{"entity": "label", "iuid": "d6f60f24e9d2426197e9823bdd5ca2ba", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/label/NGI%20Stockholm%20%28Genomics%20Production%29.json"}, "display": {"href": "https://publications.scilifelab.se/label/NGI%20Stockholm%20%28Genomics%20Production%29"}}, "value": "NGI Stockholm (Genomics Production)", "started": "2013", "ended": "2019", "created": "2017-05-02T12:10:02.503Z", "modified": "2021-03-15T14:24:16.575Z", "accounts": [{"entity": "account", "iuid": "2f6a790641494ea3b821ab973dca82db", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/renuka.kudva%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/renuka.kudva%40scilifelab.se"}}, "email": "renuka.kudva@scilifelab.se", "name": "Renuka Kudva", "orcid": "", "role": "curator", "status": "enabled", "login": "2026-07-14T17:33:20.266Z", "created": "2022-12-21T17:28:59.690Z", "modified": "2026-07-14T17:33:20.266Z"}, {"entity": "account", "iuid": "32a436398938412b93e7ddcef018c708", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/christopher.erdmann%40scilifelab.uu.se"}}, "email": "christopher.erdmann@scilifelab.uu.se", "name": "Christopher Erdmann", "orcid": "", "role": "curator", "status": "enabled", "login": "2024-08-16T11:56:57.787Z", "created": "2024-08-16T10:01:32.844Z", "modified": "2025-10-17T13:05:06.782Z"}, {"entity": "account", "iuid": "3a0653fc055b4bebbab6c164f3ac10e4", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/mattias.ormestad%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/mattias.ormestad%40scilifelab.se"}}, "email": "mattias.ormestad@scilifelab.se", "name": "Mattias Ormestad", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-11-20T13:16:54.441Z", "created": "2017-05-02T12:10:08.095Z", "modified": "2025-11-20T13:16:54.441Z"}, {"entity": "account", "iuid": "6a38350bd21f4fb6aeeb1530037a99ae", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/sune.joubert%40scilifelab.uu.se"}}, "email": "sune.joubert@scilifelab.uu.se", "name": "Sun\u00e9 Joubert", "orcid": "", "role": "curator", "status": "enabled", "login": "2025-10-31T11:15:37.113Z", "created": "2024-08-16T10:01:02.800Z", "modified": "2025-10-31T11:15:37.113Z"}, {"entity": "account", "iuid": "b68b03ae2bcb43febbfa33e1e675efc3", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/elisabet.einarsdottir%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/elisabet.einarsdottir%40scilifelab.se"}}, "email": "elisabet.einarsdottir@scilifelab.se", "name": "El\u00edsabet Einarsd\u00f3ttir", "orcid": "", "role": "curator", "status": "enabled", "login": "2023-02-22T16:10:22.529Z", "created": "2021-10-04T07:44:19.507Z", "modified": "2023-02-22T16:10:22.529Z"}, {"entity": "account", "iuid": "c272b0c5c4534a319678418310e37cc1", "timestamp": "2026-08-18T18:18:48.123Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/ellen.sherwood%40scilifelab.se.json"}, "display": {"href": "https://publications.scilifelab.se/account/ellen.sherwood%40scilifelab.se"}}, "email": "ellen.sherwood@scilifelab.se", "name": "Ellen Sherwood", "orcid": null, "role": "curator", "status": "enabled", "login": null, "created": "2017-05-03T12:52:04.270Z", "modified": "2022-03-11T12:51:25.579Z"}], "publications_count": 1566, "publications": [{"entity": "publication", "iuid": "c97265a67f72472ea537ec3be07dff36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c97265a67f72472ea537ec3be07dff36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c97265a67f72472ea537ec3be07dff36"}}, "title": "Sewage surveillance for assessing clinical antibiotic resistance prevalence: Combining metagenomic and phenotypic data", "authors": [{"family": "Flach", "given": "Carl Fredrik", "initials": "CF"}, {"family": "Berglund", "given": "Fanny", "initials": "F"}, {"family": "Osena", "given": "Gilbert", "initials": "G"}, {"family": "Huijbers", "given": "Patricia M C", "initials": "PMC"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal-article", "published": "2026-12-00", "journal": {"title": "One Health", "issn": "2352-7714", "volume": "23", "pages": "101485", "issn-l": null}, "abstract": "Surveillance of antibiotic resistance in clinical isolates is a cornerstone for the management of bacterial infections but is limited in large parts of the world, often due to lack of resources. Sewage surveillance has been proposed as a promising, resource-efficient complement to the traditional surveillance approach based on samples from many individual patients. Both phenotypic data on resistance in sewage isolates and abundance of antibiotic resistance genes in sewage have been shown to correlate with resistance prevalence in clinical isolates. Here, we aimed to directly compare and combine an isolate-based and a gene-based sewage surveillance approach to evaluate what best can reflect clinical resistance rates. The two approaches, based on susceptibility testing of collected E. coli isolates and metagenomic sequencing, respectively, were applied to municipal sewage samples collected in ten European countries. The data generated was related to available data on resistance to aminopenicillins, fluoroquinolones, third generation cephalosporins and aminoglycosides prevalence in clinical E. coli isolates using beta regression models. None of the tested individual predictors were superior across all four investigated classes of antibiotics. For modelling of aminopenicillin resistance, a clearly higher R2 value was obtained when isolate-based and gene-based data was combined as predictors, also after adjusting for the number of included variables. We conclude that there could be a value of including both isolate- and gene-based sewage data for predictions of resistance rates in clinical isolates, while emphasizing the value of linking predictors to specific species and classes of antibiotics.", "doi": "10.1016/j.onehlt.2026.101485", "pmid": "42381665", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13316215"}, {"db": "pii", "key": "S2352-7714(26)00169-2"}], "notes": [], "created": "2026-07-14T18:21:49.153Z", "modified": "2026-08-18T08:56:44.478Z"}, {"entity": "publication", "iuid": "f1c5ae1ff81a491db9527b2be7d993d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1c5ae1ff81a491db9527b2be7d993d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1c5ae1ff81a491db9527b2be7d993d6"}}, "title": "Identification of long non-coding RNAs involved in leukemogenesis and venetoclax response in acute myeloid leukemia through functional CRISPR-dCas9 interference screens", "authors": [{"family": "Cozzi", "given": "Elisabetta", "initials": "E", "orcid": "0009-0003-5311-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6657fdce5a4c8e99ad05f000ef8de3.json"}}, {"family": "Neddermeyer", "given": "Anne", "initials": "A"}, {"family": "Miliara", "given": "Sophia", "initials": "S"}, {"family": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications.scilifelab.se/researcher/b625a888935a42a89d7df3522e249413.json"}}, {"family": "Weirick", "given": "Tyler", "initials": "T", "orcid": "0000-0003-0110-5712", "researcher": {"href": "https://publications.scilifelab.se/researcher/0357a7a244b44367a7e3a60e4accb076.json"}}, {"family": "Struyf", "given": "Nona", "initials": "N", "orcid": "0000-0002-6975-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/1295c3be31024c4fa2da10cffe42c406.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Hon", "given": "Chung Chau", "initials": "CC"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0001-8374-8978", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be462a447404937857936f77677da2f.json"}}], "type": "journal-article", "published": "2026-10-00", "journal": {"title": "Noncoding RNA Res", "issn": "2468-0540", "issn-l": null, "volume": "20", "issue": null, "pages": "29-43"}, "abstract": "Acute myeloid leukemia (AML) is a malignant hematologic disease with poor prognosis, and improved understanding of its biology is critical for patient outcomes. While protein-coding genes in AML are well characterized, the role of long non-coding RNAs (lncRNAs) remains largely unexplored. Here, we investigated how lncRNAs contribute to AML biology and treatment resistance. Three high-throughput lncRNA-CRISPR-interference (CRISPRi) screens were performed in the AML cell line MOLM-13, targeting 7996 lncRNAs expressed in hematopoietic cells, with knockdowns directed to transcription start sites defined through cap analysis of gene expression (CAGE) sequencing. Effects on proliferation, differentiation, and response to the Bcl-2 inhibitor venetoclax were assessed. In total, 58, 4, and 23 lncRNAs were found to affect proliferation, differentiation, and venetoclax sensitivity, respectively. Three proliferation-associated lncRNAs (MIR17HG, CATG00000106133.1, and CATG00000056792.1) and one venetoclax-associated lncRNA (AC009299.3) were further investigated. CATG00000106133.1 was enriched in de novo and cytogenetically normal AML and correlated with NPM1 and IDH2 mutations. Gene Ontology and Reactome analyses of RNA-seq from CATG00000106133.1 knockout cells revealed roles in cytokine signaling and immune pathways. AC009299.3, linked to venetoclax response, was associated with poor outcome, adverse risk, and increased age in AML patients. Collectively, this study identifies four lncRNAs implicated in key leukemogenic processes, highlighting their potential for understanding AML biology, prognosis, and therapeutic response.", "doi": "10.1016/j.ncrna.2026.05.002", "pmid": "42388349", "labels": {"CRISPR Functional Genomics": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13318546"}, {"db": "pii", "key": "S2468-0540(26)00043-0"}], "notes": [], "created": "2026-07-13T09:01:30.068Z", "modified": "2026-08-18T08:56:59.517Z"}, {"entity": "publication", "iuid": "0ac29334eda645a1a6d1edc626fc0f09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ac29334eda645a1a6d1edc626fc0f09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ac29334eda645a1a6d1edc626fc0f09"}}, "title": "Ancestry, admixture, and pathogens in contemporaneous Neolithic farmers and foragers on the Island of Gotland", "authors": [{"family": "Fraser", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-4714-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8d9acba81e4da4a1efc097e53aa4f3.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F", "orcid": "0000-0002-0201-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/c554aeb35ee04ee1ac43c5291a8d7f3c.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Ausmees", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-6212-539X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d6a0fd5017647a7acb70bf4c667c73e.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Correa-Mendoza", "given": "Leonardo", "initials": "L"}, {"family": "Le Meur", "given": "Adrien", "initials": "A"}, {"family": "Blanchet", "given": "Antonio", "initials": "A"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef101ca28384bfabb088e7c87d0749e.json"}}, {"family": "Arrieta-Donato", "given": "Eduardo", "initials": "E", "orcid": "0009-0004-1606-1737", "researcher": {"href": "https://publications.scilifelab.se/researcher/50765f72fec044248910b7ce013ac045.json"}}, {"family": "Escobar-Rodr\u00edguez", "given": "Mariana", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Lozano-Gonzalez", "given": "Karla", "initials": "K", "orcid": "0000-0003-0329-4668", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc7c2e4b742f47688c4d48833d173778.json"}}, {"family": "Aguilar-Ordo\u00f1ez", "given": "Israel", "initials": "I"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Knutsson", "given": "Kjel", "initials": "K"}, {"family": "Wallin", "given": "Paul", "initials": "P", "orcid": "0000-0002-0916-6264", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac2463e759342bdba70ea7e40caebe2.json"}}, {"family": "Rascovan", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-2129-5878", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c1c0695dbe44d78d81ecf41265d331.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal-article", "published": "2026-07-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "9", "issue": "1", "issn-l": "2399-3642"}, "abstract": "Two archaeological cultural complexes; the Neolithic Funnelbeaker culture (FBC) and the Pitted ware culture (PWC), coexisted on Gotland for over 500 years, between ~3300 and 2800 calBCE. The ancestry of the FBC farmers and PWC marine foragers largely aligns with European Neolithic Farmers and European Mesolithic foragers, respectively, but the direct interactions between the groups on Gotland is not understood. We present a Middle Neolithic (MN) high-coverage genome and a Late Neolithic (LN) low-coverage genome from the Ansarve FBC dolmen. We investigate ancestry, admixture, and pathogens among these MN farmers (n = 6), foragers (n = 19), and the LN individual. We find that recent gene-flow between farmers and foragers could have taken place, although most gene-flow happened prior to their coexistence on the island. We also find evidence of different Yersinia pestis strains in the three cultural groups, showing that the pestis was widespread among groups with different subsistence strategies.", "doi": "10.1038/s42003-026-10498-0", "pmid": "42443543", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13376394"}, {"db": "pii", "key": "10.1038/s42003-026-10498-0"}], "notes": [], "created": "2026-07-14T17:36:10.476Z", "modified": "2026-07-30T16:05:59.748Z"}, {"entity": "publication", "iuid": "817f65055c534d8196be40bc8a8e308c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/817f65055c534d8196be40bc8a8e308c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/817f65055c534d8196be40bc8a8e308c"}}, "title": "Equal in death: Ancient genomic analysis of children's early Christian burials.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0001-8964-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3a47cc07e9d4b8592dba430785681b5.json"}}, {"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kempe Lagerholm", "given": "Vendela", "initials": "V"}, {"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2250-0463", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ed3c5d3aa804b7085c4f8a4036c09e1.json"}}, {"family": "Zachrisson", "given": "Torun", "initials": "T", "orcid": "0000-0001-7755-4982", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bdaee9400b347088474cc8a9147026b.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Sobrado", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T", "orcid": "0009-0009-3553-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a32a4e171454874a03920c915d3265f.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}], "type": "journal article", "published": "2026-07-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "28", "pages": "eaeb8588", "issn-l": "2375-2548"}, "abstract": "Sexing the skeletal remains of young individuals is crucial yet notoriously difficult in archaeology. Children, who cannot be reliably sexed morphologically, are often excluded from gender-related research, limiting our understanding of past childhood. This issue is compounded in contexts lacking grave goods, such as early Christian burials. We conducted genomic screening of 142 individuals from Sweden dating from the late Viking Age to the Medieval period, including 68 subadults and 74 adults from 27 single and 50 multiple burials. To investigate the treatment of children in death and the role of collective graves, we applied genomic sexing and kinship analyses to individuals from three sites. Contrary to the assumption that collective burials reflect close kinship, our results show that children interred with adults rarely shared close biological ties. Burial patterns indicate that gender roles were established early, with both boys and most girls mirroring adult spatial patterns. However, flexibility existed, and extended kinship likely played a central role in structuring these communities.", "doi": "10.1126/sciadv.aeb8588", "pmid": "42430491", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13353417"}], "notes": [], "created": "2026-07-14T17:36:38.635Z", "modified": "2026-07-14T17:36:39.114Z"}, {"entity": "publication", "iuid": "36ac6e2c75c94614be34596a62cdedbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36ac6e2c75c94614be34596a62cdedbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36ac6e2c75c94614be34596a62cdedbf"}}, "title": "Phylogeny-aware comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity.", "authors": [{"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Riedinger", "given": "David J", "initials": "DJ", "orcid": "0009-0002-0221-6772", "researcher": {"href": "https://publications.scilifelab.se/researcher/44aad5ff755241a7b9f8e2c29fa19b8a.json"}}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V", "orcid": "0000-0002-8090-5154", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29935a6fb20407c803cbb6b555573b6.json"}}, {"family": "Herlemann", "given": "Daniel P R", "initials": "DPR", "orcid": "0000-0002-8100-4649", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a0dc17e46354d5f99250e559b82befe.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M", "orcid": "0000-0001-7751-3187", "researcher": {"href": "https://publications.scilifelab.se/researcher/b652cb5aacc348e0a9a8bb16cfbf83fd.json"}}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Hulterstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0009-0006-1146-2827", "researcher": {"href": "https://publications.scilifelab.se/researcher/1744cf0e964d4971acc5896e9b218071.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-7943-8851", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f532d3f38142478ad0166578ca662b.json"}}, {"family": "Piwosz", "given": "Kasia", "initials": "K", "orcid": "0000-0002-3248-3364", "researcher": {"href": "https://publications.scilifelab.se/researcher/69c75bc4dc65411b9afe81b06a9398fa.json"}}, {"family": "Wo\u017aniczka", "given": "Adam", "initials": "A"}, {"family": "Benterbusch-Brockm\u00f6ller", "given": "Heike", "initials": "H"}, {"family": "Sperlea", "given": "Theodor", "initials": "T", "orcid": "0000-0003-4307-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e0963de222d42eb915c9d5b47c7a1f7.json"}}, {"family": "Dupke", "given": "Susann", "initials": "S", "orcid": "0009-0001-0639-208X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f6184e84afc44098c8d0dc2c84b9443.json"}}, {"family": "Scholz", "given": "Holger C", "initials": "HC", "orcid": "0000-0001-7224-0458", "researcher": {"href": "https://publications.scilifelab.se/researcher/c274e57dfe2a40968e3d9b046e708d26.json"}}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2026-07-08", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "17", "issue": "7", "pages": "e0020526", "issn-l": null}, "abstract": "Vibrio vulnificus, a coastal marine bacterium and opportunistic pathogen, poses increasing health risks due to rising sea water temperatures. While it harbors diverse virulence factors, its disease mechanisms remain poorly understood. To address this, we sequenced 82 environmental isolates from the Baltic Sea and combined them with 325 published genomes (clinical and environmental) for comparative analysis. Phylogenetic reconstruction revealed four major lineages, with Baltic strains restricted to L2 and L4. Clinical and environmental strains were found across all lineages, suggesting phylogeny reflects environmental adaptation more than pathogenicity. Using our newly developed PhyloBOTL pipeline, we identified 128 orthologs enriched in clinical isolates, grouped into 36 co-localization clusters. These include both known and novel virulence candidates, such as chaperone-usher pili, type VI secretion effectors, and spermidine synthases. Some clusters showed convergent loss across clades, implying niche-specific evolution. We also designed PCR primers targeting these genes to aid in the surveillance of pathogenic V. vulnificus strains.IMPORTANCEVibrio vulnificus is a naturally occurring marine bacterium that can cause life-threatening infections, with incidence increasing as coastal waters warm due to climate change. Determining which environmental strains pose the greatest risk remains a major challenge for public health surveillance. By analyzing hundreds of genomes from globally distributed strains, including extensive sampling from the rapidly warming Baltic Sea, this study shows that pathogenic potential is not restricted to specific evolutionary lineages but is instead associated with distinct sets of genes enriched in clinical strains. To support pathogen detection, we developed PCR primers targeting a subset of these clinically associated genes. Together, these findings provide new insight into the molecular basis of V. vulnificus infections and offer practical tools for improved detection, monitoring, and risk assessment of harmful strains in coastal waters and seafood under ongoing climate change.", "doi": "10.1128/mbio.00205-26", "pmid": "42307252", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13348674"}], "notes": [], "created": "2026-07-14T17:40:48.791Z", "modified": "2026-07-14T17:40:49.290Z"}, {"entity": "publication", "iuid": "23df0dc284ce4b41a3a1bc8b7a295f56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23df0dc284ce4b41a3a1bc8b7a295f56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23df0dc284ce4b41a3a1bc8b7a295f56"}}, "title": "Environmental Gradients Shape the Distribution of Free-Living and Host-Associated Syndiniales Life Stages.", "authors": [{"family": "Hanstr\u00f6m", "given": "Neea", "initials": "N", "orcid": "0009-0000-0866-2234", "researcher": {"href": "https://publications.scilifelab.se/researcher/1314ff5928be49c5a615c2932cce5a7f.json"}}, {"family": "Jan", "given": "Kinlan M G", "initials": "KMG", "orcid": "0000-0002-5579-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/503d30c9c45541db8a9bd9d37220775b.json"}}, {"family": "Winder", "given": "Monika", "initials": "M", "orcid": "0000-0001-9467-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b09dfb6b68445249b8a93c655433189.json"}}], "type": "journal article", "published": "2026-07-08", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "89", "issue": "1", "issn-l": "0095-3628"}, "abstract": "Marine alveolate parasites, particularly early-branching dinoflagellates of the order Syndiniales, play critical yet often overlooked roles in shaping marine microbial communities. These parasitoids infect diverse hosts, including dinoflagellates, copepods, and fish eggs, and rely on short-lived, free-living dinospores for transmission. Despite their ecological significance, the distributions of Syndiniales dinospores and host-associated life stages across environmental gradients remain poorly understood. We used 18S rRNA gene region DNA metabarcoding combined with size-fractionated water filtration across vertical and horizontal gradients of salinity, oxygen, and nutrients in the Baltic Sea-Skagerrak system to characterize Syndiniales life-stage distributions and identify clades producing dinospores. This approach enables the differentiation of free-living dinospores and host-associated life stages. Most reads were assigned to Syndiniales groups I and II, indicating the presence of both host associations and dinospore presence. Dinospore communities were more diverse than host-associated life stages and showed variation in spatial distribution and community composition. The spatial variation was related to salinity, oxygen, and nitrogen concentrations, emphasizing the role of environmental conditions in shaping niches suitable for host-parasite associations and infection transmission. Our findings highlight the prevalence of Syndiniales communities across an environmental gradient and the influence of environmental conditions on their distribution patterns.", "doi": "10.1007/s00248-026-02831-1", "pmid": "42418012", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00248-026-02831-1"}, {"db": "pmc", "key": "PMC13350157"}], "notes": [], "created": "2026-07-14T17:44:24.639Z", "modified": "2026-07-14T17:44:25.409Z"}, {"entity": "publication", "iuid": "0b5724836e6f4770bb25d06ab0e11807", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b5724836e6f4770bb25d06ab0e11807.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b5724836e6f4770bb25d06ab0e11807"}}, "title": "Ribosome dynamics during skeletal muscle repair and regeneration in mice and humans", "authors": [{"family": "Cui", "given": "Minying", "initials": "M"}, {"family": "Edman", "given": "Sebastian", "initials": "S", "orcid": "0000-0003-2921-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d00d020f7c84efa845fe368e7214130.json"}}, {"family": "Jude", "given": "Baptiste", "initials": "B", "orcid": "0000-0002-5506-2482", "researcher": {"href": "https://publications.scilifelab.se/researcher/60e0f4af135c4eff99a95ff1cac825bb.json"}}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "Horwath", "given": "Oscar", "initials": "O", "orcid": "0000-0002-3500-2896", "researcher": {"href": "https://publications.scilifelab.se/researcher/99970942c0114dd68a34a0524e6b5748.json"}}, {"family": "Shorter", "given": "Emily", "initials": "E"}, {"family": "Koopmans", "given": "Pieter J", "initials": "PJ", "orcid": "0000-0002-4797-5265", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4f437cb611e4327a33133c3e415c6e8.json"}}, {"family": "Chambers", "given": "Toby L", "initials": "TL", "orcid": "0000-0001-7567-1819", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ece3fb9212d4e309858701afb620180.json"}}, {"family": "Jones", "given": "Ronald G", "initials": "RG"}, {"family": "Nilsson", "given": "Abraham", "initials": "A"}, {"family": "Lanner", "given": "Johanna T", "initials": "JT", "orcid": "0000-0002-1222-9473", "researcher": {"href": "https://publications.scilifelab.se/researcher/d502479c111b4bec884fd275c2ce6384.json"}}, {"family": "Sejersen", "given": "Thomas", "initials": "T", "orcid": "0000-0001-5961-7097", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab13ad6b63424037addb7dd1afbda3b2.json"}}, {"family": "Pont\u00e9n", "given": "Eva", "initials": "E", "orcid": "0000-0001-5228-1914", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9bf1a45788a4e34be6734ce15d9de5d.json"}}, {"family": "Murach", "given": "Kevin A", "initials": "KA", "orcid": "0000-0003-2783-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/76f498f06fa0451e97123a8d5a333820.json"}}, {"family": "Schilcher", "given": "J\u00f6rg", "initials": "J"}, {"family": "von Walden", "given": "Ferdinand", "initials": "F", "orcid": "0000-0003-1134-2252", "researcher": {"href": "https://publications.scilifelab.se/researcher/903e0b7523da4a49960e677009942f67.json"}}], "type": "journal-article", "published": "2026-07-01", "journal": {"title": "Am. J. Physiol., Cell Physiol.", "issn": "0363-6143", "volume": "331", "issue": "1", "pages": "C30-C40", "issn-l": null}, "abstract": "Skeletal muscle repair requires coordinated regulation of inflammation and protein synthesis, but the roles of ribosome biogenesis and protein composition remain poorly defined. To address this, mice underwent femoral artery ligation (FAL) to induce muscle regeneration over 28 days. In humans, tibialis anterior biopsies from patients with traumatic tibial fracture were subjected to RNA sequencing. Following FAL, c-Myc mRNA increased transiently, followed by increased ribosomal DNA transcription, leading to elevated total RNA levels. Skeletal muscle-specific ribosomal protein paralog RPL3L was replaced by the ubiquitously expressed RPL3 during the initial phases of recovery, but this shift was reversed by day 28. A substantial transcriptomic response was observed in human muscle injury, with heavy emphasis on MYC-induced anabolism and inflammation. This supports a model in which MYC-driven changes in ribosomal content and composition form a core anabolic module in skeletal muscle repair, potentially representing a targetable axis to enhance recovery after muscle injury.NEW & NOTEWORTHY Our findings establish ribosome biogenesis and ribosome remodeling as core components of the skeletal muscle regenerative program conserved across species. The rapid, MYC-driven induction of translational capacity, coupled with a transient switch in ribosomal protein composition, increases ribosome heterogeneity during skeletal muscle regeneration.", "doi": "10.1152/ajpcell.00184.2026", "pmid": "42065367", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-05-11T12:28:52.694Z", "modified": "2026-07-04T19:00:44.074Z"}, {"entity": "publication", "iuid": "a7bacf7b90d34eb3aec01d340a18f9d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7bacf7b90d34eb3aec01d340a18f9d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7bacf7b90d34eb3aec01d340a18f9d9"}}, "title": "Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ephedra, Gnetales).", "authors": [{"family": "Blokzijl", "given": "Ruben", "initials": "R", "orcid": "0000-0002-5963-3537", "researcher": {"href": "https://publications.scilifelab.se/researcher/75de2e1da3244131b0cfd19ebfe0c254.json"}}, {"family": "Rydin", "given": "Catarina", "initials": "C", "orcid": "0000-0002-3347-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/70fff179e5b549c182dd7929b20f2e22.json"}}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "16", "issue": "7", "pages": "e73863", "issn-l": "2045-7758"}, "abstract": "The evolutionary history of Ephedra L. has over time proved to be a very difficult phylogenetic problem, something which probably is best reflected by the incongruent phylogenetic relationships demonstrated in and among previous studies. A low number of phylogenetically informative sites and different rooting strategies have been suggested as explanations, but the role of gene tree discordance and its underlying causes and influence on phylogenetic reconstruction in Ephedra have largely remained unexplored. In the present study, we address the phylogeny of Ephedra using information from a large set of nuclear low-copy genes obtained with a specifically designed bait set. We explore the potential effect of putative paralogy, intra-locus recombination, and chimeric sequences on phylogenetic estimation in Ephedra, while striving to minimize the risk for gene tree error. Our results indicate that recombination and putatively paralogous sequences have limited influence on phylogenetic results, although handling of putative paralogs and recombinants did improve overall species tree resolution and statistics. A robust Ephedra species phylogeny was obtained by analyzing gene trees, in which orthologous clades were inferred from data composed of orthologous and putatively paralogous sequences. The results support the division of Ephedra into three geographically defined clades, with the American clade as sister to the Mediterranean clade and the Asian clade. Relationships among species within these three clades were relatively consistent among our analytical approaches, but our results highlighted moderate to strong signals of gene tree discordance at many branches including the deepest split. Incomplete lineage sorting is a possible explanation for this discord for many branches, but hybridization/introgression is also commonly indicated.", "doi": "10.1002/ece3.73863", "pmid": "42388197", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13318514"}, {"db": "pii", "key": "ECE373863"}, {"db": "Dryad", "key": "10.5061/dryad.m63xsj4g4"}], "notes": [], "created": "2026-07-14T17:35:42.117Z", "modified": "2026-07-14T17:35:42.376Z"}, {"entity": "publication", "iuid": "7561bb26ddda43b5a3408ef3a974ac88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7561bb26ddda43b5a3408ef3a974ac88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7561bb26ddda43b5a3408ef3a974ac88"}}, "title": "Paleogenomes reveal the evolutionary relationship between modern and cave lions", "authors": [{"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Carmagnini", "given": "Alberto", "initials": "A"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Pawar", "given": "Harvinder", "initials": "H"}, {"family": "Sandoval-Velasco", "given": "Marcela", "initials": "M"}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M", "orcid": "0000-0002-0115-1797", "researcher": {"href": "https://publications.scilifelab.se/researcher/715b6d4230fb4c8eb7866c72071bc426.json"}}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V", "orcid": "0000-0002-4870-3499", "researcher": {"href": "https://publications.scilifelab.se/researcher/378b10136be74923bff019375f5d6c91.json"}}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Barnett", "given": "Ross", "initials": "R"}, {"family": "Sinding", "given": "Mikkel Holger S", "initials": "MHS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Yamaguchi", "given": "Nobuyuki", "initials": "N"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal-article", "published": "2026-07-00", "journal": {"title": "Cell", "issn": "0092-8674", "volume": "189", "issue": "14", "pages": "4425-4436.e11", "issn-l": null}, "abstract": "The Eurasian cave lion was abundant across the Northern Hemisphere before the Late Pleistocene megafaunal extinctions. However, the extent of the distinction between cave and modern lions and their adaptive differences have remained unclear. Using 12 cave lion genomes spanning more than 100,000 years, we show that modern and cave lions were distinct evolutionary lineages with separate demographic histories and unique non-synonymous variants. We also identify evidence of ancient gene flow between them, with the best modern lion proxy for this ancestry being an extinct Southwest Asian population. This admixture correlates with global ice extent, with 3.2%-4.4% modern lion ancestry detected in a \u223c20,000-year-old cave lion from Central East Asia. These findings provide insight into the evolutionary history of the cave lion, once one of the Northern Hemisphere's most ecologically impactful megafaunal species.", "doi": "10.1016/j.cell.2026.05.007", "pmid": "42235515", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(26)00524-6"}], "notes": [], "created": "2026-06-08T18:01:11.696Z", "modified": "2026-07-10T08:26:30.413Z"}, {"entity": "publication", "iuid": "3c879540016f423ca84894bb30eae1b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c879540016f423ca84894bb30eae1b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c879540016f423ca84894bb30eae1b5"}}, "title": "Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.", "authors": [{"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Meng", "given": "Lingqi", "initials": "L"}, {"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Ji", "given": "Boyu", "initials": "B"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Oktem", "given": "Ece Ozdemir", "initials": "EO"}, {"family": "Sayman", "given": "Dila", "initials": "D"}, {"family": "Karaca", "given": "Ramazan", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}, {"family": "Turkez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-7046-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbae52c6a22f4877b747a4de1ec1ca8a.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Neurobiol. Dis.", "issn": "1095-953X", "volume": "225", "pages": "107424", "issn-l": "0969-9961"}, "abstract": "While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.", "doi": "10.1016/j.nbd.2026.107424", "pmid": "42069091", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0969-9961(26)00169-5"}], "notes": [], "created": "2026-05-11T11:43:55.203Z", "modified": "2026-06-30T09:59:57.743Z"}, {"entity": "publication", "iuid": "a061e877c04d46538954ff10fdabb238", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a061e877c04d46538954ff10fdabb238.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a061e877c04d46538954ff10fdabb238"}}, "title": "Genetic diversity of late Neanderthals in northwestern Europe.", "authors": [{"family": "Bossoms Mesa", "given": "Alba", "initials": "A", "orcid": "0009-0008-7556-1722", "researcher": {"href": "https://publications.scilifelab.se/researcher/b11dd9c4aea34fb8bde542f5e983b723.json"}}, {"family": "Essel", "given": "Elena", "initials": "E", "orcid": "0000-0002-2642-8043", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c289ad6c2c443dab3e8ac7f9e85979e.json"}}, {"family": "Peyr\u00e9gne", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0002-9823-9102", "researcher": {"href": "https://publications.scilifelab.se/researcher/1659db1df364436d87f40641f0778251.json"}}, {"family": "S\u00fcmer", "given": "Arev P", "initials": "AP", "orcid": "0009-0001-4834-4414", "researcher": {"href": "https://publications.scilifelab.se/researcher/862f71c337ad4775bb2cdb7cec947e39.json"}}, {"family": "Iasi", "given": "Leonardo N M", "initials": "LNM"}, {"family": "Heide", "given": "Christian", "initials": "C", "orcid": "0000-0001-8637-9039", "researcher": {"href": "https://publications.scilifelab.se/researcher/7108e501c36345d3aaad7de0929fd1b9.json"}}, {"family": "Popli", "given": "Divyaratan", "initials": "D"}, {"family": "de Filippo", "given": "Cesare", "initials": "C"}, {"family": "Gansauge", "given": "Marie-Theres", "initials": "MT"}, {"family": "Gerullat", "given": "Lars", "initials": "L", "orcid": "0009-0005-3448-7827", "researcher": {"href": "https://publications.scilifelab.se/researcher/48e620e84ea941deb492f1c9f7cafc17.json"}}, {"family": "Lippik", "given": "Laurin", "initials": "L"}, {"family": "Nagel", "given": "Sarah", "initials": "S"}, {"family": "Nickel", "given": "Birgit", "initials": "B"}, {"family": "Schellbach", "given": "Barbara", "initials": "B"}, {"family": "Schmidt", "given": "Anna", "initials": "A"}, {"family": "Visagie", "given": "Johann", "initials": "J"}, {"family": "Weihmann", "given": "Antje", "initials": "A"}, {"family": "Zeberg", "given": "Hugo", "initials": "H", "orcid": "0000-0001-7118-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/090e842ed8ff4cf2a3fe5f8e58118e58.json"}}, {"family": "Zorn", "given": "Julia", "initials": "J"}, {"family": "Rougier", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0003-0358-0285", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f83f613a0f4d9fba2f1b9f9d6db45c.json"}}, {"family": "Crevecoeur", "given": "Isabelle", "initials": "I"}, {"family": "Semal", "given": "Patrick", "initials": "P"}, {"family": "Abrams", "given": "Gr\u00e9gory", "initials": "G", "orcid": "0000-0002-0616-4335", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5da243731a0492183b180c917afef01.json"}}, {"family": "Devi\u00e8se", "given": "Thibaut", "initials": "T", "orcid": "0000-0003-0495-7398", "researcher": {"href": "https://publications.scilifelab.se/researcher/212742d6e9d84fe1ae06bee52dce8116.json"}}, {"family": "Pirson", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0003-2955-0383", "researcher": {"href": "https://publications.scilifelab.se/researcher/5393d94f03c746b8acbc5b2ce3b778bb.json"}}, {"family": "Di Modica", "given": "K\u00e9vin", "initials": "K"}, {"family": "Cattelain", "given": "Pierre", "initials": "P"}, {"family": "Draily", "given": "Christelle", "initials": "C"}, {"family": "Toussaint", "given": "Michel", "initials": "M"}, {"family": "De Groote", "given": "Isabelle", "initials": "I"}, {"family": "Welker", "given": "Frido", "initials": "F", "orcid": "0000-0002-4846-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/7652762c05444a1d86c4b12c637b529b.json"}}, {"family": "Posth", "given": "Cosimo", "initials": "C", "orcid": "0000-0002-8206-3907", "researcher": {"href": "https://publications.scilifelab.se/researcher/828edab40ca74c89947aa70526e7e339.json"}}, {"family": "Soressi", "given": "Marie", "initials": "M", "orcid": "0000-0003-1733-7745", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecb836df3fa34bc6a678973b4213841a.json"}}, {"family": "Hublin", "given": "Jean-Jacques", "initials": "JJ", "orcid": "0000-0001-6283-8114", "researcher": {"href": "https://publications.scilifelab.se/researcher/26462f3e315a4740b9ae5337389ce99e.json"}}, {"family": "Krause", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9144-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2416e8bd2bfb4aa3988f4a37fca2de2e.json"}}, {"family": "P\u00e4\u00e4bo", "given": "Svante", "initials": "S", "orcid": "0000-0002-4670-6311", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b357300f09451a860ad33b86c76982.json"}}, {"family": "Meyer", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4760-558X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4bd87e0225d422ea165ab0670f6cb20.json"}}, {"family": "Kelso", "given": "Janet", "initials": "J", "orcid": "0000-0002-3618-322X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57db79fef05b4743bff8345f8c3dfc04.json"}}, {"family": "Peter", "given": "Benjamin M", "initials": "BM", "orcid": "0000-0003-2526-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/1860ed14a48048fdb14d9d183e1ee869.json"}}, {"family": "Hajdinjak", "given": "Mateja", "initials": "M", "orcid": "0000-0002-4064-0331", "researcher": {"href": "https://publications.scilifelab.se/researcher/cec10fd428c64857b2dc7017e390ab9b.json"}}], "type": "journal article", "published": "2026-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "655", "issue": "8122", "pages": "409-417", "issn-l": "0028-0836"}, "abstract": "Archaeological, osteological and genetic evidence suggests that Neanderthals lived in small groups1,2; however, less is known about whether these groups were part of isolated communities or belonged to larger, well-connected populations3. The dense concentration of broadly contemporaneous Neanderthal sites in the Meuse Basin, Belgium4, provides a rare opportunity to study regional populations at high resolution. Here we generated genetic data from 27 Neanderthals who lived less than approximately 52,500 years ago from ten archaeological sites in Belgium and France, including a high-coverage genome from a 45,000-year-old individual from Goyet, Belgium. We show that most of these individuals are more closely related to one another than to other contemporaneous late Neanderthals in Europe. Further, some of these individuals carry DNA from a Neanderthal lineage predating the split of late Neanderthals. Although these Neanderthals overlapped temporally with early modern humans in northwestern Europe from around 47,000 years ago, we find no evidence of recent gene flow from modern humans. They also do not show the genetic signatures of mating among close relatives found in Altai Neanderthals, suggesting that they lived in larger or better-connected groups. Moreover, genetic load did not accumulate over time, arguing against progressive genetic deterioration as a driver of Neanderthal extinction.", "doi": "10.1038/s41586-026-10625-1", "pmid": "42343123", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-026-10625-1"}, {"db": "pmc", "key": "PMC13345965"}], "notes": [], "created": "2026-07-14T17:55:22.246Z", "modified": "2026-07-14T17:55:23.277Z"}, {"entity": "publication", "iuid": "cd185537d6c1427a862c3a4040bcd21c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd185537d6c1427a862c3a4040bcd21c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd185537d6c1427a862c3a4040bcd21c"}}, "title": "MalDeepSeq panel: A targeted ultra-deep sequencing approach to trace drug resistance markers in Plasmodium falciparum.", "authors": [{"family": "Salazar", "given": "Yanka E A R", "initials": "YEAR"}, {"family": "Rezende", "given": "Antonio M", "initials": "AM"}, {"family": "Pu\u00e7a", "given": "Maria C S B", "initials": "MCSB"}, {"family": "Lagstr\u00f6m", "given": "Sonja", "initials": "S"}, {"family": "Fletcher", "given": "Danielle", "initials": "D"}, {"family": "Muwanguzi-Karugaba", "given": "Julian", "initials": "J"}, {"family": "Sutherland", "given": "Colin J", "initials": "CJ"}, {"family": "Beshir", "given": "Khalid B", "initials": "KB"}, {"family": "Mascarenhas", "given": "Maria E P", "initials": "MEP"}, {"family": "Louzada", "given": "Jaime", "initials": "J"}, {"family": "Oliveira-Ferreira", "given": "Joseli", "initials": "J"}, {"family": "Djimde", "given": "Abdoulaye", "initials": "A"}, {"family": "Lopes", "given": "Dinora", "initials": "D"}, {"family": "de Sousa", "given": "Tais N", "initials": "TN"}, {"family": "Gil", "given": "Jos\u00e9 P", "initials": "JP"}], "type": "journal article", "published": "2026-06-25", "journal": {"title": "Cell Reports Methods", "issn": "2667-2375", "pages": "101509", "issn-l": null}, "abstract": "The emergence of drug-resistant Plasmodium falciparum highlights the need for tools to detect minor parasite subpopulations before resistant lineages expand. We developed and validated a targeted ultra-deep sequencing framework for the full-length sequences of 48 antimalarial resistance genes. Performance was evaluated using 3D7:Dd2 mock mixtures and clinical samples after selective whole-genome amplification. The panel achieved high depth and breadth, including for dried blood spot samples. Using Dd2-fixed markers, Mutect2 and HaplotypeCaller reproduced expected variant-allele frequencies, with Mutect2 exhibiting lower global bias and error. A conservative truth set derived from Dd2-pure controls yielded perfect recall and no false-positives in 3D7 controls, with high recovery of true Dd2 variants in mock mixtures for both callers. In clinical samples, the panel captured within-host diversity and minority resistance alleles. Overall, these results demonstrate that targeted deep sequencing offers a cost-efficient, high-resolution approach for routine molecular surveillance of emerging drug resistance.", "doi": "10.1016/j.crmeth.2026.101509", "pmid": "42349411", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S2667-2375(26)00210-9"}], "notes": [], "created": "2026-07-14T18:12:00.160Z", "modified": "2026-07-14T18:12:00.163Z"}, {"entity": "publication", "iuid": "eebf950291ba49dc9561ebc23f759bc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eebf950291ba49dc9561ebc23f759bc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eebf950291ba49dc9561ebc23f759bc5"}}, "title": "Multi-Year Biofilm Formation on Granitic Surfaces Reveals Dynamic Microbial Communities in Fennoscandian Shield Deep Groundwaters.", "authors": [{"family": "St\u00e5hle", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1307-6181", "researcher": {"href": "https://publications.scilifelab.se/researcher/41fac36fa4aa40b58e8f53bd72d79f68.json"}}, {"family": "Johnson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2943-5158", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b87d8091975457c9bc0f362c6a874c5.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S", "orcid": "0009-0007-1915-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f779055bf334226a996f214182b41fc.json"}}, {"family": "M\u00e5rtensson", "given": "Per", "initials": "P", "orcid": "0009-0003-0538-4234", "researcher": {"href": "https://publications.scilifelab.se/researcher/434f332617c5466fb6a6473235e8987b.json"}}, {"family": "Kalinowski", "given": "Birgitta", "initials": "B", "orcid": "0000-0001-9381-6081", "researcher": {"href": "https://publications.scilifelab.se/researcher/18064bfcc18147f2ab35b842c3765134.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2026-06-19", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "89", "issue": "1", "issn-l": "0095-3628"}, "abstract": "The deep terrestrial biosphere is the vast biome beneath the soil layer that contains the majority of the Earth's prokaryotic biomass, yet it is one of the least investigated communities. Although, estimates of deep biosphere biomass suggest biofilm cells outnumber the planktonic biomass by several orders of magnitude, most investigations target planktonic communities captured from groundwaters. This multi-year study used 16S rRNA gene sequencing to compare planktonic and biofilm communities attached to natural granitic rock, demonstrating that biofilm formation selected for taxa with distinct relative abundances and exhibited temporal development. The biofilm communities also showed a decreasing influence of introduced populations on the natural rock surfaces (macadam) present at the onset of the incubations. After two- and four-years of biofilm incubation, a community developed that was dominated by sulfur/sulfate reducing Desulfocapsaceae, Desulfobacteraceae, and BM004 along with the families UBA5619, Rhodocyclaceae, Profunditerraquicolaceae, and UBA2206. This long-term community included populations predicted to be host-associated ultra-small cells. This contrasted with previous studies of early biofilm development in deep Fennoscandian Shield groundwaters that suggested biofilm initiation was mediated by lithotrophic carbon and nitrogen fixing populations. However, metabolic predictions based upon the 16S rRNA gene-based communities also showed an autotrophic and diazotrophic community including sulfur cycling in line with the previous studies. In conclusion, this study showed long-term biofilm composition to be dissimilar to the planktonic communities with a consistent strategy for energy conservation similar to previous studies of early biofilm formation from these groundwaters.", "doi": "10.1007/s00248-026-02812-4", "pmid": "42319514", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00248-026-02812-4"}, {"db": "pmc", "key": "PMC13283197"}], "notes": [], "created": "2026-07-14T17:41:19.837Z", "modified": "2026-07-14T17:41:20.049Z"}, {"entity": "publication", "iuid": "eaced373ebb042569f6b0fc22e49aec1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaced373ebb042569f6b0fc22e49aec1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaced373ebb042569f6b0fc22e49aec1"}}, "title": "Developmentally dynamic, non-convergent transcriptomic profiles in CNV models for schizophrenia risk.", "authors": [{"family": "French", "given": "Hayley", "initials": "H"}, {"family": "Yao", "given": "Shuyang", "initials": "S", "orcid": "0000-0001-9669-4470", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcd036ee020e4622ad16d020bfcd7b38.json"}}, {"family": "Bast", "given": "Lisa", "initials": "L", "orcid": "0000-0001-8489-3923", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c13ac1740034091b977ef1c421a895a.json"}}, {"family": "Roig Adam", "given": "Amparo", "initials": "A", "orcid": "0000-0003-4515-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2d2104ce15d4fd8a23209718111a9dc.json"}}, {"family": "St\u00fcmpges", "given": "Paul", "initials": "P"}, {"family": "Memic", "given": "Fatima", "initials": "F"}, {"family": "Mulle", "given": "Jennifer", "initials": "J", "orcid": "0000-0001-8593-8468", "researcher": {"href": "https://publications.scilifelab.se/researcher/56749cfe7a504674b6770af510e89f51.json"}}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J", "orcid": "0000-0002-4539-1776", "researcher": {"href": "https://publications.scilifelab.se/researcher/51675f0ff9aa47d89d6b2eb84a14820a.json"}}], "type": "journal article", "published": "2026-06-18", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "issn-l": "1359-4184"}, "abstract": "Schizophrenia is a complex psychiatric disorder with significant genetic and clinical heterogeneity. Although numerous rare copy number variations (CNVs) with high risk for schizophrenia have been identified, they show no obvious overlap in gene content or function. We hypothesized that the downstream effects of schizophrenia-associated CNVs converge on shared molecular pathways. To test this, we profiled the prefrontal cortex of five schizophrenia-associated CNV mouse models - 15q13.3del, 3q29del, 1q21.1del, 22q11.2del, and 16p11.2dup - using single-cell RNA sequencing across two developmental stages: adolescence and adulthood. From 292,943 high-quality single-cell transcriptomes, we identified distinct age- and cell type-specific patterns of differential gene expression and biological pathway perturbations in each model. Rather than converging on a shared molecular mechanism, each CNV affected unique cellular pathways in a developmentally dynamic manner. Notably, genes dysregulated in deep-layer corticothalamic projection neurons from 15q13.3del and 16p11.2dup models, and intratelencephalic neurons from adult 22q11.2del mice, showed enrichment for schizophrenia-SNP heritability. These results support a model in which rare CNVs contribute to schizophrenia genetic risk through developmentally dynamic, distinct pathways rather than through a shared molecular mechanism.", "doi": "10.1038/s41380-026-03679-0", "pmid": "42315919", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-026-03679-0"}], "notes": [], "created": "2026-07-14T18:14:38.632Z", "modified": "2026-07-14T18:14:38.938Z"}, {"entity": "publication", "iuid": "c1ef2e73b1d247049e7525192439cb19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1ef2e73b1d247049e7525192439cb19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1ef2e73b1d247049e7525192439cb19"}}, "title": "Comparative genomics reveal signatures of ecological specialization in the striped ambrosia beetle Trypodendron lineatum.", "authors": [{"family": "Montes-Ortiz", "given": "Zaide", "initials": "Z"}, {"family": "Powell", "given": "Daniel", "initials": "D"}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C"}, {"family": "Andersson", "given": "Martin N", "initials": "MN"}], "type": "journal article", "published": "2026-06-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Beetles (Coleoptera) display exceptional dietary diversity and occupy a wide range of ecological niches, often involving close associations with plants and microbes. Ambrosia beetles (Curculionidae; Scolytinae and Platypodinae) exemplify ecological specialization by cultivating mutualistic fungi within galleries excavated in their host trees' xylem, with the fungi serving as their main food source. The striped ambrosia beetle Trypodendron lineatum is a pest of conifers, relying on its nutritional mutualist Phialophoropsis ferruginea for survival. This fungiculture-based lifestyle provides a system for exploring how specialized mutualism is reflected at the genomic level. Hence, we performed a comparative genomics analysis between T. lineatum and nine other beetle species with different ecological specializations. We hypothesized that fungiculture is associated with specific genomic adaptations, including changes in gene family composition related to nutrition, detoxification, and immunity.\n\nThe small genome of T. lineatum (74.4-83.6 Mb) exhibits comparatively low levels of repetitive DNA (19.9%), including a reduced proportion of transposable elements. Annotation generated 14,830 high-quality gene predictions, most of which were supported by transcript evidence or functional domains. Comparative orthology analysis across ten beetle species identified 13,896 orthogroups, with T.lineatum having 78 species-specific orthogroups comprising 238 genes. Gene family evolution analyses revealed 33 families with significant size changes in T. lineatum, including 16 expansions and 17 contractions. Notably, gene families associated with digestion, detoxification, and immunity were contracted. These included glycoside hydrolase 28, cytochrome P450, serpin, and trypsin families, which may reflect the fungus-based, rather than plant-based, diet of T. lineatum, and reduced reliance on broad-spectrum immune defenses. In contrast, expansions in the THAP and CD80-like immunoglobulin domain families indicate diversification of genes involved in genomic regulation and immune recognition.\n\nOur results suggest that the genome of T. lineatum is characterized by low repeat content and compact gene architecture. The observed contractions in key gene families involved in plant digestion, detoxification, and immunity may represent genomic signatures of its obligate mutualistic specialization and narrow ecological niche. Our findings provide the first insights into the genomic adaptations of fungus-farming ambrosia beetles, suggesting that co-evolved insect-microbe mutualisms may lead to reductions in a variety of gene families.", "doi": "10.1186/s12864-026-13049-3", "pmid": "42298395", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-026-13049-3"}, {"db": "pmc", "key": "PMC13270666"}], "notes": [], "created": "2026-07-14T18:13:53.768Z", "modified": "2026-07-14T18:13:53.773Z"}, {"entity": "publication", "iuid": "b974baa5898a491fa7da118a6dc91e29", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b974baa5898a491fa7da118a6dc91e29.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b974baa5898a491fa7da118a6dc91e29"}}, "title": "A comparison of ancient DNA yields across ossicles and the petrous bone reveals the best preservation in the stapes and incus.", "authors": [{"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b98a6e55a69644cda1e305da05c6838d.json"}}, {"family": "Sevkar", "given": "Arda", "initials": "A", "orcid": "0000-0003-4573-6778", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c781bd3197040a3a9e4dee03b57dc65.json"}}, {"family": "Kazanc\u0131", "given": "Duygu Deniz", "initials": "DD", "orcid": "0000-0002-8333-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f28aea0bd7e4bb7b6ac3d8843cae17f.json"}}, {"family": "Garc\u00eda", "given": "Gonzalo Oteo", "initials": "GO", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Yorulmaz", "given": "Sevgi", "initials": "S", "orcid": "0000-0002-9592-6310", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ac25b5dcc84758b3f852d81133cac6.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "\u00c7akan", "given": "G\u00f6khan", "initials": "G", "orcid": "0000-0002-1840-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef6138f4d74e4270b91f894300b40d3f.json"}}, {"family": "Adilo\u011flu", "given": "G\u00f6k\u00e7en", "initials": "G", "orcid": "0009-0002-0473-8662", "researcher": {"href": "https://publications.scilifelab.se/researcher/292d044bc3524a4c8ab3aeaa6ba6c82e.json"}}, {"family": "Buldak", "given": "Duru", "initials": "D", "orcid": "0009-0006-6650-1205", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c0cb46cabd9429f88b8013db9356a77.json"}}, {"family": "Duru", "given": "G\u00fcne\u015f", "initials": "G", "orcid": "0000-0003-1870-0120", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbbcdad9813340169df6097719971ea6.json"}}, {"family": "\u00d6ztan", "given": "Aliye", "initials": "A"}, {"family": "Hassett", "given": "Brenna", "initials": "B", "orcid": "0000-0003-0509-3608", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fa8c508c2fa4261b6120432b50e040c.json"}}, {"family": "Kayacan", "given": "Nurcan", "initials": "N", "orcid": "0000-0001-6256-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f964340521f41f09a12532226c6f204.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Asl\u0131 Erim", "initials": "AE", "orcid": "0009-0002-8241-3521", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c2926f5d49240f1851cc40fb4fdcb6b.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "Erdal", "given": "\u00d6m\u00fcr Dilek", "initials": "\u00d6D", "orcid": "0000-0002-1559-4062", "researcher": {"href": "https://publications.scilifelab.se/researcher/43a1b606e9644c3794a02cf3e5c77984.json"}}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS", "orcid": "0000-0001-8143-8159", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f77cf0f580409f98004f71cf99c001.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}], "type": "journal article", "published": "2026-06-11", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051"}, "abstract": "The petrous bone is considered the most efficient source of endogenous DNA across skeletal tissues in ancient DNA (aDNA) research as well as in forensic work. Recently, ancient DNA in auditory ossicle bones was shown to be comparably well-preserved as in the petrous, although no attempt was made to distinguish among the three ossicle bones. In this study, we compare aDNA profiles across matched ossicle- and petrous-derived sequencing libraries prepared from 29 human skeletons from Neolithic Anatolia and Medieval Iberia. We find that the stapes and incus provide higher human endogenous aDNA than the petrous bone, with >2\u00d7; higher median rates of endogenous aDNA recovery, while the malleus performs similarly to the petrous. Human aDNA fragments retrieved from the stapes were 8% longer than those from the petrous, whereas postmortem damage, clonality and contamination rates were comparable among the studied bone types. These observations are corroborated by data from non-matched ossicle or petrous libraries from 81 individuals from the same contexts, with the highest endogenous aDNA content observed in the stapes. Despite being the smallest bone in the human skeleton, the stapes, along with the incus, may be among the most optimal aDNA sources yet identified.", "doi": "10.1101/gr.281213.125", "pmid": "42276740", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "gr.281213.125"}], "notes": [], "created": "2026-07-14T18:20:25.449Z", "modified": "2026-07-14T18:20:25.870Z"}, {"entity": "publication", "iuid": "b16a5df99b634091a39abab2b83d0afc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b16a5df99b634091a39abab2b83d0afc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b16a5df99b634091a39abab2b83d0afc"}}, "title": "Whole-genome sequencing with AVITI and NovaSeq X Plus reveals comparable performance with contextual biases.", "authors": [{"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f901467fc54bb3a162e533248ebb70.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d517d4f20046c08405f8aeecf4ad2a.json"}}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Hauenstein", "given": "Julia", "initials": "J"}, {"family": "F\u00e4llmar", "given": "Helena", "initials": "H"}, {"family": "Lindell", "given": "Magnus", "initials": "M"}, {"family": "Natanaelsson", "given": "Christian", "initials": "C"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "M\u00e5nsson Welinder", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}], "type": "journal article", "published": "2026-06-00", "journal": {"title": "NAR Genom Bioinform", "issn": "2631-9268", "issn-l": null, "volume": "8", "issue": "2", "pages": "lqag053"}, "abstract": "Element Biosciences' avidity sequencing has emerged as a competing technology to Illumina's short-read sequencing platform. Prior benchmarks of avidity sequencing have not included the latest Illumina NovaSeq X/X Plus instruments with XLEAP chemistry. Here, we have run polymerase chain reaction-free whole-genome sequencing on four human tumor cell lines using both Illumina NovaSeq X Plus and Element AVITI instruments. AVITI showed low duplication rates and reported higher base qualities; the latter contributed to improved mapping confidence and fewer spurious variant candidates. Both platforms were found to be highly comparable when benchmarking variant calling, with AVITI only providing a minor improvement on INDELs at lower coverages. Stratifying by genomic context revealed further differences, where AVITI genome coverage and variant calls were superior in high-GC regions while being inferior in GC homopolymers. Error-rate analysis highlighted further differences between the platforms; in particular, AVITI in some instances displayed an increased error rate on read 2 related to short fragments. AVITI error rate was also found to be more stable downstream of repetitive regions, except for GC homopolymers. We further found that AVITI sequencing was sensitive to G-quadruplex motifs. Overall, despite these identified differences, both platforms performed highly comparable for variant analysis.", "doi": "10.1093/nargab/lqag053", "pmid": "42206012", "labels": {"NGI Stockholm (Genomics Production)": "Technology development", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "NGI Long read": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13202175"}, {"db": "pii", "key": "lqag053"}], "notes": [], "created": "2026-06-08T17:20:13.126Z", "modified": "2026-08-12T15:02:18.123Z"}, {"entity": "publication", "iuid": "59d7ae58ceea4c3bb2eb1e766d18641a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59d7ae58ceea4c3bb2eb1e766d18641a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59d7ae58ceea4c3bb2eb1e766d18641a"}}, "title": "Spatiotemporal analysis reveals distinct inflammatory programs underlying chronic colitis", "authors": [{"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Castillo", "given": "Francisca", "initials": "F"}, {"family": "Chi", "given": "Yuhao", "initials": "Y"}, {"family": "He", "given": "Ning", "initials": "N"}, {"family": "Suarez-Alvarez", "given": "Martin", "initials": "M"}, {"family": "Ulloa", "given": "Maria Alejandra", "initials": "MA"}, {"family": "Morales Castro", "given": "Rodrigo A", "initials": "RA"}, {"family": "Okhovat", "given": "Ali", "initials": "A"}, {"family": "Sounart", "given": "Hailey", "initials": "H", "orcid": "0009-0000-5772-3961", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d2d0007b3d643588c5196d482cb2089.json"}}, {"family": "Zagami", "given": "Chiara", "initials": "C"}, {"family": "Cardoso", "given": "Rebeca F", "initials": "RF"}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Mechling", "given": "Anna", "initials": "A"}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH"}, {"family": "Smith", "given": "Philip", "initials": "P"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}], "type": "journal-article", "published": "2026-06-00", "journal": {"title": "Immunity", "issn": "1074-7613", "volume": "59", "issue": "6", "pages": "1599-1615.e5", "issn-l": null}, "abstract": "Inflammatory bowel disease (IBD) is a complex disorder that is often resistant to immunomodulatory treatments. Here, to understand how immune, epithelial, and stromal compartments are rewired during disease initiation and progression, we leveraged T cell transfer and Il10-/- spontaneous colitis models, including anti-IL-12p40 intervention, and integrated time-course transcriptomic analyses at bulk, single-cell, and spatial resolution. These well-established models exhibited conserved features of chronic inflammation, including neutrophil infiltration, and impaired tissue regeneration. Comparison of murine transcriptional programs and human IBD datasets revealed neutrophil-associated inflammation and cytokine signaling as the most conserved pathways across species. We identified spatial heterogeneity in inflammatory modules and described three gene programs with differential spatial and temporal distributions, including one corresponding to tertiary lymphoid structures. When used together, these models recapitulate complementary aspects of human disease at both cellular and transcriptional levels. This high-resolution spatiotemporal atlas will guide future translational research aimed at optimizing therapeutic strategies for IBD.", "doi": "10.1016/j.immuni.2026.04.005", "pmid": "42097141", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(26)00167-6"}], "notes": [], "created": "2026-05-11T11:50:48.709Z", "modified": "2026-06-29T07:40:31.984Z"}, {"entity": "publication", "iuid": "6f6a5bd19f4d4a459ee0ff3a82fc3eef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f6a5bd19f4d4a459ee0ff3a82fc3eef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f6a5bd19f4d4a459ee0ff3a82fc3eef"}}, "title": "Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.", "authors": [{"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f901467fc54bb3a162e533248ebb70.json"}}, {"family": "Pourbozorgi", "given": "Parham", "initials": "P", "orcid": "0000-0002-5957-627X", "researcher": {"href": "https://publications.scilifelab.se/researcher/520886f23ef54f008bff773ebb86f7b1.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2026-05-22", "journal": {"title": "Life (Basel)", "issn": "2075-1729", "volume": "16", "issue": "6", "issn-l": null}, "abstract": "Precision medicine is increasingly applied in the cancer clinic, adapting treatment to genomic alterations of the tumor. However, whether alterations disrupt the function of a protein can depend on if both alleles of a gene are altered. While massively parallel sequencing technologies can identify sequence aberrations, they are limited in resolving the corresponding haplotype information. In this proof-of-concept case study, we applied the linked-read droplet barcode sequencing (DBS) technology to resolve the haplotype complexity of colorectal cancer genomes on paired tumor and normal samples. Several cancer-related genes carried multiple mutations in either one or both haplotypes. Additionally, a number of haplotype-resolved large structural variants and copy number alterations were detected and phased with short somatic variants. Nearly all characterized oncogenic pathways harbored some of the identified short somatic variants. The study demonstrates that linked-read DBS technology can characterize complex genetic variations in a haplotype context and may provide essential information for personalized approaches.", "doi": "10.3390/life16060874", "pmid": "42355402", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "life16060874"}, {"db": "pmc", "key": "PMC13301505"}], "notes": [], "created": "2026-07-14T17:34:48.527Z", "modified": "2026-07-14T17:34:48.921Z"}, {"entity": "publication", "iuid": "9bafa70241894ebcab4e2bf9d0640d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40"}}, "title": "Comparing DNA metabarcoding with light microscopy to identify eukaryotic phytoplankton in the Baltic Sea, Kattegat and Skagerrak", "authors": [{"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}], "type": "journal-article", "published": "2026-05-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Marine phytoplankton monitoring has long relied on microscopy, but DNA metabarcoding has recently emerged as a complementary approach. This study assessed the applicability of DNA metabarcoding of the 18S ribosomal RNA gene in marine monitoring and compared its results with conventional microscopy. We analyzed data from 232 surface water samples from 17 monitoring stations in the Baltic Sea, Kattegat, and Skagerrak. Metabarcoding detected more orders, genera, and species than microscopy, with a 43% overlap in the most common genera identified by both methods. Despite attempts to normalize sequence reads to spike-in DNA or DNA concentrations, the correlations between abundances derived from the two methods were weak, though varied considerably between taxonomic groups and geographical areas. Correlations were consistently stronger when using carbon and biovolume concentrations than cell abundances. Our results highlight the potential of metabarcoding to expand biodiversity assessments and advance our understanding of microbial biodiversity in marine ecosystems. As a complement to microscopy, it can enhance existing monitoring efforts. Future improvements in reference database completeness, adoption of long-read sequencing technologies, and better characterization of gene copy number variability per cell are needed to further extend the applicability of metabarcoding for quantitative analyses.", "doi": "10.1038/s41598-026-48838-z", "pmid": "42156811", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13190673"}, {"db": "pii", "key": "10.1038/s41598-026-48838-z"}], "notes": [], "created": "2026-06-08T17:17:40.513Z", "modified": "2026-07-04T18:59:51.656Z"}, {"entity": "publication", "iuid": "69e64360fa0d42d4a7da65ad33e6a6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69e64360fa0d42d4a7da65ad33e6a6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69e64360fa0d42d4a7da65ad33e6a6c4"}}, "title": "Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases", "authors": [{"family": "Konstantinou", "given": "Aimiliani", "initials": "A", "orcid": "0009-0009-6955-9906", "researcher": {"href": "https://publications.scilifelab.se/researcher/adbee78c31e648518a914fd366c29be5.json"}}, {"family": "C\u00f3rdova-P\u00e9rez", "given": "Alicia", "initials": "A"}, {"family": "Varga", "given": "Julia K", "initials": "JK", "orcid": "0000-0002-5318-2798", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cce1545060342798144f3c8144d4d64.json"}}, {"family": "Madhu", "given": "Priyanka", "initials": "P"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Vieler", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-3617-1018", "researcher": {"href": "https://publications.scilifelab.se/researcher/d02f57d8ee554f1895fb5cf5d93541ef.json"}}, {"family": "Ishimura", "given": "Ryosuke", "initials": "R"}, {"family": "Lamoliatte", "given": "Frederic", "initials": "F"}, {"family": "Schueler-Furman", "given": "Ora", "initials": "O", "orcid": "0000-0002-1624-0362", "researcher": {"href": "https://publications.scilifelab.se/researcher/5332c64faf114b16bf4a5b5e789d5aa3.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/c239a7f1b8a344948d80b9104a5fcc96.json"}}, {"family": "Kulathu", "given": "Yogesh", "initials": "Y", "orcid": "0000-0002-3274-1642", "researcher": {"href": "https://publications.scilifelab.se/researcher/1646c4f2949a4a7ea47be413a9a770db.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal-article", "published": "2026-05-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity is thought to be mediated by the recognition of the ubiquitnated protein itself. In addition to their catalytic domain, USPs have one or more auxiliary domains (ADs) with key functions in regulating DUB activity and localization. We hypothesize that some ADs bind short linear motifs (SLiMs) typically found in intrinsically disordered regions of proteins to achieve targeting to substrates and multiprotein complexes. To test this, we systematically assess the potential of 29 USP-ADs and two full-length USPs for SLiM binding using a combination of proteomic-peptide phage display, peptide SPOT arrays and affinity measurements. We discover SLiM-based interactions for 14 ADs from 9 USP-DUBs, including CYLD, USP11, USP19, USP20, USP22 and USP33, and define the consensus motif and properties of the SLiM-AD binding. Interestingly, we establish that the zf-UBP and DUSP2 domains of USP20 and USP33 are SLiM binding ADs with similar binding profiles, explaining the functional redundancy between the two DUBs. Our work reveals unique motifs recognized by the auxiliary domains CAP-Gly, UBL, zf-UBP and DUSP, with potential functional implications for substrate recognition and complex assemblies.", "doi": "10.1038/s41467-026-73047-7", "pmid": "42151178", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-73047-7"}], "notes": [], "created": "2026-06-08T17:42:03.867Z", "modified": "2026-07-04T19:00:03.668Z"}, {"entity": "publication", "iuid": "b09b02fc5fff4122883cede0ca76ddbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b09b02fc5fff4122883cede0ca76ddbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b09b02fc5fff4122883cede0ca76ddbf"}}, "title": "Mitochondria serve as a holdout compartment for aggregation-prone proteins hindering efficient degradation.", "authors": [{"family": "Gierisch", "given": "Maria E", "initials": "ME", "orcid": "0000-0002-8053-4402", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe10e1b3af59418a8edbd1fea8c37faf.json"}}, {"family": "Barchi", "given": "Enrica", "initials": "E", "orcid": "0009-0007-3209-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a02a6f87294bbd96c11b502f5fba1c.json"}}, {"family": "Marogna", "given": "Mirco", "initials": "M", "orcid": "0009-0000-9866-470X", "researcher": {"href": "https://publications.scilifelab.se/researcher/61ea01f03c4b4995af9e91481cedc783.json"}}, {"family": "Walln\u00f6fer", "given": "Moritz H", "initials": "MH", "orcid": "0000-0002-7688-2359", "researcher": {"href": "https://publications.scilifelab.se/researcher/26832fc473694946b8cd60b280b2a78d.json"}}, {"family": "Ankarcrona", "given": "Maria", "initials": "M", "orcid": "0000-0002-7022-3694", "researcher": {"href": "https://publications.scilifelab.se/researcher/5deb5cb7c18647b5b37d80221b67086c.json"}}, {"family": "Naia", "given": "Luana", "initials": "L", "orcid": "0000-0002-0886-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ae78f608af4f3f8524d5ab4a3c6cdd.json"}}, {"family": "Salomons", "given": "Florian A", "initials": "FA"}, {"family": "Dantuma", "given": "Nico P", "initials": "NP", "orcid": "0000-0002-6090-4170", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ccdd02c787d4a699efd24d297040aa0.json"}}], "type": "journal article", "published": "2026-05-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "17", "issue": "1", "pages": null}, "abstract": "The accumulation of protein aggregates has been causatively linked to the pathogenesis of neurodegenerative diseases. Here, we conduct a genome-wide CRISPR-Cas9 screen to identify cellular factors that regulate the degradation of an aggregation-prone reporter. Genes encoding proteins involved in mitochondrial homeostasis, including the translation factor eIF5A, are enriched among suppressors of the degradation of the reporter. Genetic or chemical inhibition of eIF5A leads to dissociation of the aggregation-prone substrate from mitochondria, which is accompanied by enhanced ubiquitin-dependent proteasomal degradation. The presence of an aggregation-prone, amphipathic helix that localizes the reporter to mitochondria is crucial for the stimulatory effect of eIF5A inhibition on proteasomal degradation. Additionally, inhibition of eIF5A also enhances degradation of mutant huntingtin and \u03b1-synuclein, two disease-associated proteins that contain amphipathic helices and mislocalize to mitochondria. We propose that mitochondria serve as a holdout compartment for aggregation-prone proteins. Therefore, preventing mitochondrial localization of aggregation-prone proteins may offer a viable therapeutic strategy for reducing disease-associated proteins in neurodegenerative disorders.", "doi": "10.1038/s41467-026-72783-0", "pmid": "42098118", "labels": {"CRISPR Functional Genomics": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13153185"}, {"db": "pii", "key": "10.1038/s41467-026-72783-0"}], "notes": [], "created": "2026-05-11T12:46:18.151Z", "modified": "2026-07-23T19:02:15.852Z"}, {"entity": "publication", "iuid": "e7038b6561ed4a8282747388827a8dac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7038b6561ed4a8282747388827a8dac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7038b6561ed4a8282747388827a8dac"}}, "title": "Neuroinflammation and neurodegeneration trigger a specific splice form of ribosomal protein S24", "authors": [{"family": "Magadi", "given": "Srivathsa S", "initials": "SS"}, {"family": "Jonson", "given": "Maria", "initials": "M"}, {"family": "Lucena", "given": "Pablo B", "initials": "PB"}, {"family": "Caliandro", "given": "Michele F", "initials": "MF"}, {"family": "Almeida", "given": "Beatriz", "initials": "B"}, {"family": "Bilalli", "given": "Lorina", "initials": "L"}, {"family": "Budinger", "given": "Dimitri", "initials": "D", "orcid": "0000-0001-7002-1091", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc1d3189e714b89a58b392e2a05eb8e.json"}}, {"family": "Tsoi", "given": "Anna", "initials": "A"}, {"family": "Ntzouni", "given": "Maria", "initials": "M"}, {"family": "Maqdissi", "given": "Joseph Agi", "initials": "JA"}, {"family": "Kaczmarczyk", "given": "Lech", "initials": "L", "orcid": "0000-0003-2747-3134", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b192685d0c2438497741e66bfc183c9.json"}}, {"family": "Zijlstra", "given": "Jente J", "initials": "JJ"}, {"family": "Faketija", "given": "Matej", "initials": "M"}, {"family": "Perkins", "given": "Matthew", "initials": "M"}, {"family": "Paul", "given": "Gesine", "initials": "G", "orcid": "0000-0002-6806-2254", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbbb29ff13af4e28afddbf78764cad29.json"}}, {"family": "Hallbeck", "given": "Martin", "initials": "M", "orcid": "0000-0001-6716-0314", "researcher": {"href": "https://publications.scilifelab.se/researcher/17f7b361871045a1b1e3cdfec9ebe5ec.json"}}, {"family": "Ingelsson", "given": "Martin", "initials": "M", "orcid": "0000-0001-5466-8370", "researcher": {"href": "https://publications.scilifelab.se/researcher/903a14004e794693bebb8c8ca345c626.json"}}, {"family": "Watts", "given": "Joel C", "initials": "JC"}, {"family": "Reichenbach", "given": "Nicole", "initials": "N"}, {"family": "Petzold", "given": "Gabor C", "initials": "GC", "orcid": "0000-0002-0145-8641", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a64d37850384e10a8a4199ea81ae856.json"}}, {"family": "Schieweck", "given": "Rico", "initials": "R"}, {"family": "Heneka", "given": "Michael T", "initials": "MT", "orcid": "0000-0003-4996-1630", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c46f161bc8544a78eef05ee0b74bb47.json"}}, {"family": "Jackson", "given": "Walker S", "initials": "WS", "orcid": "0000-0002-3003-5509", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f49c7978954d098514c5b1bfa9e34b.json"}}], "type": "journal-article", "published": "2026-05-06", "journal": {"title": "Brain", "issn": "0006-8950", "issn-l": null}, "abstract": "Neuroinflammation, particularly that involving reactive microglia, the brain's resident immune cells, is implicated in the pathogenesis of major neurodegenerative diseases (NDs). Multiple studies have reported changes in ribosomal protein (RP) expression during neurodegeneration, but the significance of these changes remains unclear. Ribosomes are evolutionarily conserved protein-synthesizing machines, and although commonly viewed as invariant, accumulating evidence suggests functional ribosome specialization through variation in their protein composition. Among RPs, S24, encoded by RPS24 in humans and Rps24 in mice, is unique as its transcripts undergo alternative splicing to produce protein variants with different C-terminal sequences that are differentially expressed across tissues and cell types. Understanding heterogeneous RP expression patterns across brain regions and cell types could reveal mechanisms underlying selective vulnerability in NDs and provide new biomarkers for neuroinflammatory responses. To identify RP expression patterns across brain regions in neurons, astrocytes, and microglia we analyzed cell type-specific translating mRNAs from mice. To investigate Rps24 isoform-specific expression, we performed cell type-resolved transcript analysis and developed antibodies specific for the S24-PKE protein variant encoded by mRNA isoform Rps24c. We examined Rps24c/S24-PKE expression in brains from mouse models of aging and neurodegeneration, as well as in human postmortem tissue from patients with Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). This work revealed distinct RP expression patterns across brain regions and between neurons, astrocytes, and microglia, including neuron-enriched RPs Rpl13a and Rps10. Analysis of RP paralogs revealed complex expression relationships with their canonical counterparts, suggesting regulated mechanisms for generating heterogeneous ribosomes. Across brain regions and cell types, Rplp0 and Rpl13a, commonly used normalization references, showed heterogeneous expression, raising important methodological considerations for gene expression studies. Rps24 isoforms exhibited striking cell type-specific expression patterns. Rps24c was predominantly expressed in microglia and was increased by neuroinflammation caused by aging, neurodegeneration, or inflammatory chemicals. Using S24-PKE-specific antibodies, we verified increased expression of this protein variant in brains with AD, PD, and HD, and in relevant mouse models. These findings establish heterogeneous RP expression as a feature of brain cell types which may enable cell type-specific translation regulation via specialized ribosomes. This work also identifies Rps24c/S24-PKE as a potential novel marker for neuroinflammation and neurodegeneration and provides new tools for monitoring these responses.", "doi": "10.1093/brain/awag166", "pmid": "42087813", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "8670210"}], "notes": [], "created": "2026-05-11T12:23:19.422Z", "modified": "2026-07-10T08:27:01.238Z"}, {"entity": "publication", "iuid": "b87ff717143c4bf38090dc1906217558", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b87ff717143c4bf38090dc1906217558.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b87ff717143c4bf38090dc1906217558"}}, "title": "Divergent cis regulatory haplotypes at Tlr2 are associated with immune responsiveness", "authors": [{"family": "Nandakumar", "given": "Mridula", "initials": "M", "orcid": "0000-0003-4133-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/62b3ae7920a94445baa9c525a56c0973.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Nouri", "given": "Mehrnaz", "initials": "M", "orcid": "0000-0001-6188-9171", "researcher": {"href": "https://publications.scilifelab.se/researcher/7345bf18ffa64e7f8888a9c540879265.json"}}, {"family": "Valfridsson", "given": "Christine", "initials": "C", "orcid": "0009-0005-0759-0220", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cef4c3c125c4f75ba9abd19046cfc97.json"}}, {"family": "Carlsson", "given": "Fredric", "initials": "F", "orcid": "0000-0003-0875-4395", "researcher": {"href": "https://publications.scilifelab.se/researcher/d970f49b801a41eaafe818b724c03cda.json"}}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal-article", "published": "2026-05-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "0737-4038", "volume": "43", "issue": "5", "issn-l": null}, "abstract": "Positive and balancing selection on pattern recognition receptors (PRRs) is widely thought to target ligand-binding domains and affect the specificity of recognition of different pathogens. Alternatively, positive/balancing selection on PRRs could affect general responsiveness by targeting for example signaling domains or cis-regulatory variation. Studies of a wild rodent (the bank vole, Clethrionomys glareolus) have shown that Tlr2-a lipoprotein-binding PRR-is highly polymorphic with divergent haplotypes and signatures of balancing selection and that Tlr2 genotype is associated with susceptibility to Borrelia afzelii infection in the wild. To investigate what aspect of TLR2 function has been under selection, we here perform integrated population genetic and functional analyses. Ex vivo infection experiments show that the protective Tlr2 haplotype produces a stronger proinflammatory response to B. afzelii compared to the haplotype associated with susceptibility. Tlr2 genotype has a similar, albeit not statistically significant, effect on responsiveness to the phylogenetically distant pathogen Streptococcus pyogenes. We find that the strongest signature of balancing selection is 4.6 kb upstream of the Tlr2 CDS, near a putative enhancer, and that Tlr2 exhibits allele-specific expression such that the protective haplotype is more expressed. Collectively, these results indicate that balancing selection has primarily acted on cis-regulatory variation affecting the general responsiveness via TLR2 signaling rather than on polymorphisms affecting TLR2 ligand-binding specificity.", "doi": "10.1093/molbev/msag113", "pmid": "42052896", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13202456"}, {"db": "pii", "key": "8664598"}], "notes": [], "created": "2026-05-11T11:52:59.250Z", "modified": "2026-06-29T07:42:32.470Z"}, {"entity": "publication", "iuid": "c674acbfed9a4c98952dff6d7cd2f544", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c674acbfed9a4c98952dff6d7cd2f544.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c674acbfed9a4c98952dff6d7cd2f544"}}, "title": "ADAR1 Regulates Alternative Splicing Through an RNA Editing-Independent Mechanism.", "authors": [{"family": "Sagredo", "given": "Eduardo A", "initials": "EA", "orcid": "0000-0001-9984-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dfefa432364269b33bbe8a4075de65.json"}}, {"family": "Karlstr\u00f6m", "given": "Victor", "initials": "V", "orcid": "0000-0002-6985-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dbec2b963c74de7a2f9b62f9caf3267.json"}}, {"family": "Blanco", "given": "Alejandro", "initials": "A", "orcid": "0009-0005-3491-6898", "researcher": {"href": "https://publications.scilifelab.se/researcher/df541551be674916a0ce6fd6f615ce7b.json"}}, {"family": "Moraga", "given": "Paloma", "initials": "P"}, {"family": "Vergara", "given": "Matias", "initials": "M"}, {"family": "Jarvelin", "given": "Aino I", "initials": "AI"}, {"family": "Visa", "given": "Neus", "initials": "N"}, {"family": "Marcelain", "given": "Katherine", "initials": "K", "orcid": "0000-0003-4018-6623", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d278a6af5d848a9a494dc1bf943d442.json"}}, {"family": "Castello", "given": "Alfredo", "initials": "A", "orcid": "0000-0002-1499-4662", "researcher": {"href": "https://publications.scilifelab.se/researcher/476fdd8bab4644e5a137f20a3449d38c.json"}}, {"family": "Armis\u00e9n", "given": "Ricardo", "initials": "R", "orcid": "0000-0003-2567-0521", "researcher": {"href": "https://publications.scilifelab.se/researcher/25353a66f05b4944baff4de826f9ee96.json"}}], "type": "journal article", "published": "2026-04-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "27", "issue": "9", "issn-l": null}, "abstract": "Dysregulation of the RNA-editing enzyme ADAR1 is associated with human diseases, including cancer, but its RNA-editing-independent roles in alternative splicing remain largely unexplored. Comprehending these molecular mechanisms is paramount, as they may unveil novel therapeutic targets. This study elucidates how the ADAR1p110 isoform influences alternative splicing independently of its canonical editing activity. Employing RNA-sequencing, proteomic analysis of ADAR1p110 interactors, and functional assays with wild-type and mutant ADAR1 in diverse human cell lines (including cancer models), we investigated its impact on the splicing landscape. Our findings indicate that ADAR1p110 interacts with pivotal spliceosome components and auxiliary splicing regulators. Notably, ADAR1 extensively modulates alternative-splicing events, with most of these alterations occurring independently of its RNA-editing activity and often its RNA-binding capacity. Furthermore, ADAR1 alters the isoform expression of other splicing factors (e.g., ACIN1), suggesting an indirect regulatory mechanism. Importantly, this splicing reprogramming affects genes that govern therapeutic response, positioning the ADAR-splicing axis as a potential driver of drug resistance. By revealing this predominantly editing-independent mechanism, we expand the understanding of ADAR1's non-canonical functions and identify a new avenue for therapeutic intervention in cancer.", "doi": "10.3390/ijms27093952", "pmid": "42123534", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13164374"}, {"db": "pii", "key": "ijms27093952"}], "notes": [], "created": "2026-07-14T17:47:12.859Z", "modified": "2026-07-14T17:48:54.816Z"}, {"entity": "publication", "iuid": "192bc0ba645d4a9babc3be3256ac2d23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/192bc0ba645d4a9babc3be3256ac2d23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/192bc0ba645d4a9babc3be3256ac2d23"}}, "title": "Breeding for climate adaptation: genetic variation and genomic selection for drought response in Scots pine.", "authors": [{"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Estravis Barcala", "given": "Maximiliano", "initials": "M"}, {"family": "Fundova", "given": "Irena", "initials": "I"}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chen", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2026-04-27", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Drought intensity and frequency are increasing under global warming in the boreal forests, and breeding for drought resistance will facilitate adaptation of new planting material to changing climate conditions. We used a tree-ring dataset of 559 individuals to study Scots pine genetic variation and the efficiency of genomic selection of drought-response traits (drought resistance, recovery and resilience), for the first time. From genotyping-by-sequencing (GBS), 31,101 SNPs were generated and used for the study.\n\nSignificant genetic variation was detected for drought-response and other growth, wood-anatomy and wood density traits. Heritability estimates for wood-anatomical traits were higher than those for drought-response and growth traits. Genetic correlations between drought-response and wood-anatomical traits were generally high but mostly nonsignificant. In contrast, drought resistance and recovery showed positive and significant correlations with basal area increment and height. We found that the predictive ability and accuracy for drought-response traits were lower than those for wood-anatomical traits, and were comparable between GBLUP and ABLUP. Greater genetic gain per year can be achieved through genomic selection relative to pedigree-based selection if the generation interval is reduced.\n\nThe positive genetic correlation between drought-response and growth traits will enable simultaneous selection for improved growth and increased drought resistant trees in Scots pine breeding through either pedigreed-based and genomic selection.\n\nThe online version contains supplementary material available at 10.1186/s12864-026-12849-x.", "doi": "10.1186/s12864-026-12849-x", "pmid": "42045837", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13122877"}, {"db": "pii", "key": "10.1186/s12864-026-12849-x"}], "notes": [], "created": "2026-05-11T12:13:32.454Z", "modified": "2026-05-11T12:13:32.461Z"}, {"entity": "publication", "iuid": "c115bbb0dfbc4b998a5920a0fb8492e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c115bbb0dfbc4b998a5920a0fb8492e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c115bbb0dfbc4b998a5920a0fb8492e8"}}, "title": "Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia.", "authors": [{"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/891a915ffd054c57b7c0d107c4e1b7e1.json"}}, {"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Regn\u00e9ll", "given": "Carl", "initials": "C", "orcid": "0000-0002-5662-4950", "researcher": {"href": "https://publications.scilifelab.se/researcher/65820ac7ae1c4b6a87dd1334087e677d.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Gyllencreutz", "given": "Richard", "initials": "R", "orcid": "0000-0003-3193-8598", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c1d90a4e134dceb7f816725596aa6f.json"}}, {"family": "Greenwood", "given": "Sarah L", "initials": "SL", "orcid": "0000-0003-3048-7916", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4036ea604943ca9e8d0e2d7ae48d23.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2026-04-21", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "123", "issue": "16", "pages": "e2527944123", "issn-l": "0027-8424"}, "abstract": "After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two directions-from the south and the northeast-resulting in a nonoverlapping distribution of two distinct mitochondrial clades. A contact zone in central Sweden separates populations with mitochondrial clade 1a in the south from those with clade 3a in the north. However, a paucity of brown bear subfossils in Scandinavia has limited testing of this prevailing model using ancient DNA. Here, we present a high-coverage brown bear mitogenome (231\u00d7) and nuclear genome-wide data (0.05\u00d7) extracted from lake sediment dated to 9.6 cal. ka BP from northern Sweden, representing the oldest known record of brown bear in the region. At this point in the Early Holocene, the Fennoscandian Ice Sheet was in its final stages of recession. Surprisingly, our analyses suggest that this environmental genome represents one male individual carrying clade 1a and with southern brown bear nuclear ancestry, despite being found far north of the contact zone. This suggests the individual was a migratory bear and had dispersed northward from its birthplace. Our finding adds to the scarce genomic record of Early Holocene brown bears and highlights the use of sedimentary ancient DNA as a powerful source of genomic information.", "doi": "10.1073/pnas.2527944123", "pmid": "41973920", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13099568"}], "notes": [], "created": "2026-05-11T11:39:29.980Z", "modified": "2026-05-11T11:39:30.533Z"}, {"entity": "publication", "iuid": "87bf60ec792f4e9caf54376f46b3ad5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f"}}, "title": "Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Buyan", "given": "Andrey", "initials": "A", "orcid": "0000-0001-9105-4028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79c4583ae342a5ae931e39f7e282a7.json"}}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Gryzunov", "given": "Nikita", "initials": "N", "orcid": "0009-0000-0782-8650", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb53aa525ff4269936724c077b2d387.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Mauron", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0004-0909-3554", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0b2662f1bc40b682ff6923c797877e.json"}}, {"family": "Nozdrin", "given": "Vladimir", "initials": "V", "orcid": "0009-0004-3053-1387", "researcher": {"href": "https://publications.scilifelab.se/researcher/456249fbb9ef48cebc32cc15fe39a35b.json"}}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Petersson Sj\u00f6gren", "given": "Madeleine", "initials": "M"}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A", "orcid": "0000-0002-3427-9455", "researcher": {"href": "https://publications.scilifelab.se/researcher/9096109f1be94b7197fd249c4193c9d7.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Kulakovskiy", "given": "Ivan V", "initials": "IV", "orcid": "0000-0002-6554-8128", "researcher": {"href": "https://publications.scilifelab.se/researcher/41163cb5ec5d44668f9c6f06edb379ab.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}], "type": "journal article", "published": "2026-04-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Bicuspid aortic valve, a prevalent congenital malformation, predisposes individuals to severe complications. Although the condition exhibits substantial heritability, known protein-coding and common regulatory mutations explain a minority of cases. To assess the contribution of rare regulatory variants, here we integrate high-resolution three-dimensional genome organization profiling with matched whole-genome sequencing from eight individuals with bicuspid aortic valves and eight with standard tricuspid aortic valves. In bicuspid aortic valve patients, mutation-driven chromatin rewiring affected 1.8-fold more valve development genes than in healthy individuals. Genome-wide in silico analyses show that rare regulatory mutations disrupt the transcriptomes of mesenchymal cell populations necessary for endocardial cushion formation. We identify 198 candidate genes associated with bicuspid aortic valve, revealing pronounced heterogeneity and complex interplay between coding and regulatory mutations. Collectively, our findings establish rare regulatory mutations as contributors to the heritability of bicuspid aortic valve and underscore the need to elucidate their mechanistic roles in disease pathogenesis.", "doi": "10.1038/s41467-026-71758-5", "pmid": "41997951", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13090386"}, {"db": "pii", "key": "10.1038/s41467-026-71758-5"}], "notes": [], "created": "2026-05-11T11:41:45.495Z", "modified": "2026-05-11T11:41:46.015Z"}, {"entity": "publication", "iuid": "b32de9be5435484c9597989fb073c05f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b32de9be5435484c9597989fb073c05f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b32de9be5435484c9597989fb073c05f"}}, "title": "RUVBL1 and RUVBL2 are druggable MYC effector regulators in neuroblastoma cells.", "authors": [{"family": "Siaw", "given": "Joachim Tetteh", "initials": "JT"}, {"family": "Claeys", "given": "Arne", "initials": "A"}, {"family": "Lai", "given": "Wei-Yun", "initials": "WY"}, {"family": "Boren\u00e4s", "given": "Marcus", "initials": "M"}, {"family": "Hilgert", "given": "Elien", "initials": "E"}, {"family": "Bekaert", "given": "Sarah-Lee", "initials": "SL"}, {"family": "Sanders", "given": "Ellen", "initials": "E"}, {"family": "Kaya", "given": "Irem", "initials": "I"}, {"family": "Van Dorpe", "given": "Jo", "initials": "J"}, {"family": "Speleman", "given": "Frank", "initials": "F"}, {"family": "Durinck", "given": "Kaat", "initials": "K"}, {"family": "Hallberg", "given": "Bengt", "initials": "B"}, {"family": "Palmer", "given": "Ruth H", "initials": "RH"}, {"family": "Van den Eynden", "given": "Jimmy", "initials": "J"}], "type": "journal article", "published": "2026-04-17", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "4", "pages": "115236", "issn-l": "2589-0042"}, "abstract": "High-risk neuroblastoma is characterized by MYCN amplification and high MYCN or MYC gene expression. These patients have a poor prognosis and there is an urgent need for more effective drugs. While strategies to develop inhibitors that directly target the MYC proteins have remained largely unsuccessful, recent preclinical studies have identified ATR, a key protein of the DNA damage response, as a promising alternative therapeutic target. Here, we identified a strong RUVBL1 and RUVBL2 signature in transcriptomics data derived from different MYCN-driven mice tumors treated with ATR inhibitors. The RUVBL proteins form a complex with ATPase activity that has broad cellular functions and we demonstrate that pharmacological inhibition of this protein complex results in a strong reduction of MYC(N) signaling, cell-cycle arrest, DNA damage, and apoptosis. We confirmed the association with MYCN and identified the RUVBL genes as independent prognostic biomarkers in human primary neuroblastoma data.", "doi": "10.1016/j.isci.2026.115236", "pmid": "41940329", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13049659"}, {"db": "pii", "key": "S2589-0042(26)00611-5"}], "notes": [], "created": "2026-04-10T13:11:20.241Z", "modified": "2026-04-10T13:11:20.252Z"}, {"entity": "publication", "iuid": "80874800e5764f2299c86ac54a90127a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80874800e5764f2299c86ac54a90127a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80874800e5764f2299c86ac54a90127a"}}, "title": "Genomic insights into fragmentation and translocation in European green toads.", "authors": [{"family": "Walderich", "given": "Leonie Muriel", "initials": "LM"}, {"family": "Susanto", "given": "Alvin Wiwiet", "initials": "AW"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}, {"family": "Fohrman", "given": "Anna", "initials": "A"}, {"family": "Wir\u00e9n", "given": "Mats", "initials": "M"}, {"family": "O'Dwyer", "given": "Rachael", "initials": "R"}, {"family": "F\u00f6rs\u00e4ter", "given": "Kristofer", "initials": "K"}, {"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2026-04-17", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "4", "pages": "115395", "issn-l": "2589-0042"}, "abstract": "The European green toad (Bufotes viridis) is Sweden's most threatened amphibian. Its range has contracted over the past century, with many local extinctions; remaining populations are fragmented and often isolated. Since the 1990s, conservation has focused on translocations to existing breeding sites and new localities, but many efforts have had limited success. We detected lower genetic diversity in Scandinavian populations (southern Sweden and nearby Denmark) than in Poland, plus strong structure and differentiation among Scandinavian subpopulations, implying unexpectedly low gene flow despite translocations. Small, isolated populations are strongly affected by drift, and whole-genome analyses reveal inbreeding and high genetic load in some subpopulations. We recommend reassessing source populations for translocations: the stock used in captive breeding and most past releases shows intermediate diversity but also signs of divergent selection and putative local adaptation. Management should balance minimizing inbreeding depression against risks of outbreeding depression and erosion of local adaptation risks.", "doi": "10.1016/j.isci.2026.115395", "pmid": "42006334", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13084336"}, {"db": "pii", "key": "S2589-0042(26)00770-4"}], "notes": [], "created": "2026-05-11T13:10:40.099Z", "modified": "2026-05-11T13:10:40.109Z"}, {"entity": "publication", "iuid": "c67e37951ff244288a56301faa275a0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c67e37951ff244288a56301faa275a0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c67e37951ff244288a56301faa275a0d"}}, "title": "Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.", "authors": [{"family": "Fonseca", "given": "Alexis", "initials": "A"}, {"family": "Hermans", "given": "Martijn", "initials": "M"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Stranne", "given": "Christian", "initials": "C"}, {"family": "Norkko", "given": "Alf", "initials": "A"}, {"family": "Gustafsson", "given": "Bo G", "initials": "BG"}, {"family": "Humborg", "given": "Christoph", "initials": "C"}], "type": "journal article", "published": "2026-04-15", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Cable bacteria are filamentous sulphide-oxidisers capable of cm-scale electron transport. They are generally considered restricted to the upper few oxic-suboxic cm of marine sediments, where they couple sulphide oxidation to oxygen or nitrate reduction. Despite their influence on redox gradients, trace metal mobility, and nutrient cycling, their presence and activity in deeper anoxic sediment layers remain unknown. The presence and activity of marine cable bacteria (Candidatus Electrothrix) were investigated at four stations in Sweden and Finland, including deep vertical profiles of anoxic sediment layers, to assess their presence and activity under different environmental contexts.\n\nUsing metatranscriptomic data for rRNA-based community profiling and gene expression combined with porewater geochemistry, evidence of abundant and active cable bacteria was found, peaking below 20 cm depth in deep anoxic sediment layers of Kolj\u00f6 Fjord on the Swedish West Coast. This zone coincided with elevated gene expressions related to sulphide oxidation (including sqr) and nitrate reduction (napA), as well as an abundant presence of sulphide and a sharp nitrate peak. Phylogenetic analyses revealed a diverse assemblage of Ca. Electrothrix includes several potential novel taxa. The co-occurrence of cable bacteria activity, sulphide availability, and a nitrate peak at depth suggests that these organisms may be supported by local nitrate production under anoxic conditions.\n\nOur findings challenge the prevailing view that cable bacteria are restricted to shallow sediment horizons and demonstrate their activity and diversity in deep, anoxic layers. This expands the known ecological niche of cable bacteria and suggests that locally produced nitrate under anoxic conditions may facilitate their activity at depth. This discovery advances our understanding of ecology in anoxic marine environments, providing new insights into marine cable bacteria, sediment biogeochemistry, and analogues of early Earth microbial ecosystems.", "doi": "10.1186/s40793-026-00895-7", "pmid": "41987322", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13081432"}, {"db": "pii", "key": "10.1186/s40793-026-00895-7"}], "notes": [], "created": "2026-05-11T11:49:40.138Z", "modified": "2026-05-11T11:49:40.148Z"}, {"entity": "publication", "iuid": "0e45658433fb4fd68d5f344433957d24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e45658433fb4fd68d5f344433957d24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e45658433fb4fd68d5f344433957d24"}}, "title": "A transcriptional atlas of the pubertal human growth plate reveals two populations of stem cells and direct effect of growth hormone.", "authors": [{"family": "Chu", "given": "Nelson Tsz Long", "initials": "NTL", "orcid": "0000-0001-8553-6880", "researcher": {"href": "https://publications.scilifelab.se/researcher/771e0a6c700f4b4f9765f9a2811608eb.json"}}, {"family": "Dregval", "given": "Ostap", "initials": "O", "orcid": "0000-0002-9939-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d8ecff20444e9bf82f702e21e736c.json"}}, {"family": "Zaman", "given": "Farasat", "initials": "F", "orcid": "0000-0002-1832-1051", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c082df96e5c43afbca28c5c6f8e7810.json"}}, {"family": "Li", "given": "Lei", "initials": "L", "orcid": "0000-0002-8026-3665", "researcher": {"href": "https://publications.scilifelab.se/researcher/31e881d87f094a92bc6b34f734ffe12f.json"}}, {"family": "Tian", "given": "Xin", "initials": "X"}, {"family": "Liu", "given": "Xin", "initials": "X"}, {"family": "Trompet", "given": "Dana", "initials": "D", "orcid": "0000-0001-9472-6184", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ef4d02ec2e1427088522df2a759bf3a.json"}}, {"family": "Zhou", "given": "Baoyi", "initials": "B"}, {"family": "Heinonen", "given": "Jussi O", "initials": "JO"}, {"family": "Ohlsson", "given": "Claes", "initials": "C", "orcid": "0000-0002-9633-2805", "researcher": {"href": "https://publications.scilifelab.se/researcher/995dac358caa4a169fc889b7a3eef44a.json"}}, {"family": "S\u00e4vendahl", "given": "Lars", "initials": "L", "orcid": "0000-0003-1067-4976", "researcher": {"href": "https://publications.scilifelab.se/researcher/6da067b5b4a34625806e9335fa921f09.json"}}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Chagin", "given": "Andrei S", "initials": "AS", "orcid": "0000-0002-2696-5850", "researcher": {"href": "https://publications.scilifelab.se/researcher/909bca2fc68645e980a93b99dc150e4c.json"}}], "type": "journal article", "published": "2026-04-15", "journal": {"title": "Sci Transl Med", "issn": "1946-6242", "volume": "18", "issue": "845", "pages": "eadw3590", "issn-l": "1946-6234"}, "abstract": "The cartilaginous growth plate is a critical organ responsible for longitudinal bone growth. It closes after puberty in humans but remains open throughout life in mice. Although cartilage stem cells have been identified in murine growth plates, their existence in humans and their regulation by growth hormone (GH), the most widely used therapy for growth retardation, remain unknown. Here, we characterized the cellular and molecular organization of early pubertal human growth plates using unique surgical specimens from growth-restricting procedures and examined their direct responsiveness to GH. Single-cell and spatial analyses revealed two distinct stemlike populations in the resting zone, differing in proliferative activity, molecular identity, and regulatory cues. The root stem cells express multiple skeletal stem cell markers but not parathyroid hormone-related peptide and reside in a specialized microenvironment low in WNT and TGF-\u03b2 growth factors. A similar population was identified in transcriptionally profiled unsorted murine growth plates, and clonal lineage tracing demonstrated that these root cells, marked by expression of the Prrx1 gene, generate extensive chondrocyte clones and differentiate into stromal and osteoblastic lineages, confirming their stem cell properties. Human growth plate explant cultures showed that GH directly activates JAK/STAT, TGF-\u03b2, and ERK intracellular signaling pathways, inhibits AKT signaling, and stimulates cartilage growth and proliferation of cartilage stem cells and chondrocytes in the proliferative zone. Together, these findings uncover a conserved dual stem cell organization in human and mouse growth plates and define direct mechanisms of GH action, providing a framework for optimizing growth-promoting therapies.", "doi": "10.1126/scitranslmed.adw3590", "pmid": "41984930", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-05-11T12:02:43.939Z", "modified": "2026-05-11T12:02:44.448Z"}, {"entity": "publication", "iuid": "22d1c899e817411c810114fd519eebb3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22d1c899e817411c810114fd519eebb3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22d1c899e817411c810114fd519eebb3"}}, "title": "A Phytophthora infestans CRN1-derived small RNA is predicted to target the potato immune regulator EDS1.", "authors": [{"family": "Singh", "given": "Shailja", "initials": "S"}, {"family": "Hu", "given": "Xinyi", "initials": "X"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2026-04-10", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "17", "pages": "1791978", "issn-l": "1664-462X"}, "abstract": "The late blight pathogen, Phytophthora infestans (Pi), causes severe damage to plants in the Solanaceae family. Although knowledge regarding the P. infestans-mediated manipulation of critical components in the plant defense system is growing, many questions remain unanswered. Herein, we aimed to examine the role of Argonaute 1 (AGO1) associated small RNAs in this interaction. Of particular interest was the early communication between the host and the pathogen. To visualize the cellular dynamics underlying potential cross-kingdom RNA trafficking, we first examined the localization and accumulation patterns of plant extracellular vesicles (EVs) and multivesicular bodies (MVBs) using a handful of markers. MVBs were present not only at the plant plasma membrane but also in the germ tube of the invading pathogen. The enrichment of MVBs decreased as the infection process proceeded. At 3.0 days post-inoculation, co-localization between AGO1 from P. infestans and StARA6 was not seen even at the swollen tip of the germ tube. Three Crinkler effector genes encoding small RNAs were found after coimmunoprecipitation, sequencing and extensive bioinformatic analysis. PiCRN1 caused more severe disease compared with PiCRN3, which carries a typical Crinkler (CRN) LFLAK domain. This difference may result from activation of a CRN1-derived siRNA predicted to target the enhanced disease susceptibility 1 (EDS1) gene in potato. To examine whether the observed phenotypic effects can be attributed to any EV cargo from the potato host, we set up a procedure to isolate EVs from P. infestans-infected potato leaves. However, the tiny EV yield obtained during the early infection phase prevented us from such analysis. The understanding of effector cell trafficking and small RNA reprogramming of host plant genes remain elusive in this pathosystem.", "doi": "10.3389/fpls.2026.1791978", "pmid": "42040283", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13106546"}], "notes": [], "created": "2026-05-11T12:26:39.885Z", "modified": "2026-05-11T12:26:39.900Z"}, {"entity": "publication", "iuid": "b05f9a8302e1405588f93dc3cb79e0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b05f9a8302e1405588f93dc3cb79e0e5"}}, "title": "Proviral NUP153 binding to viral proteins and RNA regulates structural-nonstructural protein ratios in orthoflavivirus infection.", "authors": [{"family": "Peters", "given": "Marie B A", "initials": "MBA", "orcid": "0000-0001-8994-0864", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4733590d054742b732c2028a8f5e8a.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Yau", "given": "Wai-Lok", "initials": "WL"}, {"family": "Sengupta", "given": "Pallabi", "initials": "P", "orcid": "0000-0002-1413-9412", "researcher": {"href": "https://publications.scilifelab.se/researcher/851c95f648f242e0ba67202279725796.json"}}, {"family": "Niedermoser", "given": "Isabell", "initials": "I", "orcid": "0000-0002-5301-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b5c11f4f945a5a273c9fd040bee6f.json"}}, {"family": "Gerold", "given": "Gisa", "initials": "G", "orcid": "0000-0002-1326-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6353493de47c4ec58831f79ed94045f4.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}, {"family": "Lundmark", "given": "Richard", "initials": "R", "orcid": "0000-0001-9104-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e1b756caa79468dab0f960e43cd61d3.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723"}, "abstract": "Orthoflaviviruses are RNA viruses that cause serious diseases in humans, with currently no antivirals available. Targeting host factors is emerging as an attractive antiviral approach. However, as a first step, there is a need to understand which host proteins are hijacked and for what purpose. Here, using a combination of fluorescence microscopy, knock-down, crosslinking immunoprecipitation sequencing, mass spectrometry, and in vitro and biophysical assays, we identify nucleoporin-153 (NUP153) as a proviral factor during orthoflavivirus infection. We show that NUP153 is recruited to the virus amplification site on the endoplasmic reticulum to impact the structural to nonstructural viral protein ratios. We find that NUP153 interacts with both the viral proteins NS3 and NS5, and a highly conserved G-rich motif on the viral RNA. These interactions specifically promote the production of viral structural proteins, leading to an efficient virion assembly, virus release and spread to new cells. We propose that NUP153 acts as a key regulator in viral protein ratios, a mechanism that appears conserved among orthoflaviviruses.", "doi": "10.1038/s41467-026-71449-1", "pmid": "41951628", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71449-1"}], "notes": [], "created": "2026-04-10T12:13:07.525Z", "modified": "2026-04-10T12:13:08.280Z"}, {"entity": "publication", "iuid": "23158676211240e2a69a681a1b190fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23158676211240e2a69a681a1b190fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23158676211240e2a69a681a1b190fe0"}}, "title": "Centromeric instability and chromoanasynthesis observed in nine supernumerary marker chromosomes resolved with long-read genome sequencing.", "authors": [{"family": "Bilgrav Saether", "given": "Kristine", "initials": "K"}, {"family": "Salazar Mantero", "given": "Angelo", "initials": "A"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2026-04-07", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "36", "issue": "4", "pages": "661-670", "issn-l": "1088-9051"}, "abstract": "Small supernumerary marker chromosomes (sSMCs) remain a diagnostic challenge despite sequencing advances. As the field shifts toward cytogenomics, there is a need to establish methodologies to resolve these complex genetic variants at base pair resolution, as well as to identify their chromosomal origin and formation mechanism. Here, we apply long-read genome sequencing (lrGS) in combination with the telomere-to-telomere (T2T-CHM13) assembly to characterize the structure and genomic content of 10 clinically detected sSMCs. We use sequencing data to reconstruct the derivative chromosomes, identify breakpoint junctions (BPJs), and infer formation mechanisms. We resolve the BPJs of nine of the 10 sSMCs at base pair resolution. The analysis reveals six simple intrachromosomal rearrangements (one continuous and five discontinuous) with one to three BPJs, one complex three-way translocation with two BPJs, and two highly complex intrachromosomal rearrangements with five and nine BPJs, respectively. Breakpoint analysis reveals distinct mechanistic signatures: Simple sSMCs show features consistent with microhomology-mediated end joining (MMEJ) or microhomology-mediated break-induced replication (MMBIR), whereas complex sSMCs demonstrate evidence of translocation, chromoanasynthesis, and breakage-fusion-bridge (BFB) cycles. Haplotype analysis supports trisomy rescue in four cases, including all three complex sSMCs. In summary, our study demonstrates that lrGS combined with T2T-CHM13 enables detailed structural and mechanistic characterization of sSMCs, providing experimental support for disruption of trisomy rescue as a key formation mechanism. This work illustrates the feasibility of resolving highly challenging chromosomal abnormalities using long-read sequencing technologies.", "doi": "10.1101/gr.281175.125", "pmid": "41881544", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13138008"}, {"db": "pii", "key": "gr.281175.125"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2026-04-10T11:53:57.469Z", "modified": "2026-08-12T15:19:27.884Z"}, {"entity": "publication", "iuid": "16a8d45180854dfdb468144fa9775e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34"}}, "title": "Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fen\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyraite", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Katarzyte", "given": "Marija", "initials": "M"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2026-04-04", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.\n\nAs hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.\n\nOur results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.", "doi": "10.1186/s40793-026-00881-z", "pmid": "41935342", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13067490"}, {"db": "pii", "key": "10.1186/s40793-026-00881-z"}], "notes": [], "created": "2026-04-10T12:05:26.160Z", "modified": "2026-04-16T09:42:39.411Z"}, {"entity": "publication", "iuid": "15e539643f51433caa47680271e70979", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15e539643f51433caa47680271e70979.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15e539643f51433caa47680271e70979"}}, "title": "Limosilactobacillus reuteri metabolites modulate immune pathways and intestinal barrier repair after 5 fluorouracil exposure.", "authors": [{"family": "Lasaviciute", "given": "Gintare", "initials": "G"}, {"family": "L\u00f3pez Plana", "given": "Marta", "initials": "M"}, {"family": "Sundberg \u00d6rtegren", "given": "Sofia", "initials": "S"}, {"family": "Telli", "given": "Sevasteia", "initials": "S"}, {"family": "Kourmoulakis", "given": "Symeon", "initials": "S"}, {"family": "Ermann Lundberg", "given": "Ludwig", "initials": "L", "orcid": "0000-0001-5983-1771", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb47fe370d24b30b505f75583167a9f.json"}}, {"family": "Lidberg", "given": "Kenny", "initials": "K"}, {"family": "Peiris", "given": "Oshadi", "initials": "O"}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Jonsson", "given": "Ann-Beth", "initials": "AB"}, {"family": "Roos", "given": "Stefan", "initials": "S", "orcid": "0000-0002-1606-1794", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab7209c1ebe40d8bdcc73f99fb44b29.json"}}, {"family": "Nilsson", "given": "Anna", "initials": "A"}, {"family": "Mata Forsberg", "given": "Manuel", "initials": "M", "orcid": "0009-0008-3711-9722", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a1120ae12e54a829e523e983c5ea0d2.json"}}, {"family": "Sverremark-Ekstr\u00f6m", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2026-04-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Antimetabolites such as 5 fluorouracil are known to induce inflammation in the gut and oral cavity, underscoring the need for strategies that mitigate chemotherapy-associated toxicity. The aim of this study was to determine whether secreted components from the probiotic bacterium Limosilactobacillus reuteri DSM 17938, specifically cell-free supernatant, exopolysaccharides, and extracellular membrane vesicles, can support epithelial barrier recovery following 5 fluorouracil-induced injury. Exposure to 5 fluorouracil impaired viability, metabolic activity, and barrier integrity, and shifted the functional responses of Caco-2 cells toward increased inflammation. Stimulation with exopolysaccharides after removal of 5 fluorouracil significantly improved barrier integrity in both enterocyte-like Caco-2 cells and primary human intestinal epithelial cells, while paradoxically inducing an inflammatory protein profile in the enterocyte-like cells. Transcriptomic analysis revealed that exopolysaccharides modulate gene programs associated with extracellular matrix organization and structural remodelling. Furthermore, cell-free supernatant, membrane vesicles, and exopolysaccharides differentially influenced monocyte polarization pathways when monocytes were cultured with supernatant from 5 fluorouracil-exposed Caco-2 cells. Together, these findings demonstrate that bacterial metabolites such as exopolysaccharides influence intestinal barrier recovery upon inflammation and activate immune cell recruitment that could have consequences for the intestinal epithelial integrity during inflammation.", "doi": "10.1038/s41598-026-45524-y", "pmid": "41927663", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13049081"}, {"db": "pii", "key": "10.1038/s41598-026-45524-y"}], "notes": [], "created": "2026-04-10T12:45:16.030Z", "modified": "2026-05-04T07:55:34.771Z"}, {"entity": "publication", "iuid": "00a23e638c504441b0a54f8ee8dec96b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00a23e638c504441b0a54f8ee8dec96b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00a23e638c504441b0a54f8ee8dec96b"}}, "title": "Single-Cell Triomics Analysis of Tumor Cells Infiltrating Patient-Derived Breast Cancer Scaffolds", "authors": [{"family": "Filges", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5994-6699", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d546bd6e774a639c45968aa81c0c1b.json"}}, {"family": "Jonasson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0463-9373", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddcca3a85ea848c5afdae4d5cf066b44.json"}}, {"family": "Leiva Arrabal", "given": "Maria Del Carmen", "initials": "MDC"}, {"family": "Andersson", "given": "Lisa", "initials": "L"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Dhingra", "given": "Dalia", "initials": "D"}, {"family": "Mendez", "given": "Pedro", "initials": "P"}, {"family": "Ooi", "given": "Aik", "initials": "A", "orcid": "0000-0002-9101-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/817965235259489cb9e029059b9451e3.json"}}, {"family": "Sciambi", "given": "Adam", "initials": "A"}, {"family": "Landberg", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-9004-9403", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3b79caacba4566897f136a1200476f.json"}}, {"family": "Ruff", "given": "David", "initials": "D", "orcid": "0000-0003-2260-3163", "researcher": {"href": "https://publications.scilifelab.se/researcher/f48bd314d7494e819be6ae6d4d2ea1ca.json"}}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "journal-article", "published": "2026-04-00", "journal": {"title": "Am. J. Pathol.", "issn": "0002-9440", "volume": "196", "issue": "4", "pages": "1016-1027", "issn-l": null}, "abstract": "Cellular heterogeneity plays a critical role in tissues and diseases, including cancer. Single-cell technologies are required to provide detailed information about the phenotype and genotype of individual cells. Despite several approaches to analyzing different analytes at the single-cell level, it is challenging to assess DNA, RNA, and protein simultaneously. Here, a single-cell triomics method to assess DNA, RNA, and proteins from the same cell using a targeted sequencing approach is shown. Breast cancer cells cultured in monolayers and in patient-derived scaffolds that mimic in vivo-like growth conditions, both with and without chemotherapy treatment, were analyzed. Data showed that DNA, RNA, and protein biomarkers could be reliably analyzed, providing biological insights into breast cancer cell heterogeneity. In addition, chemotherapy treatment caused changes in subpopulations and expressions of biomarkers. Furthermore, cells growing in patient-derived scaffolds generated from various breast cancers affected cell heterogeneity and drug resistance differently as a result of the unique tumor-specific microenvironments. The data show that single-cell triomics provides new means to assess cancer cell heterogeneity at DNA, RNA, and protein levels.", "doi": "10.1016/j.ajpath.2025.12.013", "pmid": "41580235", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9440(26)00008-8"}], "notes": [], "created": "2026-02-09T12:51:37.488Z", "modified": "2026-03-24T09:14:15.522Z"}, {"entity": "publication", "iuid": "4314ddab9c19449c8f14a8a5c00981fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4314ddab9c19449c8f14a8a5c00981fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4314ddab9c19449c8f14a8a5c00981fa"}}, "title": "Pan-Continental Genomic Analysis of Eurasian Perch Uncovers Global Diversity Hotspots and Postglacial Recolonization Patterns.", "authors": [{"family": "Lichman", "given": "Vitalii", "initials": "V", "orcid": "0009-0007-5955-0479", "researcher": {"href": "https://publications.scilifelab.se/researcher/379b94bfc1184a189ee57c449956ffad.json"}}, {"family": "Ozerov", "given": "Mikhail", "initials": "M"}, {"family": "L\u00f3pez", "given": "Mar\u00eda-Eugenia", "initials": "ME"}, {"family": "Noreikiene", "given": "Kristina", "initials": "K"}, {"family": "Kahar", "given": "Siim", "initials": "S"}, {"family": "Pukk", "given": "Lilian", "initials": "L"}, {"family": "Burimski", "given": "Oksana", "initials": "O"}, {"family": "Japoshvili", "given": "Bella", "initials": "B"}, {"family": "Blazhekovikj-Dimovska", "given": "Dijana", "initials": "D"}, {"family": "Lajus", "given": "Dmitry", "initials": "D"}, {"family": "Nikoli\u0107", "given": "Du\u0161an", "initials": "D"}, {"family": "Ribeiro", "given": "Filipe", "initials": "F"}, {"family": "Gebauer", "given": "Tatyana", "initials": "T"}, {"family": "Kou\u0159il", "given": "Jan", "initials": "J"}, {"family": "Peterka", "given": "Ji\u0159\u00ed", "initials": "J"}, {"family": "Blabolil", "given": "Petr", "initials": "P"}, {"family": "\u010cech", "given": "Martin", "initials": "M"}, {"family": "J\u016fza", "given": "Tom\u00e1\u0161", "initials": "T"}, {"family": "Kube\u010dka", "given": "Jan", "initials": "J"}, {"family": "Mu\u0161ka", "given": "Milan", "initials": "M"}, {"family": "\u0160mejkal", "given": "Marek", "initials": "M"}, {"family": "Va\u0161ek", "given": "Mojm\u00edr", "initials": "M"}, {"family": "Kahilainen", "given": "Kimmo", "initials": "K"}, {"family": "Lo\u017eys", "given": "Linas", "initials": "L"}, {"family": "Carlsson", "given": "Jens", "initials": "J"}, {"family": "Corcoran", "given": "William", "initials": "W"}, {"family": "Yilmaz", "given": "\u00d6zgen", "initials": "\u00d6"}, {"family": "Ekl\u00f6v", "given": "Peter", "initials": "P", "orcid": "0000-0002-8981-1453", "researcher": {"href": "https://publications.scilifelab.se/researcher/461265784bf643658985483277624d66.json"}}, {"family": "Tak\u00e1cs", "given": "P\u00e9ter", "initials": "P"}, {"family": "B\u00e1n\u00f3", "given": "B\u00e1lint", "initials": "B"}, {"family": "Pallos", "given": "R\u00e9ka", "initials": "R"}, {"family": "Kazakov", "given": "Stefan", "initials": "S"}, {"family": "Pehlivanov", "given": "Luchezar", "initials": "L"}, {"family": "Lecocq", "given": "Thomas", "initials": "T"}, {"family": "Lambert", "given": "Sophie", "initials": "S"}, {"family": "Lauridsen", "given": "Torben", "initials": "T"}, {"family": "Berthelsen", "given": "Andreas", "initials": "A"}, {"family": "Raposeiro", "given": "Pedro", "initials": "P"}, {"family": "Verreycken", "given": "Hugo", "initials": "H"}, {"family": "Britton", "given": "Robert", "initials": "R"}, {"family": "Borcheling", "given": "Jost", "initials": "J"}, {"family": "Kutsokon", "given": "Yuliia", "initials": "Y"}, {"family": "Didenko", "given": "Oleksandr", "initials": "O"}, {"family": "Jurajda", "given": "Pavel", "initials": "P"}, {"family": "Miranda", "given": "Rafael", "initials": "R", "orcid": "0000-0003-4798-314X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb0fd0fe7d34dc4b24af564521382bd.json"}}, {"family": "Gross", "given": "Riho", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A"}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "16", "pages": "e73502", "issn-l": "2045-7758"}, "abstract": "The contemporary distribution of genetic diversity in widespread freshwater species reflects a complex interplay between historical processes and recent demographic events. We investigated the postglacial recolonization history of the Eurasian perch (Perca fluviatilis L.) across its native range spanning Europe and Western Siberia, aiming to understand how historical and recent demographic processes have shaped contemporary genetic diversity in a widespread freshwater species. Using an integrative genomic approach, we combined whole mitochondrial genome resequencing with nuclear SNP-array genotyping (3660 SNPs) for 382 individuals from 188 locations to reconstruct patterns of lineage divergence, population structure, and admixture. We identified five highly divergent mitochondrial lineages, consistent with the existence of multiple glacial refugia across Southwestern, Southeastern, and Central Europe, as well as Siberia. Nuclear data (3660 SNPs) revealed three major genetic clusters corresponding to Western, Northern, and Southeastern Europe, along with strong regional admixture. The Baltic Sea region emerged as a contemporary hotspot of genetic diversity, likely resulting from the admixture and convergence of distinct maternal lineages during the postglacial recolonization of Northern Europe. Signals of isolation by distance were evident both within and across lineages, highlighting the role of limited dispersal in shaping current genetic patterns. The integration of mitochondrial and nuclear genomic data provided a comprehensive view of the evolutionary history of P. fluviatilis, revealing both deep historical divergence and recent admixture events. The existence of multiple glacial refugia and subsequent secondary contact underscores the complexity of postglacial recolonization processes in freshwater fauna. These findings advance our understanding of how historical and contemporary factors interact to shape biodiversity across Europe.", "doi": "10.1002/ece3.73502", "pmid": "42023045", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13099172"}, {"db": "pii", "key": "ECE373502"}], "notes": [], "created": "2026-05-11T11:47:22.623Z", "modified": "2026-05-11T11:47:22.933Z"}, {"entity": "publication", "iuid": "d07dfbb5faf14d66a0758d483af8d8b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07dfbb5faf14d66a0758d483af8d8b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07dfbb5faf14d66a0758d483af8d8b4"}}, "title": "Bite-DNA Shows Substantial Browsing on Willows (Salix spp.) by North American Bison in Yellowstone National Park.", "authors": [{"family": "Jansson", "given": "Julia L", "initials": "JL"}, {"family": "Spitzer", "given": "Robert", "initials": "R", "orcid": "0000-0003-2753-1912", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c48a231a06f41b395bd2c7d98b2b0b2.json"}}, {"family": "Brealey", "given": "Jaelle Caitlin", "initials": "JC"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1246-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccdce43407204828b73bce24fc4e6453.json"}}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "16", "issue": "4", "pages": "e73354"}, "abstract": "Riparian willows (Salix spp.) in Yellowstone National Park have long been shaped by ungulate browsing, yet the specific contribution of individual herbivore species remains unclear. We applied a bite-DNA metabarcoding approach, extracting saliva DNA from browsed willow twigs, to directly identify the browsing community across six northern range riparian sites. Mammalian DNA was successfully assigned for more than half of the collected bite samples, revealing browsing by moose (Alces alces), North American bison (Bison bison), elk (Cervus canadensis), deer (Odocoileus sp.), bighorn sheep (Ovis canadensis), and jackrabbit (Lepus townsendii). Contrary to the traditional view of bison as primarily grazers, bite-DNA showed that bison were the most frequent browsers of willows, present at all sites and contributing the majority of browsing bites. Elk, historically considered the primary browser on riparian shrubs, were detected less often, whereas mule deer browsing was consistently recorded and frequently exceeded elk. Browsing height largely overlapped among species and was significantly higher for bighorn sheep than for bison and mule deer. Diameter of browsed twigs did not differ significantly between species. Browsing composition varied locally without clear spatial patterns, suggesting that site-level factors shape where different ungulates browse willows. Our results demonstrate substantial bison browsing on riparian willows and highlight shifting herbivore impacts on Yellowstone's riparian ecosystems.", "doi": "10.1002/ece3.73354", "pmid": "42040859", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13106989"}, {"db": "pii", "key": "ECE373354"}, {"db": "Dryad", "key": "10.5061/dryad.gtht76j1w"}], "notes": [], "created": "2026-06-08T17:24:50.294Z", "modified": "2026-06-08T17:26:16.368Z"}, {"entity": "publication", "iuid": "fecec34336824e84b6c3dd0f90675ef4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fecec34336824e84b6c3dd0f90675ef4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fecec34336824e84b6c3dd0f90675ef4"}}, "title": "Contrasting population genomic structuring of northern pike ( Esox lucius L.) in fresh\u2010 and brackish water environments: Implications for management and conservation", "authors": [{"family": "Diaz\u2010Suarez", "given": "Alfonso", "initials": "A", "orcid": "0000-0002-1726-2563", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f3f9866fe543b78c91c9c62c362cdd.json"}}, {"family": "L\u00f3pez", "given": "Mar\u00eda\u2010Eugenia", "initials": "M"}, {"family": "Sundblad", "given": "G\u00f6ran", "initials": "G"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}], "type": "journal-article", "published": "2026-03-30", "journal": {"title": "J. Fish Biol.", "issn": "0022-1112", "issn-l": null}, "abstract": "Understanding the factors that shape population genetic structure is crucial for advancing evolutionary studies and developing effective management and conservation strategies. The northern pike (Esox lucius L.) is a top teleost predator that inhabits fresh and brackish water environments in the northern hemisphere. Pike populations in the brackish Baltic Sea typically display strong genetic structuring, with coastal sympatric populations that separate during spring for spawning in either shallow, sheltered brackish bays or in freshwater tributaries and wetlands. In contrast to the Baltic Sea, genomic structuring in freshwater environments, particularly in large lacustrine systems, remains poorly understood. To address this gap, we used restriction site-associated DNA-sequencing to assess the genetic structure and diversity of northern pike in two ecologically contrasting habitats: freshwater V\u00e4nern Lake, Sweden (8932 single nucleotide polimorphisms [SNPs]), and the brackish Baltic Sea around Saaremaa, Estonia (6899 SNPs). The results show strong genetic structuring and lower genetic diversity in brackish environment compared to the higher genetic diversity and extremely low genetic structuring observed in freshwater habitat. We found no evidence of divergent selection within environments. However, we identified 187 outlier SNPs and 62 outlier genes distinguishing the brackish and freshwater environments, potentially reflecting adaptation to salinity. Notably, several of these genes are associated with key biological processes, including osmotic stress regulation (akap13), early development (tfap2a) and pathogens response (tlr18). From a fisheries management perspective, our results indicate that the freshwater system can be managed as a single stock, while strong population structuring among Baltic coastal pike likely requires either large-scale solutions and/or population-specific fine-scale management efforts to maintain the genetic and life-history diversity among brackish coastal pike populations.", "doi": "10.1111/jfb.70417", "pmid": "41912439", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-04-10T13:09:47.227Z", "modified": "2026-04-16T09:42:58.777Z"}, {"entity": "publication", "iuid": "853fcd087cf147129106a699a63b80ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/853fcd087cf147129106a699a63b80ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/853fcd087cf147129106a699a63b80ef"}}, "title": "Tumor-infiltrating immature innate lymphoid cells in colorectal cancer are biased toward ILC1/tissue-resident NK cell differentiation.", "authors": [{"family": "Marchalot", "given": "Anne", "initials": "A", "orcid": "0000-0002-3042-8206", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b674db5dc349eaa4438563f2256290.json"}}, {"family": "Ljunggren", "given": "Malin", "initials": "M"}, {"family": "Stamper", "given": "Christopher", "initials": "C"}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Tibbitt", "given": "Christopher Andrew", "initials": "CA"}, {"family": "Meininger", "given": "Isabel", "initials": "I"}, {"family": "Pandey", "given": "Ram Vinay", "initials": "RV"}, {"family": "Franklin", "given": "Miriam", "initials": "M", "orcid": "0000-0002-9402-9976", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64100c086a644b8b1b7dd56f4f09da5.json"}}, {"family": "Bassett", "given": "John Washington", "initials": "JW"}, {"family": "Wirth", "given": "Lorenz", "initials": "L"}, {"family": "Colorectal Study Group", "given": "", "initials": ""}, {"family": "Lindforss", "given": "Ulrik", "initials": "U"}, {"family": "Jansson-Palmer", "given": "Gabriella", "initials": "G"}, {"family": "Nordenvall", "given": "Caroline", "initials": "C"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}], "type": "journal article", "published": "2026-03-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Peritoneal metastases (PM) occur in 10% of patients with colorectal cancer (CRC) and are linked to poor outcomes. Although dysregulated innate lymphoid cells (ILC) have been described in CRC, their function in CRC-PM remains unclear. Here, we analyze tumor samples from CRC and CRC-PM patients using single-cell RNA sequencing (11 patients), flow cytometry (8 patients) and differentiation assays (24 patients). Healthy colon, primary CRC and CRC-PM tumors are infiltrated by heterogeneous populations of ILC3, ILC2, ILC1, tissue resident (tr)NK cells and conventional (c)NK cells. Compared to healthy colons, primary CRC and CRC-PM tumors are depleted of ILC3 but enriched for ILC1, trNK cells and cNK cells. CRC and CRC-PM tumors harbor two immature ILC populations, early NK and na\u00efve (n)ILC, with nILCs being transcriptionally skewed toward ILC1 and trNK cells. Indeed, co-culture of isolated nILCs with OP9-DL1 cells induces intratumoral nILC differentiation into ILC1/trNK-like cells. These findings help understand the immune pathogenesis of CRC and CRC-PM and provide insights for future ILC1 and NK cell-based therapies.", "doi": "10.1038/s41467-026-71085-9", "pmid": "41896575", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13035902"}, {"db": "pii", "key": "10.1038/s41467-026-71085-9"}], "notes": [], "created": "2026-04-10T12:22:32.013Z", "modified": "2026-04-10T12:22:32.241Z"}, {"entity": "publication", "iuid": "bccea3aeba8b476eb4902896a66d3d62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bccea3aeba8b476eb4902896a66d3d62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bccea3aeba8b476eb4902896a66d3d62"}}, "title": "Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Mas-Sandoval", "given": "Alex", "initials": "A"}, {"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Fortes-Lima", "given": "Cesar A", "initials": "CA", "orcid": "0000-0002-9310-5009", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1afb9addfa42b4aa92a74ed8a8586b.json"}}, {"family": "Garc\u00eda Rubio", "given": "Almudena", "initials": "A"}, {"family": "M\u00e1rquez-Grant", "given": "Nicholas", "initials": "N"}, {"family": "Mar\u00ed", "given": "Juanjo", "initials": "J"}, {"family": "Graziani", "given": "Glenda", "initials": "G"}, {"family": "Ferrer Ab\u00e1rzuza", "given": "Antoni", "initials": "A"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Lorca-Francisco", "given": "Lander", "initials": "L", "orcid": "0009-0000-5486-1509", "researcher": {"href": "https://publications.scilifelab.se/researcher/306a8399107a4c078493180672a3a1b7.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "Arauna", "given": "Lara R", "initials": "LR", "orcid": "0000-0003-3317-4261", "researcher": {"href": "https://publications.scilifelab.se/researcher/111d8114dc6f448c9516f8f246ef7925.json"}}, {"family": "P\u00e9rez-Ramallo", "given": "Patxi", "initials": "P", "orcid": "0000-0002-1142-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb111a8997c4fc4a3167bbeabcac042.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2026-03-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of C\u00f3rdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.", "doi": "10.1038/s41467-026-70615-9", "pmid": "41888119", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13021928"}, {"db": "pii", "key": "10.1038/s41467-026-70615-9"}], "notes": [], "created": "2026-04-10T12:08:45.109Z", "modified": "2026-04-10T12:08:45.877Z"}, {"entity": "publication", "iuid": "af8e8e9ebf9c485889bde183fd55210f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af8e8e9ebf9c485889bde183fd55210f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af8e8e9ebf9c485889bde183fd55210f"}}, "title": "Temporal genomics reveals widespread but unexpected consequences of a bottleneck in the Scandinavian brown bear", "authors": [{"family": "Lindahl", "given": "Amanda", "initials": "A"}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Ravasini", "given": "Francesco", "initials": "F"}, {"family": "Meleg", "given": "Ioana N", "initials": "IN", "orcid": "0000-0002-0836-4971", "researcher": {"href": "https://publications.scilifelab.se/researcher/01e901f9e2924bee8e3de6bfbcd8fe62.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}], "type": "journal-article", "published": "2026-03-25", "journal": {"title": "R. Soc. open sci.", "issn": "2054-5703", "issn-l": "2054-5703", "volume": "13", "issue": "3", "pages": null}, "abstract": null, "doi": "10.1098/rsos.251947", "pmid": null, "labels": {"Ancient DNA": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-03-26T13:53:56.827Z", "modified": "2026-04-16T09:43:31.467Z"}, {"entity": "publication", "iuid": "dcc99177f164437e8a1a681594fa0445", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcc99177f164437e8a1a681594fa0445.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcc99177f164437e8a1a681594fa0445"}}, "title": "Ribonuclease 4 Functions in Nociceptor-Mediated Nerve Homeostasis.", "authors": [{"family": "Feng", "given": "Xiaona", "initials": "X", "orcid": "0000-0001-6186-1160", "researcher": {"href": "https://publications.scilifelab.se/researcher/ade5499e48344e448626eef177bf1b27.json"}}, {"family": "Zhang", "given": "Kaiwen", "initials": "K", "orcid": "0009-0001-0790-1616", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1880c8da747467795a011858ca2c9bf.json"}}, {"family": "Techameena", "given": "Prach", "initials": "P", "orcid": "0009-0005-9380-2428", "researcher": {"href": "https://publications.scilifelab.se/researcher/835cc139cbbd4e08afd433a817f74ac6.json"}}, {"family": "Quadros", "given": "Rolen M", "initials": "RM"}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Murtazina", "given": "Aliia", "initials": "A"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Biagini", "given": "Sofia", "initials": "S", "orcid": "0009-0001-8033-1568", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6a1c687a2e945c0a01cd9ea4729fcd0.json"}}, {"family": "Bayramlik", "given": "Ozun Gokce", "initials": "OG", "orcid": "0009-0006-2130-9674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecf0118536354092bddc54ca48594444.json"}}, {"family": "Lallemend", "given": "Francois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}, {"family": "Gurumurthy", "given": "Channabasavaiah B", "initials": "CB"}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}], "type": "journal article", "published": "2026-03-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "The regulation of nociceptor identity and function is essential, as disruptions can significantly influence pain sensation, yet our understanding of the molecular mechanisms involved remains incomplete. In this study, we identified ribonuclease 4 (RNase4) as selectively expressed in the unmyelinated nociceptor lineage. Analysis of RNase4-deficient mice and single-cell transcriptomic data revealed a cell-autonomous role for RNase4 in regulating nociceptor function. Moreover, in a neuropathic pain model, RNase4 expression was upregulated in nociceptors during the pain and recovery phases, and its deletion altered mechanical sensation. Additionally, RNase4 exerted non-cell- autonomous effects on the myelin structural organization of adjacent myelinated axons. Together, these findings implicate RNase4 as a dual regulator of nociceptor biology and myelin integrity, revealing a molecular pathway for pain regulation and nerve repair.", "doi": "10.1038/s41467-026-70365-8", "pmid": "41876491", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13022371"}, {"db": "pii", "key": "10.1038/s41467-026-70365-8"}], "notes": [], "created": "2026-04-10T12:49:18.049Z", "modified": "2026-04-10T12:49:18.431Z"}, {"entity": "publication", "iuid": "b2a677b49fcd4cea828daa238d38fc87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2a677b49fcd4cea828daa238d38fc87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2a677b49fcd4cea828daa238d38fc87"}}, "title": "Transcription factor NFYA directs male meiotic entry by regulating accessible chromatin at meiotic promoters in mice", "authors": [{"family": "S\u00e4flund", "given": "Martin", "initials": "M", "orcid": "0009-0004-0450-1088", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2621fb0a17c498b8ea57d8db518c544.json"}}, {"family": "Askari", "given": "Masomeh", "initials": "M"}, {"family": "Eghbali", "given": "Atiyeh", "initials": "A"}, {"family": "Abdi", "given": "Mukhtar Mohamed", "initials": "MM", "orcid": "0009-0008-9207-7705", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ccfcd44f2d045338ebaff37a4481e01.json"}}, {"family": "Er", "given": "Dilay Deren", "initials": "DD", "orcid": "0009-0000-2441-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/72ed4229936e4ddeb92c9af2b029ff11.json"}}, {"family": "\u00d6stlund Farrants", "given": "Ann Kristin", "initials": "AK", "orcid": "0000-0001-9225-3264", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39df17c335240939cad1d413beb13b0.json"}}, {"family": "Yu", "given": "Tianxiong", "initials": "T", "orcid": "0000-0003-1151-4624", "researcher": {"href": "https://publications.scilifelab.se/researcher/921557bbdcf34a1c822995b09d2700ea.json"}}, {"family": "\u00d6zata", "given": "Deniz M", "initials": "DM", "orcid": "0000-0001-5215-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/933850bed34c4517b01e915cf8831686.json"}}], "type": "journal-article", "published": "2026-03-19", "journal": {"title": "EMBO J.", "issn": "1460-2075", "issn-l": "0261-4189"}, "abstract": "Meiotic prophase I, characterized by homologous recombination and synapsis, is a critical step in spermatogenesis. This process entails extensive changes to chromatin and transcription. Prior to prophase I, accessible chromatin bound by paused Pol II at meiotic gene promoters is essential for their timely activation later during meiosis. However, the factors responsible for establishing accessible chromatin at meiotic gene promoters before entry into prophase I are unknown. Here, we discovered that NFYA, expressed in pre-meiotic germ cells, regulates accessible chromatin at meiotic gene promoters, including those activated by the STRA8/MEISON axis. Concordantly, conditional germline deletion of Nfya in male mice blocks meiotic entry. Single-cell ATAC-seq analysis shows that loss of NFYA in pre-meiotic cells disrupts accessible chromatin at poised meiotic gene promoters. These findings establish NFYA as a regulator of accessible chromatin at meiotic gene promoters and of the timely activation of the meiotic genetic program.", "doi": "10.1038/s44318-026-00756-6", "pmid": "41857150", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s44318-026-00756-6"}], "notes": [], "created": "2026-03-23T13:24:24.304Z", "modified": "2026-03-24T09:12:12.298Z"}, {"entity": "publication", "iuid": "59eca9ec25b940089924c25b003d94a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59eca9ec25b940089924c25b003d94a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59eca9ec25b940089924c25b003d94a3"}}, "title": "Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs.", "authors": [{"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Agirre", "given": "Eneritz", "initials": "E", "orcid": "0000-0002-5012-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/a507b19745c64c3bb8ef5dce800c8687.json"}}, {"family": "Carlstr\u00f6m", "given": "Karl E", "initials": "KE", "orcid": "0000-0002-3001-2403", "researcher": {"href": "https://publications.scilifelab.se/researcher/3aa5f65acad34b5790a2b9f607521825.json"}}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6", "orcid": "0000-0002-9980-2702", "researcher": {"href": "https://publications.scilifelab.se/researcher/8288edd47f70479e93e1fc441d486997.json"}}, {"family": "Lor", "given": "Yuk Kit", "initials": "YK"}, {"family": "Pohl", "given": "Fabio Baldivia", "initials": "FB", "orcid": "0000-0003-1695-4936", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7913023dd124c8f96f5d072af0eff56.json"}}, {"family": "Ruffin", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3698-5505", "researcher": {"href": "https://publications.scilifelab.se/researcher/991af3c2719f4c0b9d4feeae24c5161a.json"}}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Seeker", "given": "Luise A", "initials": "LA"}, {"family": "Bestard-Cuche", "given": "Nadine", "initials": "N"}, {"family": "Lederer", "given": "Alex R", "initials": "AR", "orcid": "0000-0001-6381-5088", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa3aa57bbddf4845b2d2c438ecfb2bff.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J"}, {"family": "Ahola", "given": "Virpi", "initials": "V"}, {"family": "Goldman", "given": "Steven A", "initials": "SA"}, {"family": "Edstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Arvidsson", "given": "Lisa", "initials": "L", "orcid": "0000-0003-2129-5357", "researcher": {"href": "https://publications.scilifelab.se/researcher/654ca67f559842669ed19aefa16f878b.json"}}, {"family": "Moreira", "given": "Tiago Holm", "initials": "TH"}, {"family": "Bartosovic", "given": "Marek", "initials": "M", "orcid": "0000-0003-2057-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce3c36916eb844e7bc10f73b95f6494a.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}, {"family": "Williams", "given": "Anna", "initials": "A", "orcid": "0000-0002-6329-382X", "researcher": {"href": "https://publications.scilifelab.se/researcher/80c29c92194a4af3a6ed8f9d18dbddfe.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2026-03-19", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Neural cells in the adult human central nervous system (CNS) display extensive transcriptional heterogeneity. How different layers of epigenetic regulation underpin this heterogeneity is poorly understood. Here we profile, at the single-nuclei epigenomic level, distinct regions of the adult human CNS, for chromatin accessibility and simultaneously for the histone modifications H3K27me3 and H3K27ac. We unveil a putative SOX10 enhancer and primed chromatin signatures at HOX loci in spinal-cord-derived human oligodendroglia (OLG) and astrocytes, but not microglia. These signatures in adult OLG were reminiscent of developmental profiles but were decoupled from robust gene expression. Moreover, using high-resolution Micro-C, we show that induced pluripotent stem-cell-derived human OLGs exhibit a HOX chromatin architecture compatible with the primed chromatin in adult OLGs, bearing a strong resemblance not only to OLG developmental architecture but also to high-grade pontine gliomas. Thus, epigenetic memory from developmental states in adult OLG not only enables them to promptly transcribe Hox family genes during regeneration but also makes them susceptible to gliomagenesis.", "doi": "10.1038/s41593-026-02208-0", "pmid": "41857393", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02208-0"}], "notes": [], "created": "2026-03-23T13:16:33.192Z", "modified": "2026-03-23T13:16:34.150Z"}, {"entity": "publication", "iuid": "4e526893cc21459f8c1e48d163b14e3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e526893cc21459f8c1e48d163b14e3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e526893cc21459f8c1e48d163b14e3f"}}, "title": "Glioma-induced DNMT3A reduction in microglia promotes an anti-tumoral phenotype.", "authors": [{"family": "Cheray", "given": "Mathilde", "initials": "M", "orcid": "0000-0002-7551-6357", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0f0d5fdd40b4113a4fb3222107d4dc9.json"}}, {"family": "Posada-P\u00e9rez", "given": "Mercedes", "initials": "M"}, {"family": "Fragkopoulou", "given": "Adamantia", "initials": "A", "orcid": "0000-0001-7715-652X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f473bbe876e49b9bb6320f89c80746f.json"}}, {"family": "Rodrigues", "given": "Carlos F D", "initials": "CFD", "orcid": "0000-0003-1685-9883", "researcher": {"href": "https://publications.scilifelab.se/researcher/3229cd2cdb57449f82d0bd7c53d8cf95.json"}}, {"family": "Murgoci", "given": "Adriana-Natalia", "initials": "AN", "orcid": "0000-0002-4492-6804", "researcher": {"href": "https://publications.scilifelab.se/researcher/81d6c5a032534b1587dc3224728d95ee.json"}}, {"family": "Osman", "given": "Ahmed M", "initials": "AM", "orcid": "0000-0002-5255-2136", "researcher": {"href": "https://publications.scilifelab.se/researcher/91eb7159bac6486e897aa8b65cef1b5a.json"}}, {"family": "V\u00e1zquez-Cabrera", "given": "Guillermo", "initials": "G", "orcid": "0000-0003-1708-6712", "researcher": {"href": "https://publications.scilifelab.se/researcher/67769c07cbd044f790ad3f8cca983b01.json"}}, {"family": "\u0160kand\u00edk", "given": "Martin", "initials": "M", "orcid": "0000-0003-2060-9553", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c20184259e14fff9d5ec1cbabe80745.json"}}, {"family": "Hong", "given": "Christine C", "initials": "CC"}, {"family": "Engskog-Vlachos", "given": "Pinelopi", "initials": "P"}, {"family": "Kanatani", "given": "Shigeaki", "initials": "S"}, {"family": "Li", "given": "Yue", "initials": "Y", "orcid": "0000-0003-0584-1119", "researcher": {"href": "https://publications.scilifelab.se/researcher/12c8feb7f8914821905e56b6b81473ef.json"}}, {"family": "Spulber", "given": "Stefan", "initials": "S", "orcid": "0000-0001-8122-6738", "researcher": {"href": "https://publications.scilifelab.se/researcher/270f8d26bc1c4a36a712e61006002696.json"}}, {"family": "Friess", "given": "Lara", "initials": "L"}, {"family": "Sylaidi", "given": "Theodora", "initials": "T"}, {"family": "St-Pierre", "given": "Marie-Kim", "initials": "MK", "orcid": "0000-0001-5307-1580", "researcher": {"href": "https://publications.scilifelab.se/researcher/30f930c6b38547b6a59ae50fba6e1088.json"}}, {"family": "Carlson", "given": "Lena-Maria", "initials": "LM"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c3e953634140b8974186ac0d7eac85.json"}}, {"family": "Kamme", "given": "Fredrik", "initials": "F"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}, {"family": "Joseph", "given": "Bertrand", "initials": "B", "orcid": "0000-0001-5655-9979", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cbb8902d726446fa0a3b25b649f82aa.json"}}], "type": "journal article", "published": "2026-03-18", "journal": {"title": "Cell Death Differ.", "issn": "1476-5403", "issn-l": "1350-9047"}, "abstract": "Glioblastoma, IDH1 wildtype, aggressive primary brain tumors with a dismal prognosis, promote the recruitment of microglia, brain resident innate immune cells, and ultimately their activation toward a tumor-supportive phenotype that increases gliomal proliferation and invasion capability. Here, we report that upon stimulation by glioma cells, microglia transit via a reactive state holding anti-tumoral properties coupled to reduced DNA methyltransferase 3 A (DNMT3A) chromatin occupancy and DNA demethylation that promote the expression of gene sets related to the transforming growth factor beta (TGF-\u03b2)-dependent microglial homeostasis and the microglial sensome. We find that upon repression of Dnmt3a expression in microglia, those cells maintain anti-tumoral attributes in vitro and in vivo. In a syngeneic immunocompetent glioblastoma mouse model, brain delivery of antisense oligonucleotide targeting Dnmt3a expression led to microglial activation and reduced tumor growth. Taken together, our results reveal the involvement of DNA demethylation in the control of glioma cells-induced microglia activation and indicate that microglial DNMT3A is a potentially therapeutic target to treat brain neoplasms such as glioblastoma that include a microglial component.", "doi": "10.1038/s41418-026-01712-x", "pmid": "41844900", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41418-026-01712-x"}], "notes": [], "created": "2026-07-15T07:04:36.683Z", "modified": "2026-07-15T07:04:37.448Z"}, {"entity": "publication", "iuid": "8a88693e35b444ce876a3dd11d760a8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a88693e35b444ce876a3dd11d760a8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a88693e35b444ce876a3dd11d760a8e"}}, "title": "FGFR signaling establishes spatial gradients of secretory cell identities along the airway proximal-distal axis.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Eliot", "given": "Orane", "initials": "O"}, {"family": "Koepke", "given": "Janine", "initials": "J"}, {"family": "Millar-B\u00fcchner", "given": "Pamela", "initials": "P"}, {"family": "Manner\u00e5s-Holm", "given": "Louise", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Fysikopoulos", "given": "Athanasios", "initials": "A", "orcid": "0000-0002-8081-0198", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c94301c7ab74979ae2db1c606d9387b.json"}}, {"family": "Kelm", "given": "Antonia", "initials": "A"}, {"family": "Bouloukou", "given": "Eleni", "initials": "E"}, {"family": "Gaengel", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-2682-2833", "researcher": {"href": "https://publications.scilifelab.se/researcher/b405d74174ae47749815a091affb9aea.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Seeger", "given": "Werner", "initials": "W", "orcid": "0000-0003-1946-0894", "researcher": {"href": "https://publications.scilifelab.se/researcher/36385e53dcd7475ab3f100b63179807b.json"}}, {"family": "Bellusci", "given": "Saverio", "initials": "S"}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2026-03-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Secretory cells are major structural and functional constituents of the lung airways. Their heterogeneity, spatial organization and specification mechanisms are partially understood. Here, we analyze secretory lung cell-types at single-cell resolution. In the airway epithelium, we find opposing, partially overlapping gene-expression gradients along the proximal-distal airway axis superimposed on a general gene program encoding detoxification. One graded program is elevated proximally and relates to innate immunity, whereas the other is enriched distally, encoding lipid metabolism and antigen presentation. Intermediately positioned cells express moderate levels of both graded programs creating a differentiation continuum towards each end. Lineage tracing analysis during development reveals the sequential establishment of the gradients in common epithelial progenitors postnatally. We show that Fgfr2b regulates the airway patterning by inducing and maintaining high levels of lipid biosynthesis and vesicle trafficking in distal airways and down-regulating innate-immunity genes in vivo and in airway organoids. Our analysis offers a framework for studying epithelial and lung tissue organization to better understand cellular roles in tissue-level pathology.", "doi": "10.1038/s41467-026-70842-0", "pmid": "41851103", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-70842-0"}, {"db": "pmc", "key": "PMC13004988"}], "notes": [], "created": "2026-03-23T13:53:27.906Z", "modified": "2026-03-23T13:53:28.385Z"}, {"entity": "publication", "iuid": "483493d2904b4314872a2fb14d09bb93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/483493d2904b4314872a2fb14d09bb93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/483493d2904b4314872a2fb14d09bb93"}}, "title": "The population structure in the Baltic herring reflects natural selection and local adaptation.", "authors": [{"family": "Goodall", "given": "Jake", "initials": "J"}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Andersson", "given": "Anastasia", "initials": "A"}, {"family": "Dahlin", "given": "Iris", "initials": "I"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "St\u00e5hl", "given": "Gunnar", "initials": "G"}, {"family": "Wennerstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L"}], "type": "journal article", "published": "2026-03-17", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "123", "issue": "11", "pages": "e2526500123", "issn-l": "0027-8424"}, "abstract": "How species time reproduction and adapt to environmental conditions are key topics in ecology and evolutionary biology. Here, we conducted a high-resolution population genetic analysis of Baltic herring, a subspecies of Atlantic herring (Clupea harengus). Genotypes at >4,500 SNPs were generated from >4,500 spawning individuals, sampled from 150 locations spanning Swedish's eastern coast. Abiotic factors-week of spawning, latitude, temperature, salinity-were used to assess how genetic variation is shaped by temporal, spatial, and environmental gradients. Our results reaffirm strong genetic differentiation between spring- and autumn-spawning ecotypes, despite hybridization suggesting ongoing gene flow between the two ecotypes. We document significant substructuring within the spring-spawning ecotype, delineating three main, previously unidentified, genetic clusters underpinned by adaptative genetic variation associated with latitude, salinity, temperature, and spawning time. Complementary linkage disequilibrium (LD) partitioning showed that adaptive loci-especially those in inversion regions-exhibit strong elevated among-population LD, consistent with divergence maintained by local selection despite ongoing gene flow. Clinal variation in allele frequencies indicated regionally distinct selection pressures, including shifts in allele frequencies at two major supergenes (inversions) and at a suite of genes correlated with abiotic factors. Importantly, rare genetic outlier populations are identified within each geographic region which further illustrates the unexpected fine-grained population structure of Baltic herring and implies a strong homing behavior in this abundant marine fish. Overall, this study demonstrates the capacity for targeted population genetic studies to detect adaptive variation in natural populations, the outcomes of which have direct implications for sustainable fisheries and biodiversity management.", "doi": "10.1073/pnas.2526500123", "pmid": "41802067", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12993978"}], "notes": [], "created": "2026-03-23T14:00:34.838Z", "modified": "2026-03-23T14:00:34.939Z"}, {"entity": "publication", "iuid": "999289be0c1e406bb30bd4b40e7a2f00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/999289be0c1e406bb30bd4b40e7a2f00"}}, "title": "Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost", "authors": [{"family": "Selvatici", "given": "Sofia", "initials": "S"}, {"family": "Jin", "given": "Chenyu", "initials": "C"}, {"family": "Zazula", "given": "Grant", "initials": "G", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Moots", "given": "Hannah M", "initials": "HM", "orcid": "0000-0002-6637-6321", "researcher": {"href": "https://publications.scilifelab.se/researcher/5105354f578c480ba144061ffbb49bf5.json"}}, {"family": "Sharif", "given": "Bilal", "initials": "B"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Parducci", "given": "Laura", "initials": "L", "orcid": "0000-0003-1956-4757", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed4c737e2c7c4266b598a89aa2116a91.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}], "type": "journal-article", "published": "2026-03-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ond\u00ebk Hw\u00ebch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as \"Ts'ey\" in the H\u00e4n language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.", "doi": "10.1038/s41598-026-44540-2", "pmid": "41845022", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996357"}, {"db": "pii", "key": "10.1038/s41598-026-44540-2"}], "notes": [], "created": "2026-03-23T13:18:35.892Z", "modified": "2026-03-24T09:12:30.461Z"}, {"entity": "publication", "iuid": "49030089ac5e463a815a0459fdcfe9a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49030089ac5e463a815a0459fdcfe9a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49030089ac5e463a815a0459fdcfe9a2"}}, "title": "Paralog-aware assembly and filtering strategies reveal minimal nucleotide variation on the macro germline-restricted chromosome of the zebra finch.", "authors": [{"family": "Chen", "given": "Augustin", "initials": "A", "orcid": "0000-0002-2016-3048", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db30961a7d74af8992748220415b643.json"}}, {"family": "Ruiz-Ruano", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0002-5391-301X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37ccedb49884e27aeffed3b49085ddf.json"}}, {"family": "Contreras-L\u00f3pez", "given": "Orlando", "initials": "O", "orcid": "0000-0002-4048-6637", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b2d9f2bfc8843d4a2f75eae2cbe76a4.json"}}, {"family": "Fouch\u00e9", "given": "Simone", "initials": "S", "orcid": "0000-0003-0601-6073", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b5335a456624aaeac268a1489c00b1f.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-2411-4454", "researcher": {"href": "https://publications.scilifelab.se/researcher/af91cebf5fa04abb9656aaf9123ad53b.json"}}, {"family": "Pei", "given": "Yifan", "initials": "Y", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2026-03-16", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X"}, "abstract": "The germline-restricted chromosome (GRC) of passerines is a remarkable tissue-specific chromosome that accumulated paralogs of genes from the regular \"A chromosomes\" over millions of years, often amplified into dozens of gene copies. In addition to its repetitive content, typically uniparental inheritance, and lack of recombination, the GRC resembles non-recombining sex chromosomes and some B chromosomes, for all of which assembly and single-nucleotide polymorphisms (SNPs) calling are difficult. Here, we first show that much of the Australian zebra finch macro-GRC can be assembled using accurate long reads. We then describe a paralog-aware Snakemake pipeline, ParaVar, to map short reads from the GRC to retrieve GRC regions suitable for haplotype-based analysis. ParaVar reliably calls hundreds of SNPs across the GRC, thereby providing an estimate of nucleotide diversity on the highly repetitive zebra finch macro-GRC. Our results show significantly lower nucleotide diversity (20- to 50-fold lower) on the GRC compared to the mitogenome and autosomes, and a strong phylogenetic discordance between the GRC and the mitochondrial genome. Beyond the contribution of background selection, our results suggest that a single GRC haplotype recently spread through the populations while jumping across matrilines via occasional paternal inheritance. We anticipate that our paralog-aware pipeline will be useful for SNP calling and population genetics analyses of repetitive GRCs, sex chromosomes, and B chromosomes.", "doi": "10.1038/s41437-026-00830-z", "pmid": "41840191", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-026-00830-z"}], "notes": [], "created": "2026-03-23T15:23:33.935Z", "modified": "2026-08-12T15:17:48.266Z"}, {"entity": "publication", "iuid": "e5ec787139724ab0bcd41b3b3b928147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5ec787139724ab0bcd41b3b3b928147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5ec787139724ab0bcd41b3b3b928147"}}, "title": "Persistent interferon signaling causes sensory neuron plasticity and pain before and during arthritis.", "authors": [{"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Kwak", "given": "Dongoh", "initials": "D"}, {"family": "Picton", "given": "Laurence", "initials": "L"}, {"family": "Xu", "given": "Bingze", "initials": "B"}, {"family": "do Nascimento", "given": "Leandro Flores", "initials": "LF"}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Gonzalez", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-7513-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/df94b05dc87c4d5f9e9939170f4d001f.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Xu", "given": "Zhongwei", "initials": "Z", "orcid": "0000-0001-5178-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/f056000b3af842bda8cdd411da7d44ad.json"}}, {"family": "Szczot", "given": "Marcin", "initials": "M", "orcid": "0000-0002-3902-059X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4fef830b2914f37b100c433fbdd4fd0.json"}}, {"family": "El Manira", "given": "Abdeljabbar", "initials": "A", "orcid": "0000-0001-5920-9384", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c6e1ed8fbb547b1844b979220d8514a.json"}}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2026-03-10", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Although inflammatory processes in rheumatoid arthritis have been described, mechanisms driving pain are poorly defined. Here, we used a multitude of approaches to uncover the neural basis and causes of inflammatory pain. We show in mice with cartilage autoantibody-induced arthritis that early immune activation and a cytokine storm were mainly driven by vascular cells and monocytes/macrophages in the dorsal root ganglion. However, persistently elevated interferons and receptor activation of the MNK1/MNK2-eIF4E signaling pathway at all disease phases caused sensory-motor dysfunction and pain by inducing hyperexcitability and sensitization of a GFRA3+ C-fiber subtype of joint-innervating sensory neurons. Signaling pathway inhibition in vivo reversed pain and restored limb function. Like mice, human sensory neurons expressed interferon receptors, and type 1 interferons and signaling were increased only in individuals with painful rheumatoid arthritis. The finding that joint pain before and during arthritis is caused by a defined cytokine and signaling pathway holds promise for targeted therapies for pain relief in arthritis.", "doi": "10.1038/s41593-026-02234-y", "pmid": "41807847", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02234-y"}], "notes": [], "created": "2026-03-23T15:25:03.672Z", "modified": "2026-03-23T15:25:04.053Z"}, {"entity": "publication", "iuid": "0e1dde47e7304f09b029297f6c8335fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1dde47e7304f09b029297f6c8335fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1dde47e7304f09b029297f6c8335fb"}}, "title": "Whole genomes reveal subpopulations and isolation-by-distance patterns in the Norwegian lemming.", "authors": [{"family": "Feinauer", "given": "Isabelle Sofie", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Ravasini", "given": "Francesco", "initials": "F"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "M\u00e5sviken", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2660-7081", "researcher": {"href": "https://publications.scilifelab.se/researcher/b060865f580a44f29d46bf1bb6030f1f.json"}}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-Wera", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ehrich", "given": "Dorothee", "initials": "D", "orcid": "0000-0002-3028-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/c056bc462f8e433ba76bc65bb308df9b.json"}}, {"family": "Ims", "given": "Rolf A", "initials": "RA"}, {"family": "Henttonen", "given": "Heikki", "initials": "H"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9707-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/40450a7e8cda45ba8292b9a677b3fb29.json"}}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2026-03-06", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "24", "issue": "1", "issn-l": "1741-7007"}, "abstract": "The Norwegian lemming (Lemmus lemmus) is a small rodent endemic to the Fennoscandian alpine and arctic tundra. The species is known for cyclic population outbreaks and mass movements during peak years. Previous research based on microsatellites revealed high genetic variation but a weak population structure in the Norwegian lemming.\n\nIn this study, we revisit the population structure of the species using genome-wide data. To do this, we generated a high-quality de novo reference genome for Lemmus lemmus, and resequenced genomes to 2.5-5 \u00d7 coverage, from 86 lemmings sampled across the species' entire geographic distribution. Our results reveal that the population is geographically structured into distinct subpopulations, with an overall pattern characterised by isolation-by-distance among subpopulations. Furthermore, our results are consistent with earlier work suggesting that the species survived the last ice age within a northern refugium.\n\nTogether, these findings provide a genome-wide perspective on today's population structure of the Norwegian lemming. In addition, we provide a de novo reference genome, which we believe will be a valuable resource to the research community.", "doi": "10.1186/s12915-026-02568-w", "pmid": "41787358", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Long read": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13064042"}, {"db": "pii", "key": "10.1186/s12915-026-02568-w"}], "notes": [], "created": "2026-03-23T13:20:06.509Z", "modified": "2026-08-12T15:24:41.766Z"}, {"entity": "publication", "iuid": "79685133481d424091f6bbe60bed024e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79685133481d424091f6bbe60bed024e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79685133481d424091f6bbe60bed024e"}}, "title": "Resource Availability Modulates Gene Expression Across Life Stages in a Migratory Butterfly.", "authors": [{"family": "Shipilina", "given": "D", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "H\u00f6\u00f6k", "given": "L", "initials": "L"}, {"family": "N\u00e4svall", "given": "K", "initials": "K"}, {"family": "Talla", "given": "V", "initials": "V"}, {"family": "Palah\u00ed", "given": "A", "initials": "A"}, {"family": "Parkes", "given": "E", "initials": "E"}, {"family": "Vila", "given": "R", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Talavera", "given": "G", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}, {"family": "Backstr\u00f6m", "given": "N", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "35", "issue": "5", "pages": "e70293", "issn-l": "0962-1083"}, "abstract": "Natural populations are in constant need of balancing resource allocation to compensate for seasonal environmental variation. In many insects, a well-established trade-off between migration and reproduction exists. While this trade-off has been characterised phenotypically for decades, the underlying regulatory pathways are poorly understood. Here, we examined how resource-related environmental cues shape transcription across development in the long-distance migrant butterfly Vanessa cardui. In a multi-cue, developmental stage-specific design, adult females were exposed to host-plant presence or absence, while larvae experienced food limitation or crowding. Adult exposure to host plants was associated with differential expression in ecdysteroid and juvenile-hormone pathways, consistent with endocrine regulation of reproductive readiness and predictions of the oogenesis-flight syndrome. Larval resource limitation altered developmental and metabolic pathways, suggesting molecular predispositions and potential carry-over effects to adult traits. Across all contrasts, metabolism emerged as a shared axis linking responses across life stages. Together, our results show that resource-driven cues leave both stage-specific and general transcriptional signatures that connect environmental context with the molecular basis of migratory behaviour.", "doi": "10.1111/mec.70293", "pmid": "41797265", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12968515"}], "notes": [], "created": "2026-03-23T13:21:43.409Z", "modified": "2026-03-23T13:21:43.572Z"}, {"entity": "publication", "iuid": "e05c68328fed4b66bdae56b5a53a8183", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e05c68328fed4b66bdae56b5a53a8183.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e05c68328fed4b66bdae56b5a53a8183"}}, "title": "Enrichment of Neural Crest Cells by Antibody Labeling and Flow Cytometry for Single-Cell Transcriptomics in a Lizard.", "authors": [{"family": "Pranter", "given": "Robin", "initials": "R", "orcid": "0000-0003-3615-0281", "researcher": {"href": "https://publications.scilifelab.se/researcher/02c2a85e333a477597ff77429646a0a9.json"}}, {"family": "Patthey", "given": "Cedric", "initials": "C", "orcid": "0000-0002-2627-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7707e8bd3d4e029fb1e1f43df86ad4.json"}}, {"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Evol Dev", "issn": "1525-142X", "volume": "28", "issue": "1", "pages": "e70030", "issn-l": null}, "abstract": "Neural crest cells (NCCs) are a key component of the vertebrate body plan and contribute to a variety of different traits. Recent advances in single-cell transcriptomics (scRNA-seq) have significantly improved our understanding of NCC biology. However, their dynamic migratory behavior and spatiotemporal heterogeneity in the developing embryo pose significant challenges for their identification and isolation. Consequently, most studies of NCCs have been confined to model organisms with established transgenic tools or established methods for in ovo manipulation. To overcome this limitation, we present a novel approach that combines antibody labeling with fluorescence activated cell sorting to enrich for NCCs and we demonstrate the approach in the common wall lizard (Podarcis muralis). Through microscopy, reverse transcription quantitative polymerase chain reaction and single-cell RNA sequencing, we show that the method enriches for NCCs as efficiently as methods relying on transgenic animals. Using this technique, we successfully characterize transcriptional profiles of NCCs in wall lizard embryos. We anticipate that this method can be applied to a wide range of vertebrates that lack transgenic tools, enabling deeper insights into the diverse roles of neural crest cells in development and evolution.", "doi": "10.1111/ede.70030", "pmid": "41709476", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12917300"}], "notes": [], "created": "2026-02-26T15:21:38.415Z", "modified": "2026-03-24T09:08:52.661Z"}, {"entity": "publication", "iuid": "4ae3dd53948e468a890cf7c38b75b085", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ae3dd53948e468a890cf7c38b75b085.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ae3dd53948e468a890cf7c38b75b085"}}, "title": "Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.", "authors": [{"family": "Saitoh", "given": "Takema", "initials": "T", "orcid": "0000-0003-4982-4724", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea03b39f2134b55bae9e444bb0e1fe5.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Xia", "given": "Canwei", "initials": "C", "orcid": "0000-0003-1432-1019", "researcher": {"href": "https://publications.scilifelab.se/researcher/006d6dc9454d4e0db595691b2e0b8cb5.json"}}, {"family": "Zhang", "given": "Lijun", "initials": "L"}, {"family": "Seki", "given": "Shin-Ichi", "initials": "SI", "orcid": "0000-0002-5140-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/c00a2e3811cb4c7c9d591dbf5b6a4aaa.json"}}, {"family": "Olsson", "given": "Urban", "initials": "U"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "PNAS Nexus", "issn": "2752-6542", "volume": "5", "issue": "3", "pages": "pgag037", "issn-l": null}, "abstract": "Despite the escalating biodiversity crisis, many species remain unknown to science and may even disappear unnoticed. This is particularly true for many island populations. We illustrate the problem of detecting overlooked species and its consequences by exploring a rare and geographically restricted migratory songbird. We find that this consists of two-hence even rarer-species: the Japanese endemic Ijima's Leaf Warbler Phylloscopus ijimae from the Izu Islands and the Tokara Leaf Warbler from the Tokara Islands. We describe the latter as a new cryptic species, ie one that is morphologically highly similar to, but genetically distinct from, a known species. The genetic divergence is revealed by analyses of nuclear genome-wide and mitochondrial DNA and supported by differences in vocalizations, while the morphological differences are minimal. We evaluate key conservation genomic indicators, showing that both species show low levels of genetic diversity and signs of a decrease of effective population size. Our genome-wide analysis revealed short runs of homozygosity and a low estimated deleterious load, suggesting limited recent inbreeding and possible purging of harmful alleles-indicators of genetic recovery after past demographic fluctuations. Ijima's Leaf Warbler is already classified as Vulnerable as well as a \"Natural Monument\" in Japan, and we propose that the Tokara Leaf Warbler should retain this status, with continued focused monitoring. Our study not only highlights the importance of integrating genomics with taxonomy for uncovering cryptic avian diversity but also provides a critical foundation for future conservation efforts.", "doi": "10.1093/pnasnexus/pgag037", "pmid": "41852645", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12993812"}, {"db": "pii", "key": "pgag037"}], "notes": [], "created": "2026-03-24T08:59:52.573Z", "modified": "2026-03-24T08:59:53.096Z"}, {"entity": "publication", "iuid": "8901ae491c224ece95ecca7bcd0fb242", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8901ae491c224ece95ecca7bcd0fb242.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8901ae491c224ece95ecca7bcd0fb242"}}, "title": "An Equatorial Hemispheric Barrier Shapes the Diversification of Migratory Belenois Butterflies.", "authors": [{"family": "Janiczek", "given": "Anna", "initials": "A", "orcid": "0009-0002-8654-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/57a0474b15674fb08e3572896dd004ee.json"}}, {"family": "Palah\u00ed", "given": "Aleix", "initials": "A", "orcid": "0000-0002-1373-4949", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee01ff0f2c3746939dbf64a7fca04439.json"}}, {"family": "Dapporto", "given": "Leonardo", "initials": "L", "orcid": "0000-0001-7129-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/17d272c2c8214d8fb107f095ac656297.json"}}, {"family": "D\u00edaz-Mart\u00ednez", "given": "Gemma", "initials": "G", "orcid": "0009-0003-4084-4734", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbfd1115d0274688a24ca44352e00d6d.json"}}, {"family": "Nazari", "given": "Vazrick", "initials": "V", "orcid": "0000-0001-9064-8959", "researcher": {"href": "https://publications.scilifelab.se/researcher/47148cc85ab042d78cfcaf5b406e3a95.json"}}, {"family": "Garc\u00eda-Berro", "given": "Aurora", "initials": "A", "orcid": "0000-0002-2419-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fdb6dd337074a89bf36e3b06458f042.json"}}, {"family": "Bahleman", "given": "Farid", "initials": "F", "orcid": "0000-0002-5439-0804", "researcher": {"href": "https://publications.scilifelab.se/researcher/f22a3054ef304d08972c52077aeceaa9.json"}}, {"family": "Collins", "given": "Steve C", "initials": "SC"}, {"family": "Akite", "given": "Perpetra", "initials": "P", "orcid": "0000-0002-0302-1822", "researcher": {"href": "https://publications.scilifelab.se/researcher/19097e8ac2ed4f8580906122df0da105.json"}}, {"family": "Braby", "given": "Michael F", "initials": "MF", "orcid": "0000-0002-5438-587X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c15f10e0aa48488f51ddec5282dfb9.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Suchan", "given": "Tomasz", "initials": "T", "orcid": "0000-0002-0811-8754", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b3c7df2089e4060a8ad426a5570654c.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "35", "issue": "6", "pages": "e70310", "issn-l": "0962-1083"}, "abstract": "Biogeographic barriers are typically considered prominent geographic features that block or severely restrict dispersal and gene flow. However, mating barriers can also emerge within continuous suitable habitats, driven by ecological or behavioural constraints. Migratory insects show an extraordinary capacity to traverse vast geographic ranges, as well as notable landscape features like mountains, deserts and oceans. Yet, their movements are not unrestricted: they are shaped by seasonal dynamics that dictate the feasibility of migration across these landscapes. Hemisphericity, the existence of inverted seasonal regimes and orientation cues in the two latitudinal hemispheres, has been proposed as a potential abiotic barrier involved in the diversification of migratory insects. Here, we use population genomic data to investigate patterns of diversification in migratory caper butterflies (Belenois spp.) across Africa. We identify a striking phylogeographic break around the equator in Belenois aurota, and emerging population structure between northern and southern African populations in Belenois creona, consistent with migratory divides aligned with hemispheric barriers. These divergences largely predate the Last Glacial Maximum, when major environmental changes such as contractions-expansions of equatorial rainforests and savannahs occurred. This reinforces the hypothesis that long-term abiotic factors, such as hemisphericity, had a role in limiting north-south dispersal. Given the absence of detectable gene flow detected even in sympatric populations of B. aurota in their contact zone in Kenya, Uganda, and Tanzania, we argue that populations from the Northern and Southern Hemispheres represent different species, and reinstate the taxon Belenois syrinx (Wallengren 1860) reinst. stat. for the Southern African lineage. Our findings provide genomic evidence of migratory divides in insects, which surprisingly emerge in the absence of physical barriers in the landscape, highlighting a role of hemisphere-specific adaptations in driving reproductive isolation and diversification in migratory insects.", "doi": "10.1111/mec.70310", "pmid": "41860563", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13004182"}], "notes": [], "created": "2026-03-23T13:39:58.929Z", "modified": "2026-03-23T13:39:59.651Z"}, {"entity": "publication", "iuid": "78404c951982420f9ae4b56a148a989c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78404c951982420f9ae4b56a148a989c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78404c951982420f9ae4b56a148a989c"}}, "title": "A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3.", "authors": [{"family": "Biswas", "given": "Soumi", "initials": "S"}, {"family": "Tavaf", "given": "Zohreh", "initials": "Z"}, {"family": "Benz", "given": "Caroline", "initials": "C"}, {"family": "Khalil", "given": "Moustafa", "initials": "M"}, {"family": "Becht", "given": "Dustin C", "initials": "DC"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Blanco", "given": "M Andres", "initials": "MA"}, {"family": "Affar", "given": "El Bachir", "initials": "EB"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}, {"family": "Kutateladze", "given": "Tatiana G", "initials": "TG"}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "volume": "302", "issue": "3", "pages": "111189", "issn-l": "0021-9258"}, "abstract": "The human methyltransferases mixed lineage leukemia 4 and 3 (MLL4 and MLL3) play pivotal roles in the regulation of epigenetic and transcriptional programs. Here, we report the identification and characterization of a tryptophan-phenylalanine binding motif recognized by MLL4 and MLL3. Binding of the sixth PHD finger of MLL4 and the seventh PHD finger of MLL3 to the tryptophan-phenylalanine motif derived from a set of human proteins was detected in a proteomic peptide-phage screening of intrinsically disordered regions of the human proteome and confirmed in NMR and MST assays. Mutational, genetic and binding interface analyses reveal the molecular mechanism underlying the direct interaction of MLL4 and MLL3 with the motif. A high correlation of expression of MLL4/MLL3 and the motif containing proteins in several tumor types suggests shared roles in oncogenic transcriptional programs. In conclusion, our findings highlight a potential relationship between the MLL4/MLL3 methyltransferases and diverse motif-containing epigenetic coregulators.", "doi": "10.1016/j.jbc.2026.111189", "pmid": "41581869", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12934300"}, {"db": "pii", "key": "S0021-9258(26)00059-1"}], "notes": [], "created": "2026-07-15T07:07:36.153Z", "modified": "2026-07-15T07:07:36.160Z"}, {"entity": "publication", "iuid": "0b48959ee84c4ee890a0e427e268d9c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b48959ee84c4ee890a0e427e268d9c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b48959ee84c4ee890a0e427e268d9c6"}}, "title": "Novel activating SNRNP70-ALK fusion in congenital infant-type hemispheric glioma displays clinical response to lorlatinib: a case-report", "authors": [{"family": "Arthur", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0645-6530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b07104d934d413a9c9546e7e9933051.json"}}, {"family": "Georgantzi", "given": "Kleopatra", "initials": "K"}, {"family": "de St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD"}, {"family": "Guan", "given": "Jikui", "initials": "J", "orcid": "0000-0003-1723-0307", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39044157aa7475485fb489a003b63d1.json"}}, {"family": "Oder", "given": "Blaz", "initials": "B", "orcid": "0000-0001-7984-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9851f9fc65fc44aea55d0c1567be7887.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Illies", "given": "Christopher", "initials": "C"}, {"family": "Sandgren", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6776-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d5b6b16fdbe470f83de8748227f8987.json"}}, {"family": "Svoboda", "given": "Jan", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Sandvik", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-9273-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/72b8c0bf76054dc8ba15fa80fa78918e.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Hallberg", "given": "Bengt", "initials": "B"}, {"family": "Palmer", "given": "Ruth", "initials": "R", "orcid": "0000-0002-2735-8470", "researcher": {"href": "https://publications.scilifelab.se/researcher/808281ecc2634b66a274895e58a122bd.json"}}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal-article", "published": "2026-02-26", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "We report a child with an antenatally detected brain tumor that progressed over three years' time despite surgery, chemo- and proton therapy. Retrospective whole-genome and transcriptome sequencing with methylation analysis of primary tumor tissue led to the molecular diagnosis infant-type hemispheric glioma, and identified a novel SNRNP70::ALK fusion, providing a therapeutic target for compassionate-use precision treatment with the ALK tyrosine kinase inhibitor lorlatinib. Functional studies confirmed the fusion protein to be expressed and active in the patient's tumor. After two years of therapy, the child has sustained partial tumor regression on MRI and no new neurological symptoms. We conclude that comprehensive multi-omics analyses are required for correct molecular diagnosis in childhood CNS tumors and can radically impact patient outcome by identifying molecular targets for precision treatment.", "doi": "10.1038/s41698-026-01336-x", "pmid": "41748687", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996540"}, {"db": "pii", "key": "10.1038/s41698-026-01336-x"}], "notes": [], "created": "2026-03-23T15:20:36.846Z", "modified": "2026-03-24T09:13:14.286Z"}, {"entity": "publication", "iuid": "85a0aeb18c244eb99a86ed0f415586e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85a0aeb18c244eb99a86ed0f415586e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85a0aeb18c244eb99a86ed0f415586e3"}}, "title": "Accuracy of occurrence and abundance estimates from insect metabarcoding.", "authors": [{"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Granqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "Nowak", "given": "Karol H", "initials": "KH"}, {"family": "Valdivia", "given": "Catalina", "initials": "C"}, {"family": "Buczek", "given": "Mateusz", "initials": "M"}, {"family": "Srivathsan", "given": "Amrita", "initials": "A", "orcid": "0000-0002-7988-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/194d94be10214bf7bde05418745b1d1a.json"}}, {"family": "Hartop", "given": "Emily", "initials": "E"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P"}, {"family": "Meier", "given": "Rudolf", "initials": "R"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2026-02-22", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "DNA metabarcoding-high-throughput sequencing of barcode regions from bulk samples-has become a key tool for insect biodiversity assessment. Yet, how methodological choices affect the accuracy of metabarcoding data remains insufficiently explored. In this paper, we ask: (1) How does the lysis method (non-destructive lysis vs. destructive homogenization) affect community recovery? (2) How comprehensively does metabarcoding capture species richness? (3) To what extent can spike-ins improve abundance estimates? (4) How accurately can species abundances be estimated?We evaluated the accuracy of insect metabarcoding using 4,749 bulk samples from a large-scale biodiversity survey subjected to mild lysis. Of these samples, 856 were also homogenized, allowing a systematic comparison of the effect of alternative treatments. To potentially improve abundance estimates, we added six biological spike-ins (i.e., foreign insects) to all samples, and two synthetic spike-ins (artificial DNA fragments) to the homogenization treatment. In addition, we established the contents of 15 samples by individually barcoding all specimens, enabling direct assessment of occurrence and abundance estimates.Our results revealed consistent differences between destructive and non-destructive treatments. While both methods reliably detected the majority of species, small and soft-bodied taxa were more often recovered after mild lysis than after homogenization, while the reverse was true for heavily sclerotized, hairy, and large taxa. Using biological spike-ins for calibration reduced the variance in read numbers per specimen considerably, especially in homogenized samples, while synthetic spike-ins were less effective. In a Bayesian analysis, where species data were matched to the best-fitting spike-in calibration curve, accurate abundance estimates (+/-1 individual) were obtained for 72.9% of species occurrences.Our results show that it is possible to obtain reasonably accurate abundance estimates from metabarcoding data, and that mild lysis and homogenization result in different taxon-specific biases in terms of occurrence data, with neither method outperforming the other. Accuracy is improved by homogenization rather than mild lysis of samples, and by the use of biological rather than synthetic spike-ins. Together, these findings provide a major step towards robust, quantitative biodiversity monitoring using DNA-metabarcoding.", "doi": "10.64898/2026.02.20.707016", "pmid": "41756968", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12934785"}, {"db": "pii", "key": "2026.02.20.707016"}], "notes": [], "created": "2026-07-15T07:05:21.156Z", "modified": "2026-07-15T07:05:21.268Z"}, {"entity": "publication", "iuid": "0f47f664e3e4473d9f72b07bc5730cd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f47f664e3e4473d9f72b07bc5730cd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f47f664e3e4473d9f72b07bc5730cd2"}}, "title": "Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.", "authors": [{"family": "\u00c1sgr\u00edmsd\u00f3ttir", "given": "Emil\u00eda Sif", "initials": "ES", "orcid": "0000-0003-1509-6853", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fc060425ec4835b3bbef9ef2eb90a1.json"}}, {"family": "Bassini", "given": "Luca Fusar", "initials": "LF", "orcid": "0009-0005-8256-8074", "researcher": {"href": "https://publications.scilifelab.se/researcher/69009a47fd394ed5ac1372076eb1be28.json"}}, {"family": "Sun", "given": "Ting", "initials": "T", "orcid": "0000-0002-7104-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/521fca43267242fca06da0f5fc823e6a.json"}}, {"family": "Puigsasllosas Pastor", "given": "Cl\u00e0udia", "initials": "C", "orcid": "0009-0007-6498-5223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ee97e4af1854228ab68a0bc94619ef3.json"}}, {"family": "di Val Cervo", "given": "Pia Rivetti", "initials": "PR", "orcid": "0000-0001-5999-1230", "researcher": {"href": "https://publications.scilifelab.se/researcher/45578a8b146d4eaf8b7f5e1391e6a5e3.json"}}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Lee", "given": "Kawai", "initials": "K"}, {"family": "Grigsby", "given": "Christopher L", "initials": "CL", "orcid": "0000-0002-0105-3847", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4407a0f102b4ee596d7944155d9226e.json"}}, {"family": "Jude", "given": "Baptiste", "initials": "B", "orcid": "0000-0002-5506-2482", "researcher": {"href": "https://publications.scilifelab.se/researcher/60e0f4af135c4eff99a95ff1cac825bb.json"}}, {"family": "Abaurre", "given": "Carmen", "initials": "C", "orcid": "0000-0002-7800-2829", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a55672674314bf593124300d5c2840f.json"}}, {"family": "Islam", "given": "Saiful", "initials": "S"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Villaescusa", "given": "Carlos", "initials": "C"}, {"family": "Salt\u00f3", "given": "Carmen", "initials": "C"}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Castelo-Branco", "given": "Goncalo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "La Manno", "given": "Gioele", "initials": "G", "orcid": "0000-0003-1428-8757", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dab6b6e789a46eba434ceadf38b6601.json"}}, {"family": "Toledo", "given": "Enrique M", "initials": "EM", "orcid": "0000-0002-1460-4708", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa05854e643c499c8efe6781d3457167.json"}}, {"family": "Arenas", "given": "Ernest", "initials": "E", "orcid": "0000-0003-0197-6577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3bb18ad1c4b4dae99b60ab0ae13e36a.json"}}], "type": "journal article", "published": "2026-02-16", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Understanding the development of midbrain dopaminergic (mesDA) neurons is essential for advancing cell replacement therapies for Parkinson's disease. In the developing ventral midbrain (VM), radial glia (Rgl) cells are the progenitors of mesDA neurons. However, distinct Rgl subtypes have recently been identified, and their individual roles are unclear. Here we analyze transcriptomic data from mouse and human VM Rgl to define their contributions to mesDA neuron development. We identify Rgl1 as the progenitor of the mesDA lineage, and reveal a Rgl1 transcriptional network coordinated by BMAL1, which we validate as a new regulator of mesDA neurogenesis. Moreover, we uncover Rgl3 as a key signaling subtype and show that factors expressed by Rgl3 promote the survival and yield of human stem cell-derived mesDA neurons. Our findings delineate distinct roles of Rgl subtypes, elucidate lineage relationships in the developing VM and uncover new factors that improve the derivation of clinically relevant human mesDA neurons.", "doi": "10.1038/s41593-026-02200-8", "pmid": "41699318", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-026-02200-8"}], "notes": [], "created": "2026-02-26T13:31:00.279Z", "modified": "2026-02-26T13:31:01.932Z"}, {"entity": "publication", "iuid": "f8a7ffd49cad48eb8cb108d82f8b32ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8a7ffd49cad48eb8cb108d82f8b32ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8a7ffd49cad48eb8cb108d82f8b32ab"}}, "title": "Exploring microbial diversity using cell-size fractionated enrichment incubations from subsurface aquifers at \u00c4sp\u00f6, Sweden.", "authors": [{"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S", "orcid": "0009-0007-1915-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f779055bf334226a996f214182b41fc.json"}}, {"family": "Hevele", "given": "Patrik", "initials": "P"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2026-02-14", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642"}, "abstract": "The continental subsurface hosts energy-constrained groundwaters with a high diversity of ecologically elusive microorganisms adapted to the prevailing low-energy conditions. This study explored potential interactions among microbes using anaerobic enrichment incubations with three types of groundwater of contrasting hydrochemistry from the \u00c4sp\u00f6 Hard Rock Laboratory, Sweden. Removing cells larger than 0.45 \u00b5m from the inoculum resulted in incubations enriched in populations characterized by very small genomes, including Patescibacteria, Nanobdellota, and Omnitrophota. These incubations had a higher diversity than non-fractionated incubations. However, cell numbers and community structure of the fractionated incubations did not change over an incubation period up to four months, despite high microbial diversity and experimental amendments with either simple (acetate) or more complex (cell lysate) carbon sources. In addition, network analysis on the groundwaters revealed multiple co-occurrences between populations affiliated with the Patescibacteria and the Desulfobacterota. Overall, these findings support that a considerable part of microbial diversity has a small cell size in these low energy groundwaters and strong co-occurrences among populations as an important survival strategy.", "doi": "10.1038/s42003-026-09706-8", "pmid": "41691100", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-026-09706-8"}], "notes": [], "created": "2026-02-26T13:35:39.634Z", "modified": "2026-02-26T13:35:39.923Z"}, {"entity": "publication", "iuid": "a4925370cf2840a29d01394990c7cb68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4925370cf2840a29d01394990c7cb68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4925370cf2840a29d01394990c7cb68"}}, "title": "Spatial overlap and temporal synchrony between guilds of insect hosts and parasitoids", "authors": [{"family": "van Dijk", "given": "Laura J A", "initials": "LJA", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "Goodsell", "given": "Robert M", "initials": "RM", "orcid": "0000-0002-3349-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/84f42755a394403b95486707bf4a83bd.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Fisher", "given": "Brian L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Iwaszkiewicz\u2010Eggebrecht", "given": "Elzbieta", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Lukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Pe\u00f1a\u2010Aguilera", "given": "Pablo", "initials": "P"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}], "type": "journal-article", "published": "2026-02-10", "journal": {"title": "Journal of Animal Ecology", "issn": "0021-8790", "issn-l": null}, "abstract": "How communities are structured into functional groups and trophic layers is key to understanding ecosystem functioning. Nonetheless, we lack insights about spatiotemporal variation in guild composition of communities and its causes. To investigate spatial and temporal patterns and drivers of variation in insect feeding guilds, we combined data from a nationwide survey of Swedish insects using Malaise traps and DNA metabarcoding with a comprehensive trait database. We assigned species into one of three feeding guilds (phytophages, saprophages, predators) or into one of three associated parasitoid guilds. We then analysed patterns in species richness for each guild. Species richness declined with latitude in all guilds. Beyond this gradient, local variation in species richness matched between hosts and their parasitoids. Yet, hosts and their parasitoids responded differently to habitat. The phenological peak of parasitoid species richness appeared later than the peak of their hosts, but the length of time lags varied among guilds. Spatiotemporal patterns were driven by guild-specific responses to temperature, though much variation remained between seasons and locations even when controlling for temperature. Overall, these patterns suggest that shifts in both climate and land use may alter the synchrony of insect trophic layers, with unknown consequences.", "doi": "10.1111/1365-2656.70228", "pmid": "41665095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-27T13:20:10.573Z", "modified": "2026-03-24T09:07:39.535Z"}, {"entity": "publication", "iuid": "d7cadda1f9044aed80babd0395773f5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7cadda1f9044aed80babd0395773f5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7cadda1f9044aed80babd0395773f5c"}}, "title": "Genome Sequencing in 19 Families With Bladder Exstrophy and Epispadias Complex Indicates Involvement of the ADGR-Gene Family.", "authors": [{"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A", "orcid": "0000-0001-6638-4631", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ffe8956663241938ad4c01e8f3474ec.json"}}, {"family": "Alm", "given": "Samara", "initials": "S", "orcid": "0000-0002-8339-4783", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d6cb147d9614153ad9b7c64f82d6536.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Cao", "given": "Jia", "initials": "J", "orcid": "0009-0000-4321-8147", "researcher": {"href": "https://publications.scilifelab.se/researcher/f34d15bd603c4a2394cf0ddff9c4af7c.json"}}, {"family": "Anderberg", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4505-338X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7615d8e407d4ce8bc517220db17c2f8.json"}}, {"family": "Barker", "given": "Gillian", "initials": "G"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Holmdahl", "given": "Gundela", "initials": "G"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K", "orcid": "0000-0001-9848-0468", "researcher": {"href": "https://publications.scilifelab.se/researcher/63d275105d9b4253944abaa311c986ee.json"}}], "type": "journal article", "published": "2026-02-10", "journal": {"title": "Am. J. Med. Genet. A", "issn": "1552-4833", "issn-l": "1552-4825"}, "abstract": "Bladder exstrophy and epispadias complex (BEEC) is one of the most severe congenital malformations of the urogenital tract, significantly impacting continence, sexual function, and renal function. To date, the only recurrent genetic aberration identified is the 22q.11.2 microduplication, but several candidate regions and genes including components of the WNT signaling pathway have been proposed. This study aimed to identify additional genes contributing to the pathogenesis of BEEC and to verify previously suggested candidate genes. We performed trio-based whole genome sequencing on 19 individuals with BEEC and their unaffected parents; of those, five carried earlier reported microdeletions. The genome data was also filtered in silico for variants in 204 candidate genes selected from databases, publications, and in-house findings. Variants were prioritized based on allele frequency and predicted functional impact. In 8 of the 19 trios, our findings highlight members of the ADGR-gene family as novel candidate genes for BEEC, alongside other implicated genes such as TRANK1, CSNK1E, IFT122, SDK1, SDK2, and KIF19 and propose two more CNVs as risk factors for BEEC; on chromosome regions 1p36 and 16p11.2. This study identifies novel candidate genes for BEEC within the ADGR gene family. The results also further implicate a complex molecular background of BEEC.", "doi": "10.1002/ajmga.70074", "pmid": "41668247", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-26T15:18:15.537Z", "modified": "2026-02-26T15:18:16.369Z"}, {"entity": "publication", "iuid": "2c3956defcf44e96ad1976508cd8f7ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c3956defcf44e96ad1976508cd8f7ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c3956defcf44e96ad1976508cd8f7ed"}}, "title": "Molecular interactome of HNRNPU reveals regulatory networks in neuronal differentiation and DNA methylation.", "authors": [{"family": "Oksanen", "given": "Marika", "initials": "M", "orcid": "0000-0003-4140-4282", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a8727638dc49fe88b15052d5741fd5.json"}}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F", "orcid": "0000-0003-4237-2446", "researcher": {"href": "https://publications.scilifelab.se/researcher/30aece0009c94ace82728640c71682f7.json"}}, {"family": "Mazan-Mamczarz", "given": "Krystyna", "initials": "K", "orcid": "0009-0005-1545-0500", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c526906891841359c173a86c8ab6414.json"}}, {"family": "Martindale", "given": "Jennifer L", "initials": "JL", "orcid": "0000-0002-3234-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/46adaad64bfc479eb2452956f6a25cc3.json"}}, {"family": "Ye", "given": "Xuan", "initials": "X"}, {"family": "Arora", "given": "Abishek", "initials": "A", "orcid": "0000-0002-6149-4417", "researcher": {"href": "https://publications.scilifelab.se/researcher/384ef4f8d6eb49d6873c87556843a7a2.json"}}, {"family": "Banskota", "given": "Nirad", "initials": "N"}, {"family": "Gorospe", "given": "Myriam", "initials": "M", "orcid": "0000-0001-5439-3434", "researcher": {"href": "https://publications.scilifelab.se/researcher/d946f33774fc424fa0ae365eb8079646.json"}}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2026-02-05", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "4", "issn-l": "0305-1048"}, "abstract": "HNRNPU is an RNA-binding protein with diverse roles in transcriptional and post-transcriptional regulation. Pathogenic genetic variants of HNRNPU cause a severe neurodevelopmental disorder (NDD), but the underlying molecular mechanisms are unclear. Here, we comprehensively investigate the HNRNPU molecular interactome by integrating protein-protein interaction (PPI) mapping, RNA target identification, and genome-wide DNA methylation profiling in human neuroepithelial stem cells and differentiating neural cells. We identified extensive HNRNPU-centered networks, including an association with the mammalian SWI/SNF chromatin-remodeling complex, and uncovered a previously unrecognized role in translation. We present evidence that HNRNPU associates with messenger RNAs (mRNAs) encoding proteins important for neuronal development, including several linked to NDDs. Silencing HNRNPU reprogrammed methylation dynamics at regulatory regions, particularly at active and bivalent promoters of neurodevelopmental transcription factors. Integrative analysis across PPI, RNA, and methylome datasets identified 19 converging genes at all three molecular levels, including NDD genes within the SWI/SNF complex, SMARCA4 and SMARCC2, and RNA-processing machinery such as SYNCRIP. Together, these data showcase HNRNPU as a central coordinator of RNA metabolism and epigenetic remodeling during neural differentiation, linking RNA-binding, chromatin organization, and DNA methylation to the pathogenesis of HNRNPU-related NDDs.", "doi": "10.1093/nar/gkag107", "pmid": "41674383", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12895067"}, {"db": "pii", "key": "8474399"}], "notes": [], "created": "2026-02-27T13:05:08.621Z", "modified": "2026-03-24T09:06:45.961Z"}, {"entity": "publication", "iuid": "3857360785ca4b5d9ed1b660982a2c92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3857360785ca4b5d9ed1b660982a2c92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3857360785ca4b5d9ed1b660982a2c92"}}, "title": "Warming Causes a Decline in Baltic Sea Coastal Sediment Microbial Abundance.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L", "orcid": "0000-0002-2620-914X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0923436cd0a42cea933771b57ae8c94.json"}}, {"family": "Li", "given": "Songjun", "initials": "S", "orcid": "0009-0008-4816-2451", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0c5a7e34da45c2aca6f8de83af14b5.json"}}, {"family": "Hanna-Elias", "given": "Shahinez", "initials": "S", "orcid": "0009-0007-7894-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a1167e7920f47e188b705992727a776.json"}}, {"family": "Rula", "given": "Iryna", "initials": "I"}, {"family": "Ahlberg", "given": "Louise", "initials": "L", "orcid": "0009-0006-8777-8588", "researcher": {"href": "https://publications.scilifelab.se/researcher/da605765d18c4f5b8bc62bc894b3c3ea.json"}}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2026-02-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "28", "issue": "2", "pages": "e70256", "issn-l": "1462-2912"}, "abstract": "Long-term ocean warming impacts the marine environment, and these effects will be exacerbated by future climate change affecting, e.g., biogeochemical processes and microbial communities. However, how the sediment microbial cell abundance and live/dead ratio respond to warming is poorly understood. In this study, sediment core samples were collected from a Baltic Sea bay artificially heated on average 5\u00b0C for > 50 years above a nearby (control) bay unaffected by the heating. Contrary to the expected increased productivity in the heated bay, qPCR-based sediment cell abundances showed decreased cell numbers along the sediment depth gradient in the heated bay compared to the control bay. This could reflect that a portion of the cells' metabolic energy was diverted to a heat related stress response rather than being used for replication. In addition, live/dead cell ratios showed no clear differences in either bay suggesting the majority of the cells were alive. Finally, sediment depth gradient 16S rRNA gene sequencing confirmed previous studies, showing that prolonged warming shallows sediment biogeochemical zones and related microbial communities. In conclusion, future climate change related warming will likely decrease microbial cell abundances that form part of the food web base, potentially impacting the entire ecosystem.", "doi": "10.1111/1462-2920.70256", "pmid": "41712959", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12920023"}], "notes": [], "created": "2026-02-27T07:59:56.449Z", "modified": "2026-02-27T07:59:57.339Z"}, {"entity": "publication", "iuid": "a13b9b2a120741f2af40dbd525b2c748", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a13b9b2a120741f2af40dbd525b2c748"}}, "title": "Exploration of immune phenotypes in self-sampling citizens", "authors": [{"family": "Dahl", "given": "Leo", "initials": "L", "orcid": "0000-0003-1492-3052", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4df506f315c4289935b935a503efd56.json"}}, {"family": "Bendes", "given": "Annika", "initials": "A", "orcid": "0000-0001-9329-2353", "researcher": {"href": "https://publications.scilifelab.se/researcher/50dffce4f4444dd8b5ff8f9294146a0b.json"}}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB", "orcid": "0000-0002-2669-7796", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a18cc0ce34429a91758206cedb5d60.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V", "orcid": "0009-0003-1985-7733", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d422e623e9e449f98853e6830cdd401.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Bj\u00f6rkander", "given": "Sophia", "initials": "S", "orcid": "0000-0002-4600-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/310af30b841741a790046af03a3cee6d.json"}}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK", "orcid": "0000-0001-5974-7676", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7a04c6538814b089994c7a822ecf07f.json"}}, {"family": "Mezger", "given": "Anja", "initials": "A", "orcid": "0000-0002-7337-9547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebf61fe41e6f43e4aec2be101de688d4.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Fredolini", "given": "Claudia", "initials": "C", "orcid": "0000-0002-7674-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/40ac3a5823cb4f998cc8bdb96dcbf195.json"}}, {"family": "Naluai", "given": "\u00c5sa Torinsson", "initials": "\u00c5T"}, {"family": "Beck", "given": "Olof", "initials": "O"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}, {"family": "Bauer", "given": "Stefan", "initials": "S"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M", "orcid": "0000-0002-2357-1020", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b50df8c8ecc45b89574dc76e244b07e.json"}}, {"family": "Roxhed", "given": "Niclas", "initials": "N", "orcid": "0000-0002-7147-6730", "researcher": {"href": "https://publications.scilifelab.se/researcher/3739210caaf14a28898849f20bf6ece5.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal-article", "published": "2026-02-00", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "29", "issue": "2", "pages": "114611", "issn-l": "2589-0042"}, "abstract": "Blood proteins have provided essential insights into how humans responded to the recent pandemic. To expand our understanding beyond patients seeking medical care, we conducted a citizen-centric survey with 2,000 random residents (age: 18-69 years) from Sweden's two largest cities in 2021. With self-sampled dried blood spots (DBS) and health information from 437 (22%) volunteers, we performed multi-analyte COVID-19 serology, measured autoantibodies (AAbs) against 22 interferons, and quantified 502 circulating low-abundant immune-related blood proteins. Antibody assays confirmed self-reported infections (26%) and vaccinations (40%), showed timing-dependent discrepancies in the immune response, and revealed anti-type I interferon AAbs co-occurring frequently alongside natural infections. Proteomics data added plausible mechanistic insights into cell-mediated processes: data-driven analyses revealed 24% of participants presented deviating immune phenotypes linked to infections, immunity, respiratory effects, and age. Multi-molecular DBS analysis of random layperson samples captured the broader spectrum of immune system states, adding relevant insights for clinical and public health investigations.", "doi": "10.1016/j.isci.2025.114611", "pmid": "41630906", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12860695"}, {"db": "pii", "key": "S2589-0042(25)02872-X"}], "notes": [], "created": "2026-02-26T13:37:49.302Z", "modified": "2026-03-24T09:13:34.204Z"}, {"entity": "publication", "iuid": "dfd322f75400494482ef1a0ccf538954", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd322f75400494482ef1a0ccf538954.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd322f75400494482ef1a0ccf538954"}}, "title": "SOX21 suppresses glioblastoma growth by repressing AP-1 activity", "authors": [{"family": "Rrapaj", "given": "Eltjona", "initials": "E", "orcid": "0000-0003-3601-4888", "researcher": {"href": "https://publications.scilifelab.se/researcher/40451faaeadb4c29bf77bb83ba383d52.json"}}, {"family": "Yuan", "given": "Juan", "initials": "J"}, {"family": "Kurtsdotter", "given": "Idha", "initials": "I"}, {"family": "Misyurin", "given": "Vsevolod", "initials": "V"}, {"family": "Baselli", "given": "Guido Alessandro", "initials": "GA"}, {"family": "Holmberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-3018-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f84bece88a264d228d3770ca634b4a19.json"}}, {"family": "Persson", "given": "Oscar", "initials": "O"}, {"family": "Bergsland", "given": "Maria", "initials": "M"}, {"family": "Muhr", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0704-0788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a665f02acc432e9d80feb5c61f4572.json"}}], "type": "journal-article", "published": "2026-01-31", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "17", "issue": "1", "pages": "191", "issn-l": "2041-4889"}, "abstract": "Treatment-resistant glioblastoma stem and precursor cells (GPCs) drive glioblastoma (GBM) growth and recurrence. Thus, targeting the molecular machinery that sustains GPCs in an undifferentiated and self-renewing state is a promising therapeutic strategy. The transcription factor SOX21 effectively suppresses the tumorigenic capacity of GPCs, but the mechanism by which SOX21 impedes GPC features is unknown. By engineering patient-derived GPCs with a transgenic TetOn system we show that SOX21 expression induces an anti-tumorigenic transcriptional program, aligning with clinical data demonstrating a positive correlation between SOX21 levels and improved GBM patient survival. Induced SOX21 expression in GPCs within pre-established GBM reduces their capacity to sustain tumor growth and significantly extends the survival of the orthotopically transplanted mice. Mechanistically, SOX21 functions as a tumor suppressor by binding a large set of AP-1-targeted chromatin regions, leading to epigenetic repression of AP-1-activated genes. Consistently, the anti-tumorigenic activities of SOX21 are largely replicated by AP-1 inhibitors, which decrease GPC proliferation and survival, while overexpression of the AP-1 family member, c-JUN, counteracts these effects. Our findings identify SOX21 as a key regulator that prevents GPC malignancy by targeting and repressing an AP-1-driven, tumor-promoting gene expression program. These results highlight SOX21-regulated pathways as promising therapeutic targets for GBM.", "doi": "10.1038/s41419-026-08442-5", "pmid": "41620461", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12876893"}, {"db": "pii", "key": "10.1038/s41419-026-08442-5"}], "notes": [], "created": "2026-02-06T08:02:53.704Z", "modified": "2026-03-24T09:13:46.564Z"}, {"entity": "publication", "iuid": "2eb354120b4e4f18a6b6912af75d7656", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2eb354120b4e4f18a6b6912af75d7656.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2eb354120b4e4f18a6b6912af75d7656"}}, "title": "Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effects", "authors": [{"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Rangani", "given": "Fatemeh", "initials": "F"}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C", "orcid": "0000-0002-9088-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ead2e8f98754d1586891eda5adb9e1a.json"}}, {"family": "Zheleznyakova", "given": "Galina", "initials": "G"}, {"family": "Kalomoiri", "given": "Maria", "initials": "M"}, {"family": "Kenny", "given": "Lea", "initials": "L"}, {"family": "Raghavan", "given": "Anika", "initials": "A"}, {"family": "Rao Prakash", "given": "Chandana", "initials": "C"}, {"family": "van den Hoeven", "given": "Gabe", "initials": "G"}, {"family": "Venkata S. Badam", "given": "Tejaswi", "initials": "T"}, {"family": "Covacu", "given": "Ruxandra", "initials": "R"}, {"family": "Andreou", "given": "Ioanna", "initials": "I"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}], "type": "journal-article", "published": "2026-01-31", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "27", "issue": "1", "pages": null}, "abstract": "CRISPR/dCas9-based epigenome editing systems, including DNA methylation epimodifiers, have greatly advanced molecular functional studies, revolutionizing their precision and applicability. Despite their promise, challenges such as the magnitude and stability of the on-target editing and unwanted off-target effects underscore the need for improved tool characterization and design.\n\nWe systematically compare specific targeting and genome-wide off-target effects of available and novel dCas9-based DNA methylation editing tools over time. We demonstrate that multimerization of the catalytic domain of DNA methyltransferase 3A enhances editing potency but also induces widespread, early methylation deposition at low-to-medium methylated promoter-related regions with specific gRNAs and also with non-targeting gRNAs. A small fraction of the methylation changes associated with transcriptional dysregulation and mapped predominantly to bivalent chromatin associating both with transcriptional repression and activation. Additionally, specific non-targeting control gRNAs cause pervasive and long-lasting methylation-independent transcriptional alterations particularly in genes linked to RNA and energy metabolism. CRISPRoff emerges as the most efficient tool for stable promoter targeting, with fewer and less stable off-target effects compared to other epimodifiers but with persistent transcriptome alterations.\n\nOur findings highlight the delicate balance between potency and specificity of epigenome editing and provide critical insights into the design and application of future tools to improve their precision and minimize unintended consequences.", "doi": "10.1186/s13059-026-03967-6", "pmid": "41620608", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12924462"}, {"db": "pii", "key": "10.1186/s13059-026-03967-6"}], "notes": [], "created": "2026-02-06T08:02:40.826Z", "modified": "2026-03-24T09:10:47.840Z"}, {"entity": "publication", "iuid": "0a1bc06aed8944028dbc6a1adb526828", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a1bc06aed8944028dbc6a1adb526828.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a1bc06aed8944028dbc6a1adb526828"}}, "title": "Skeletal Muscle Microbiopsies in Children and Adults-Tolerability, Sample Yield, and Analyzability.", "authors": [{"family": "H\u00f6gelin", "given": "Emil Rydell", "initials": "ER", "orcid": "0000-0002-0155-6655", "researcher": {"href": "https://publications.scilifelab.se/researcher/a797176a0ef44f38b35727870aa42099.json"}}, {"family": "Edman", "given": "Sebastian", "initials": "S"}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "L\u00f6fgren", "given": "Axel", "initials": "A"}, {"family": "Thulin", "given": "Kajsa", "initials": "K"}, {"family": "Michno", "given": "Piotr", "initials": "P"}, {"family": "Norrbom", "given": "Jessica", "initials": "J"}, {"family": "Alkner", "given": "Bj\u00f6rn A", "initials": "BA"}, {"family": "von Walden", "given": "Ferdinand", "initials": "F", "orcid": "0000-0003-1134-2252", "researcher": {"href": "https://publications.scilifelab.se/researcher/903e0b7523da4a49960e677009942f67.json"}}, {"family": "Fornander", "given": "Lotta", "initials": "L", "orcid": "0000-0003-2077-8445", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bceecb024cd4adeb8032e41449c7a36.json"}}], "type": "journal article", "published": "2026-01-30", "journal": {"title": "Muscle Nerve", "issn": "1097-4598", "issn-l": null}, "abstract": "Traditional methods of sampling skeletal muscle tissue are invasive. This study aimed to evaluate a sub-millimeter core-biopsy (microbiopsy) as a potentially more tolerable method, with further regard to tissue yield and analyzability of RNA expression.\n\nChildren (9-13 years, n = 11) and adults (18-50 years, n = 16) were recruited. Microbiopsy and venipuncture were performed, with prior application of local anesthesia cream. Additionally, adults underwent a Bergstr\u00f6m muscle biopsy, with infiltrative local anesthesia. Pain was rated using the visual analog scale (VAS), reported as medians (95% CI). Microbiopsy samples were freeze-dried and weighed. To evaluate RNA sequencing performance at low tissue sample weights, a six-step incremental tissue ladder (10-500 \u03bcg) was analyzed.\n\nChildren rated venipunctures and microbiopsies low, at VAS = 0.1 (0.0-0.6) and 1.6 (0.9-3.9), respectively. Microbiopsy pain ratings were slightly higher than venipuncture, p < 0.001. Pain ratings in adults were 0.0 (0.0-0.5), 1.8 (1.3-2.4), 2.9 (2.4-3.8), and 2.7 (2.2-3.8) for venipuncture, microbiopsy, Bergstr\u00f6m biopsy, and infiltrative local anesthesia, respectively. Microbiopsy was rated less painful than Bergstr\u00f6m biopsy and local anesthesia (p < 0.05). Children did not rate microbiopsy more painful than adults (p = 0.82). Microbiopsies yielded on average 303 (SD 121.8) \u03bcg. RNA sequencing detected similar transcriptomic signatures across the tissue ladder.\n\nThe generally low pain ratings for the microbiopsy procedure support its use as a tolerable method of acquiring skeletal muscle samples in both children and adults. It represents a less painful alternative to Bergstr\u00f6m biopsies while still rendering adequate material for RNA sequencing.", "doi": "10.1002/mus.70161", "pmid": "41618578", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2026-02-09T12:51:02.135Z", "modified": "2026-02-09T12:51:03.068Z"}, {"entity": "publication", "iuid": "b4356e6f236f4a27b987ac01aea346a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4356e6f236f4a27b987ac01aea346a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4356e6f236f4a27b987ac01aea346a2"}}, "title": "Allergen-specific human IgE isolated through an allergen-agnostic pipeline\u2014understanding immune response and allergen recognition", "authors": [{"family": "Th\u00f6rnqvist", "given": "Linnea", "initials": "L"}, {"family": "Franciskovic", "given": "Eric", "initials": "E"}, {"family": "Godzwon", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-9745-1160", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fa85685e9e149d8a341effcb1b924d0.json"}}, {"family": "Kristensen", "given": "Bjarne", "initials": "B"}, {"family": "Sultan", "given": "Kristin", "initials": "K", "orcid": "0009-0002-5619-517X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7288f4347b8440479e0f908b705f9df5.json"}}, {"family": "Nordstr\u00f6m", "given": "Franziska", "initials": "F", "orcid": "0000-0003-3730-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa587c1b382f4cd1b9486ba50eb8bb0e.json"}}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Todorovic", "given": "Nikolina", "initials": "N"}, {"family": "Keller", "given": "Walter", "initials": "W", "orcid": "0000-0002-2261-958X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dfdfb31e5a24ceb93609f4166c06f5c.json"}}, {"family": "Lindstedt", "given": "Malin", "initials": "M", "orcid": "0000-0001-9136-1087", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc58fdfd7f0a40e2bf2fa21c2d2bea36.json"}}, {"family": "Greiff", "given": "Lennart", "initials": "L", "orcid": "0000-0002-7004-1989", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a6c63fee50b446da172ddbb30f69fb2.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2026-01-28", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "9", "issue": "1", "issn-l": "2399-3642"}, "abstract": "Allergy, characterised by antibody responses of the IgE isotype, is a major health concern. The set of monoclonal human IgE used for studying the molecular mechanisms of allergies is limited. Single-cell sequencing offers opportunities to establish novel antibodies for researching, diagnosis, and treatment of allergies. We describe and exploit a pipeline for generating recombinant IgE directly from the immune repertoires of allergic subjects. It uses single-cell sequencing of IgM- B cells of bone marrow and peripheral blood in an allergen-agnostic manner, combined with high-throughput transcriptome sequencing to identify clonotypes populating the IgE repertoire. Immunochemical and immunoprecipitation analyses are used to deconvolute the specificity of identified antibodies. High-affinity antibodies were raised against four grass pollen allergens, antibodies that illustrated aspects of the development of allergen-specific humoral immunity. The pipeline provides a streamlined approach for the development and characterisation of native allergen-specific antibodies as they occur in allergy and during allergy desensitisation.", "doi": "10.1038/s42003-026-09600-3", "pmid": "41606257", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12953631"}, {"db": "pii", "key": "10.1038/s42003-026-09600-3"}], "notes": [], "created": "2026-02-09T12:51:20.129Z", "modified": "2026-03-24T09:14:00.807Z"}, {"entity": "publication", "iuid": "342a4ab7fa284801b476886e85244b3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/342a4ab7fa284801b476886e85244b3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/342a4ab7fa284801b476886e85244b3e"}}, "title": "NUP98 regulates orthoflavivirus replication through interaction with vRNA and can be targeted for antiviral purposes.", "authors": [{"family": "Peters", "given": "Marie B A", "initials": "MBA", "orcid": "0000-0001-8994-0864", "researcher": {"href": "https://publications.scilifelab.se/researcher/df4733590d054742b732c2028a8f5e8a.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Madhu", "given": "Priyanka", "initials": "P"}, {"family": "Lundmark", "given": "Richard", "initials": "R"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}], "type": "journal article", "published": "2026-01-22", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "3", "issn-l": "0305-1048"}, "abstract": "The nuclear pore complex (NPC) is composed of multiple nucleoporins (NUPs) and enables the exchange of RNA and proteins between the nucleus and cytoplasm. NUP98 is one of the major components of the NPC, being involved in the RNA export pathway by interacting with several transport factors. Previous studies have suggested both proviral and antiviral functions of NUP98 in viral infection, yet little is known about its function in orthoflavivirus infection. In this study we show that NUP98 is a proviral cellular protein that is recruited to the cytoplasm during orthoflavivirus infection. We observe that NUP98 is found specifically in the vicinity of the replication vesicles during infections with tick-borne encephalitis virus, Japanese encephalitis virus, and yellow fever virus. Furthermore, using surface plasmon resonance, cross-link immunoprecipitation, and cross-link immunoprecipitation-sequencing we observe that the C-terminal domain of NUP98 directly interacts with a conserved site of the viral RNA (vRNA) in the E coding region promoting viral replication. We identified a peptide that binds to NUP98 that is antivirally active against several orthoflaviviruses by outcompeting the binding between NUP98 and vRNA, making NUP98 an attractive target for antiviral development.", "doi": "10.1093/nar/gkag027", "pmid": "41591840", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12839527"}, {"db": "pii", "key": "8442274"}], "notes": [], "created": "2026-02-27T08:03:17.950Z", "modified": "2026-06-01T11:13:48.642Z"}, {"entity": "publication", "iuid": "1e5708bc6c1c4c099e773f1d29e68641", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e5708bc6c1c4c099e773f1d29e68641.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e5708bc6c1c4c099e773f1d29e68641"}}, "title": "Anoctamin-2-specific T cells link Epstein-Barr virus to multiple sclerosis.", "authors": [{"family": "Thomas", "given": "Olivia G", "initials": "OG", "orcid": "0000-0002-2011-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea07f812ffee4db893c6f98548563525.json"}}, {"family": "Rykaczewska", "given": "Urszula", "initials": "U"}, {"family": "Gale\u0161i\u0107", "given": "Marina", "initials": "M"}, {"family": "van der Burgt", "given": "Rianne T M", "initials": "RTM"}, {"family": "Hall\u00e9n", "given": "Nils", "initials": "N"}, {"family": "Ferro", "given": "Filippo", "initials": "F", "orcid": "0000-0002-6023-8227", "researcher": {"href": "https://publications.scilifelab.se/researcher/27810903638948feb4391fa537a7eda3.json"}}, {"family": "Bronge", "given": "Mattias", "initials": "M", "orcid": "0000-0002-1258-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/691b77352a57408896ef1fb486980ccd.json"}}, {"family": "Marti", "given": "Zoe", "initials": "Z"}, {"family": "Li", "given": "Yue", "initials": "Y"}, {"family": "Riqu\u00e9", "given": "Alexandra Hill", "initials": "AH"}, {"family": "Lin", "given": "Jianing", "initials": "J"}, {"family": "Krstic", "given": "Aleksa", "initials": "A"}, {"family": "Gromadzka", "given": "Alicja", "initials": "A"}, {"family": "Szonder", "given": "Andr\u00e1s Levente", "initials": "AL"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Reina-Campos", "given": "Mar\u00eda", "initials": "M"}, {"family": "Sun", "given": "Ting", "initials": "T", "orcid": "0000-0002-7104-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/521fca43267242fca06da0f5fc823e6a.json"}}, {"family": "Rubio Rodr\u00edguez-Kirby", "given": "Leslie A", "initials": "LA", "orcid": "0000-0003-4467-2661", "researcher": {"href": "https://publications.scilifelab.se/researcher/9790e215a63d40aa8fac497b537999f9.json"}}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6", "orcid": "0000-0002-9980-2702", "researcher": {"href": "https://publications.scilifelab.se/researcher/8288edd47f70479e93e1fc441d486997.json"}}, {"family": "Berglund", "given": "Rasmus", "initials": "R"}, {"family": "Kakhki", "given": "Majid Pahlevan", "initials": "MP"}, {"family": "Adzemovic", "given": "Milena Z", "initials": "MZ"}, {"family": "Zeitelhofer", "given": "Manuel", "initials": "M"}, {"family": "Akpinar", "given": "Birce", "initials": "B"}, {"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Nilsson", "given": "Ola B", "initials": "OB", "orcid": "0000-0002-7516-1760", "researcher": {"href": "https://publications.scilifelab.se/researcher/096ce3bf888b4ad395d53bb3c11f6946.json"}}, {"family": "Holmgren", "given": "Erik", "initials": "E", "orcid": "0000-0002-2656-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/6160949c45cf4daaab3991d051db5a16.json"}}, {"family": "Cucuzza", "given": "Chiara Starvaggi", "initials": "CS"}, {"family": "H\u00f6gelin", "given": "Klara Asplund", "initials": "KA"}, {"family": "Gafvelin", "given": "Guro", "initials": "G", "orcid": "0000-0003-1618-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/870294f4604744ccb212a3c299887ecc.json"}}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T", "orcid": "0000-0002-5391-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52adbc739e274652bbf877facf4f0959.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fe4902c355449e4812008d4ad7a37e0.json"}}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c3e953634140b8974186ac0d7eac85.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Martin", "given": "Roland", "initials": "R"}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2026-01-22", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "189", "issue": "2", "pages": "585-602.e38"}, "abstract": "Epstein-Barr virus (EBV) infection constitutes a prerequisite for multiple sclerosis (MS) development, and cross-reactivity between EBV nuclear antigen 1 (EBNA1) and anoctamin-2 (ANO2) antibodies was previously demonstrated in persons with MS (pwMS). Here, we show that ANO2-specific CD4+ T cells are more frequent in pwMS. Immunization of SJL/J mice with ANO2 or EBNA1 led to cross-reactive CD4+ T cell and antibody responses. ANO2 pre-immunization led to exacerbated experimental autoimmune encephalomyelitis (EAE), an effect mediated by CD4+ T cells, as confirmed by adoptive transfer experiments. T cell clones with cross-reactivity to EBNA1 and ANO2 could be isolated from natalizumab-treated pwMS, and sequencing of EBNA1- and ANO2-specific T cell receptors (TCRs) revealed a significant repertoire overlap. We thus report the first mechanistic evidence that EBNA1 CD4+ T cells can target the MS autoantigen ANO2, thereby establishing a link between EBV infection and neuroinflammation.", "doi": "10.1016/j.cell.2025.12.032", "pmid": "41534529", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)01481-3"}], "notes": [], "created": "2026-01-15T20:23:02.729Z", "modified": "2026-03-24T09:17:16.086Z"}, {"entity": "publication", "iuid": "f74db641b67b4485b01bf07e453d5dd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f74db641b67b4485b01bf07e453d5dd0"}}, "title": "Draft assemblies for 177 bird species enhance genus-level coverage", "authors": [{"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Wang", "given": "Shuang", "initials": "S", "orcid": "0009-0008-9451-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/186a6001c26a403e8b0640a3cb516a1a.json"}}, {"family": "Bilyeli\u00a0\u00d8ksnebjerg", "given": "Daniel", "initials": "D"}, {"family": "Nielsen", "given": "Sascha Dreyer", "initials": "SD", "orcid": "0000-0003-2485-9314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ff8708bff74ea4b0c80c5f434329a8.json"}}, {"family": "Dai", "given": "Wei", "initials": "W", "orcid": "0000-0001-9286-759X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7c48f0de21d478ab23bc18b439472e0.json"}}, {"family": "Jiang", "given": "Wei", "initials": "W", "orcid": "0000-0003-1570-1208", "researcher": {"href": "https://publications.scilifelab.se/researcher/9908e45f950149e2963961d88783dabb.json"}}, {"family": "Liang", "given": "Jing", "initials": "J"}, {"family": "Han", "given": "Wei", "initials": "W"}, {"family": "Zhou", "given": "Chengran", "initials": "C", "orcid": "0000-0002-9468-5973", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d36e1d73bb440184212119bf82858c.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Monadjem", "given": "Ara", "initials": "A", "orcid": "0000-0003-1906-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/94671b1f708d49f5b9eebc0e6b78b82e.json"}}, {"family": "Bhembe", "given": "Zamekile D", "initials": "ZD", "orcid": "0009-0006-5354-5751", "researcher": {"href": "https://publications.scilifelab.se/researcher/d276b65085fa48bdb17d12ecb8b014ac.json"}}, {"family": "Maphalala", "given": "Machawe", "initials": "M", "orcid": "0000-0002-9304-1391", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eebd8acec5a4084b64c3be4a3627b67.json"}}, {"family": "Ocampo", "given": "Diego", "initials": "D"}, {"family": "Sandoval", "given": "Luis", "initials": "L", "orcid": "0000-0002-0793-6747", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8f560d617c2432aa26f9700d2311ac1.json"}}, {"family": "Fickel", "given": "J\u00f6rns", "initials": "J", "orcid": "0000-0002-0593-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/40018134351a481ab2d00b4113404c47.json"}}, {"family": "Greenwood", "given": "Alex D", "initials": "AD", "orcid": "0000-0002-8249-1565", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab62cca19d7641918b6dd9adbff919c5.json"}}, {"family": "Szentiks", "given": "Claudia A", "initials": "CA"}, {"family": "Roller", "given": "Marco", "initials": "M"}, {"family": "Birks", "given": "Sharon M", "initials": "SM"}, {"family": "Leach\u00e9", "given": "Adam D", "initials": "AD", "orcid": "0000-0001-8929-6300", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c9502316d344a1282bec0f444638222.json"}}, {"family": "Rico-Guevara", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-4067-5312", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe305adf4d234dce94a9c74ca873169d.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Vy", "given": "Nguyen Tran", "initials": "NT"}, {"family": "Hvilsom", "given": "Christina", "initials": "C", "orcid": "0000-0001-7870-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e68386a9414dad9162026abafad7ce.json"}}, {"family": "Berner", "given": "Juliana Andrea", "initials": "JA"}, {"family": "Lifjeld", "given": "Jan Terje", "initials": "JT"}, {"family": "Johnsen", "given": "Arild", "initials": "A", "orcid": "0000-0003-4864-6284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d610052c8e134f9a9ddff3eee7ed864d.json"}}, {"family": "Johannessen", "given": "Lars Erik", "initials": "LE", "orcid": "0000-0001-5981-9190", "researcher": {"href": "https://publications.scilifelab.se/researcher/838c1d1eb4bb4861a2408a5d83b616cb.json"}}, {"family": "Labuschagne", "given": "Kim", "initials": "K", "orcid": "0000-0003-2784-4767", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa0e1dbf2194c5bbcfb36769d1b2cf4.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Hellgren", "given": "Olof", "initials": "O", "orcid": "0000-0002-4062-7276", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bca3b673a2447ecbc55eaf9edf56a02.json"}}, {"family": "Brumfield", "given": "Robb T", "initials": "RT", "orcid": "0000-0003-2307-0688", "researcher": {"href": "https://publications.scilifelab.se/researcher/71a3a36f83154d3dbe14e1a5290f425f.json"}}, {"family": "Burg", "given": "Theresa M", "initials": "TM", "orcid": "0000-0001-5096-3479", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab837fec0ea64df5bd66001038f505c5.json"}}, {"family": "Illera", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0002-4389-0264", "researcher": {"href": "https://publications.scilifelab.se/researcher/d137c193d3cd4f8c8b9fe09a6443033c.json"}}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Smit", "given": "Ben", "initials": "B"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE", "orcid": "0000-0001-8946-7085", "researcher": {"href": "https://publications.scilifelab.se/researcher/744276ae56e24e7295f672854fbaf3d9.json"}}, {"family": "Lee", "given": "Jessica", "initials": "J", "orcid": "0000-0003-0757-4237", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec08a3cbe214f22b05c730bf94613aa.json"}}, {"family": "Nishiumi", "given": "Isao", "initials": "I"}, {"family": "Quesada", "given": "Javier", "initials": "J", "orcid": "0000-0002-6010-8473", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c4e889bf2fd424c915c6487038f7950.json"}}, {"family": "Dumbacher", "given": "John P", "initials": "JP", "orcid": "0000-0001-8942-1554", "researcher": {"href": "https://publications.scilifelab.se/researcher/6221be035944462989353d66f126a5c5.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Andersen", "given": "Michael J", "initials": "MJ", "orcid": "0000-0002-7220-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/15d3b310f2f34fc4969520d431a14f6d.json"}}, {"family": "Witt", "given": "Christopher C", "initials": "CC", "orcid": "0000-0003-2781-1543", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a535b32f94e59acf1398df72a8cd1.json"}}, {"family": "Phillips", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-0208-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/f35746710d7c4ae6a86d1b12e805ea14.json"}}, {"family": "Prum", "given": "Richard O", "initials": "RO", "orcid": "0000-0002-4741-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/28d15772cf924924b7e5630bfbdb5b89.json"}}, {"family": "Zyskowski", "given": "Kristof", "initials": "K", "orcid": "0000-0002-5680-6412", "researcher": {"href": "https://publications.scilifelab.se/researcher/49aadb5fab7b4fbebf1c65c9f3a04217.json"}}, {"family": "Goodman", "given": "Steven M", "initials": "SM"}, {"family": "Raherilalao", "given": "Marie Jeanne", "initials": "MJ", "orcid": "0000-0002-8618-7157", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5653450df494d96b15d77a12d77e932.json"}}, {"family": "Ottosson", "given": "Ulf", "initials": "U", "orcid": "0000-0001-7914-0484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b035efe180248eaa188b0e1d23f2007.json"}}, {"family": "Barshep", "given": "Yahkat", "initials": "Y"}, {"family": "Ivande", "given": "Sam", "initials": "S", "orcid": "0000-0003-4949-1376", "researcher": {"href": "https://publications.scilifelab.se/researcher/181e4fbbf6ae40d1bebe504c5c24f797.json"}}, {"family": "Brl\u00edk", "given": "Vojt\u011bch", "initials": "V", "orcid": "0000-0002-7902-8123", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ed62d45f978413d9c983e53b07b7ad8.json"}}, {"family": "Okposio", "given": "Emmanuel", "initials": "E"}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Rahbek", "given": "Carsten", "initials": "C", "orcid": "0000-0003-4585-0300", "researcher": {"href": "https://publications.scilifelab.se/researcher/341ee33c55904249b6e70a9b55b5509a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Hosner", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-7499-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/87a4c8cd6229436d9a39761aa77eeec2.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal-article", "published": "2026-01-21", "journal": {"title": "Gigascience", "issn": "2047-217X", "volume": "15", "issn-l": "2047-217X"}, "abstract": "With over 10,000 recognized species, birds constitute one of the most diverse and widely distributed vertebrate groups. Although avian genomics has advanced rapidly over the past decade, substantial gaps remain across the global avifauna. Filling these gaps is essential for understanding macroevolutionary patterns, population structure, and the molecular basis of ecological and behavioral diversity. Worldwide museum collections represent invaluable resources for filling these gaps, yet the typically degraded DNA and limited quantities from historical specimens have posed significant challenges for generating high-quality genome assemblies.\n\nHere, the Bird Genome 10 K Project adopted low-input sequencing strategies that reduce costs while improving assembly quality compared with earlier order- and family-level genomes. Using mainly stLFR, complemented by 10X Genomics and standard next-generation sequencing, we assembled 177 avian genomes from museum specimens and tissue collections representing 161 genera, including 102 newly sequenced at the genomic level. The assemblies average \u223c1.2 Gb in size, with scaffold N50 = 8.03 Mb, contig N50 = 120 kb, 93% BUSCO completeness, and Merqury Quality Value score of 56.\n\nThese genomes greatly expand avian taxonomic coverage and demonstrate the efficiency of low-input sequencing for generating high-quality assemblies from limited and often degraded material sourced from museum specimens. This resource provides a foundation for comparative genomics, conservation genetics, and evolutionary studies across the avian tree of life.", "doi": "10.1093/gigascience/giag045", "pmid": "42104960", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8675036"}, {"db": "pmc", "key": "PMC13274736"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-29T07:41:18.996Z"}, {"entity": "publication", "iuid": "4f13015ae8624d2280a97f539bbf89b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f13015ae8624d2280a97f539bbf89b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f13015ae8624d2280a97f539bbf89b0"}}, "title": "Dealing with phosphorus deficiency: contrasting strategies in marine phytoplankton and bacteria", "authors": [{"family": "Delgadillo-Nu\u00f1o", "given": "Erick", "initials": "E"}, {"family": "Teira", "given": "Eva", "initials": "E", "orcid": "0000-0002-4333-0101", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed7047ae09241a182466fee66736dbd.json"}}, {"family": "Fern\u00e1ndez", "given": "Emilio", "initials": "E", "orcid": "0000-0001-7985-0814", "researcher": {"href": "https://publications.scilifelab.se/researcher/748dd6833e474966b5c7b79ef52dd1c7.json"}}, {"family": "Justel-D\u00edez", "given": "Maider", "initials": "M"}, {"family": "Di Leo", "given": "Danilo", "initials": "D"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S", "orcid": "0000-0002-5476-7499", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc1a03d6cd414b748807788a0c8e11fb.json"}}], "type": "journal-article", "published": "2026-01-14", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "6", "issue": "1", "pages": "ycag035", "issn-l": null}, "abstract": "Phosphorus (P) and nitrogen (N) are essential nutrients for microbial growth, playing crucial roles in regulating the biological productivity of marine ecosystems. Over the last decades, the relatively higher increase in anthropogenic N compared to P inputs is causing a continuous increase in the N:P supply ratio to the global biosphere. The high N:P ratio of riverine discharge may seasonally cause P limitation in estuaries and river-dominated continental shelf waters. We conducted a mesocosm experiment simulating a P-deplete and a P-replete riverine discharge to coastal waters in NW Spain to assess the functional response of marine microplankton using a metatranscriptomic approach. By examining the expression of 40 well-documented genes related to P-metabolism in prokaryotic and eukaryotic gene expression, we uncovered pronounced changes in microbial P-metabolism induced by riverine N:P ratio in this productive system. Remarkably, heterotrophic bacteria and eukaryotic phytoplankton exhibited contrasting phosphate metabolism strategies in response to P deficiency, with the former mostly expressing genes coding for high-affinity transporters and the latter mostly transcribing genes related with low-affinity transporters. Our results also highlight distinct regulatory and adaptive mechanisms across different members of the prokaryotic and eukaryotic communities when exposed to varying P concentrations. Our findings shed light on the broader ecological and functional roles of these genes in nutrient cycling within aquatic ecosystems, with potential application for the design of diagnostic tools for P status in coastal productive systems.", "doi": "10.1093/ismeco/ycag035", "pmid": "41835132", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12981677"}, {"db": "pii", "key": "ycag035"}], "notes": [], "created": "2026-03-23T13:43:18.783Z", "modified": "2026-03-24T09:16:03.978Z"}, {"entity": "publication", "iuid": "20af1880766c43ec92b67618ebf96e75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20af1880766c43ec92b67618ebf96e75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20af1880766c43ec92b67618ebf96e75"}}, "title": "Single-Cell Omics Analysis of Human Basophils Reveals Two Transcriptionally Distinct Populations.", "authors": [{"family": "Papavasileiou", "given": "Sofia", "initials": "S", "orcid": "0000-0002-4066-5715", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bdcde693814787b551baca99852eb7.json"}}, {"family": "Mo", "given": "Jiezhen", "initials": "J"}, {"family": "Boey", "given": "Daryl", "initials": "D"}, {"family": "Wu", "given": "Chenyan", "initials": "C"}, {"family": "Tronstad", "given": "Magnus", "initials": "M"}, {"family": "Margerie", "given": "Lucille", "initials": "L", "orcid": "0000-0001-9537-1231", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5acd66266474d168d31cc60aa92294a.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Low", "given": "Jing Hui", "initials": "JH"}, {"family": "Ong", "given": "Jocelyn", "initials": "J"}, {"family": "Blom", "given": "Lars Heede", "initials": "LH", "orcid": "0000-0003-2027-727X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a5bcf890d60428b9e6569c0d435c08d.json"}}, {"family": "Andiappan", "given": "Anand Kumar", "initials": "AK"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G", "orcid": "0000-0001-6795-5512", "researcher": {"href": "https://publications.scilifelab.se/researcher/258ef97611dd4441a38e1baf2b517ecd.json"}}, {"family": "Dahlin", "given": "Joakim S", "initials": "JS", "orcid": "0000-0003-3007-9875", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d022071f86a451aba84b18fb0774461.json"}}], "type": "journal article", "published": "2026-01-07", "journal": {"title": "Allergy", "issn": "1398-9995", "issn-l": "0105-4538"}, "abstract": "Basophils are implicated in various diseases including allergies, but a comprehensive single-cell characterization of human basophils has yet to be performed. Here, we aimed to generate a single-cell omics-based reference resource of circulating human basophils, integrating transcriptomic and large-scale immunoprofiling data. We also sought to investigate basophil heterogeneity at the molecular level.\n\nCirculating basophils were analyzed using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Both short- and long-read single-cell RNA-sequencing platforms were used to capture the transcriptomic data.\n\nCITE-seq enabled accurate identification and profiling of side scatterlow lineage- CCR3+ Fc\u03b5RI+ basophils. Short-read single-cell RNA-sequencing data revealed two previously unresolved basophil populations, defined by 66 differentially expressed genes and reproducibly identified across donors. Despite the transcriptional differences, the populations displayed similar immunophenotypes based on more than 100 investigated cell surface markers. Long-read single-cell RNA-sequencing analysis confirmed the existence of the two populations and provided further insights into their gene expression profiles.\n\nWe present a multimodal single-cell resource that defines two novel transcriptionally distinct basophil populations. This resource, accessible through a user-friendly web interface, constitutes a cellular and molecular reference map for future studies of basophils in health and disease.", "doi": "10.1111/all.70209", "pmid": "41498390", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Single cell": "Collaborative", "NGI Short read": "Service", "NGI Long read": "Collaborative"}, "xrefs": [], "notes": [], "created": "2026-01-08T07:58:10.538Z", "modified": "2026-01-08T07:58:10.841Z"}, {"entity": "publication", "iuid": "438c9e5e841c43789942d0c391dbba77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/438c9e5e841c43789942d0c391dbba77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/438c9e5e841c43789942d0c391dbba77"}}, "title": "TGF\u03b2 signaling mediates microglial resilience to spatiotemporally restricted myelin degeneration.", "authors": [{"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b85d1ae8136464788be19d62a8863d7.json"}}, {"family": "Liu", "given": "Yun", "initials": "Y", "orcid": "0000-0001-5753-1265", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa51ce95224f46d8ac2a25652a0cded3.json"}}, {"family": "Min", "given": "Jin-Hong", "initials": "JH"}, {"family": "Joshua", "given": "Vijay", "initials": "V", "orcid": "0000-0002-2606-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/60cae01031724ad7b8d67851bc0d9b78.json"}}, {"family": "Lin", "given": "Jianing", "initials": "J"}, {"family": "Li", "given": "Yue", "initials": "Y", "orcid": "0000-0003-0584-1119", "researcher": {"href": "https://publications.scilifelab.se/researcher/12c8feb7f8914821905e56b6b81473ef.json"}}, {"family": "Kreutzmann", "given": "Judith C", "initials": "JC"}, {"family": "Guo", "given": "Yuxi", "initials": "Y"}, {"family": "Xia", "given": "Wenlong", "initials": "W"}, {"family": "Mohammadi", "given": "Elyas", "initials": "E"}, {"family": "Pieber", "given": "Melanie", "initials": "M"}, {"family": "Suerth", "given": "Valerie", "initials": "V"}, {"family": "Xia", "given": "Yiming", "initials": "Y"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Hugnot", "given": "Jean-Philippe", "initials": "JP"}, {"family": "Kanatani", "given": "Shigeaki", "initials": "S", "orcid": "0000-0003-2226-4288", "researcher": {"href": "https://publications.scilifelab.se/researcher/355335d5d964416883ccf63a312b69db.json"}}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P", "orcid": "0000-0003-1446-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/91c3e953634140b8974186ac0d7eac85.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Fancy", "given": "Stephen P J", "initials": "SPJ", "orcid": "0000-0002-2818-8258", "researcher": {"href": "https://publications.scilifelab.se/researcher/0afaa662c4d943579e4823dba3dae348.json"}}, {"family": "Sarlus", "given": "Heela", "initials": "H", "orcid": "0000-0001-7880-9828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9985f00d25dc4440b4e9a10ec5c3a69f.json"}}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b0733d3c25145139f42cad897d6726b.json"}}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fe4902c355449e4812008d4ad7a37e0.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256"}, "abstract": "Microglia survey and regulate central nervous system myelination during embryonic development and adult homeostasis. However, whether microglia-myelin interactions are spatiotemporally regulated remains unexplored. Here, by examining spinal cord white matter tracts in mice, we determined that myelin degeneration was particularly prominent in the dorsal column (DC) during normal aging. This was accompanied by molecular and functional changes in DC microglia as well as an upregulation of transforming growth factor beta (TGF)\u03b2 signaling. Disrupting TGF\u03b2 signaling in microglia led to unrestrained microglial responses and myelin loss in the DC, accompanied by neurological deficits exacerbated with aging. Single-nucleus RNA-sequencing analyses revealed the emergence of a TGF\u03b2 signaling-sensitive microglial subset and a disease-associated oligodendrocyte subset, both of which were spatially restricted to the DC. We further discovered that microglia rely on a TGF\u03b2 autocrine mechanism to prevent damage of myelin in the DC. These findings demonstrate that TGF\u03b2 signaling is crucial for maintaining microglial resilience to myelin degeneration in the DC during aging. This highlights a previously unresolved checkpoint mechanism of TGF\u03b2 signaling with regional specificity and spatially restricted microglia-oligodendrocyte interactions.", "doi": "10.1038/s41593-025-02161-4", "pmid": "41482590", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-025-02161-4"}], "notes": [], "created": "2026-01-07T10:54:23.366Z", "modified": "2026-01-07T10:54:23.929Z"}, {"entity": "publication", "iuid": "053ef45f515a4c6d94ba0ee3a1b5a74a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/053ef45f515a4c6d94ba0ee3a1b5a74a"}}, "title": "Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.", "authors": [{"family": "Gu\u00f0j\u00f3nsd\u00f3ttir", "given": "S\u00f3lveig M", "initials": "SM", "orcid": "0009-0002-6435-4409", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d580e28f1f4e9ea90b46b330b6dcff.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Leme\u017e", "given": "\u0160pela", "initials": "\u0160", "orcid": "0000-0002-0387-1421", "researcher": {"href": "https://publications.scilifelab.se/researcher/381dee4d331a43369d747adc51275fea.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}], "type": "journal article", "published": "2026-01-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "18", "issue": "1", "issn-l": "1759-6653"}, "abstract": "Using temporarily spaced high-coverage ancient genomes, we can assess population decline prior to extinction. However, finding suitable ancient remains for recovering this type of data is challenging. Here, we sequenced a high-coverage genome from muscle tissue of a 14,400-year-old woolly rhinoceros (Coelodonta antiquitatis)-a cold-adapted herbivore that went extinct \u223c14,000-years ago-found inside a permafrost-preserved wolf's stomach. We compared genome-wide diversity, inbreeding, genetic load, and population size changes in this sample with two other Late Pleistocene Siberian woolly rhinoceros. We found no evidence of population size decline, nor any genomic erosion, shortly prior to the species' demise. Given the few long homozygous segments, typically indicative of recent inbreeding, we infer a stable population size only a few centuries before extinction. Thus, the woolly rhinoceros' extinction likely happened rapidly, during the B\u00f8lling-Aller\u00f8d interstadial. This study demonstrates the ability to recover high-quality DNA from unlikely sources to elucidate species' extinction dynamics.", "doi": "10.1093/gbe/evaf239", "pmid": "41530912", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12799484"}, {"db": "pii", "key": "8414728"}], "notes": [], "created": "2026-01-22T13:27:26.594Z", "modified": "2026-01-22T13:27:27.263Z"}, {"entity": "publication", "iuid": "cc47692d5ce54490b075f561042eafa5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc47692d5ce54490b075f561042eafa5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc47692d5ce54490b075f561042eafa5"}}, "title": "Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells", "authors": [{"family": "Deligiannis", "given": "Spyridon Panagiotis", "initials": "SP"}, {"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Moussaud-Lamodi\u00e8re", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-2359-6519", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a0f932253042239c1d38ea00ca0018.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "Akos", "initials": "A", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Lavogina", "given": "Darja", "initials": "D"}, {"family": "Papaikonomou", "given": "Kiriaki", "initials": "K"}, {"family": "Zubarev", "given": "Roman", "initials": "R", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/e971b9cdec2b4411934f9c5d535da8b4.json"}}, {"family": "Acharya", "given": "Ganesh", "initials": "G"}, {"family": "Velthut-Meikas", "given": "Agne", "initials": "A", "orcid": "0000-0003-1927-9016", "researcher": {"href": "https://publications.scilifelab.se/researcher/3371af7256714f478d42af5cf868134d.json"}}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}, {"family": "Salumets", "given": "Andres", "initials": "A", "orcid": "0000-0002-1251-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dcf4bacf5c4792bbfd111495d43595.json"}}, {"family": "Di Nisio", "given": "Valentina", "initials": "V", "orcid": "0000-0002-8435-7925", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee1509ba58840f597b7fccc778a0a20.json"}}], "type": "journal-article", "published": "2026-01-02", "journal": {"title": "J Ovarian Res", "issn": "1757-2215", "issn-l": null, "volume": "19", "issue": "1", "pages": null}, "abstract": "Radiotherapy is a cornerstone of cancer treatment; however, its effects on healthy ovarian somatic cells remain largely unexplored. This study addresses this gap by investigating how human cortical and medullary primary ovarian cells (cPOCs and mPOCs, respectively) respond to acute, high-dose X-ray exposure in vitro.\n\nOvarian tissue was obtained from eight patients (aged 23\u201336 years) undergoing gender-affirming surgery at Karolinska University Hospital in Huddinge, Sweden. The tissue was separated into cortex and medulla and dissociated into cPOCs and mPOCs. Monolayer cultures of cPOCs and mPOCs were exposed to 10 Gy X-rays upon reaching confluency, or left unexposed as paired controls. Following irradiation, cells were assessed for ATP content and mitochondrial dehydrogenase activity, followed by immunofluorescence staining, bulk RNA sequencing (Illumina Stranded mRNA Prep Ligation protocol; sequencing on the Illumina NovaSeq 6000 platform), bulk proteomic analysis (liquid chromatography\u2013tandem mass spectrometry), and a functional assay for assessing their ability to form 3D Silk-Ovarioids.\n\nWhile irradiation did not significantly affect cell viability, immunofluorescence analyses revealed alterations in DNA damage response, apoptosis, and cell cycle regulation. Transcriptomic analysis showed minimal changes at 1 h post-irradiation in both cPOCs and mPOCs. However, marked shifts in transcriptomic profiles were observed at 4 h (2,810 and 2,540 DEGs in cPOCs and mPOCs, respectively) and at 24 h (2,462 and 2,802 DEGs, respectively), including upregulation of the p53 pathway and downregulation of MYC targets, E2F targets, the G2/M checkpoint, and the mTORC1 pathway. At the proteomic level, differentially expressed proteins associated with cell adhesion, focal adhesion, and cadherin binding were detected at 24 h post-irradiation. Functionally, irradiated cells demonstrated an impaired capacity to self-organize into 3D Silk-Ovarioids, indicating compromised cell\u2013cell adhesion.\n\nThese findings reveal a novel mechanism by which radiotherapy may damage ovarian tissue independently of follicular loss, underscoring the need for targeted strategies to preserve somatic cell function in fertility preservation protocols.\n\nThe online version contains supplementary material available at 10.1186/s13048-025-01932-8.", "doi": "10.1186/s13048-025-01932-8", "pmid": "41485059", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC12930946"}, {"db": "pii", "key": "10.1186/s13048-025-01932-8"}], "notes": [], "created": "2026-01-07T10:51:06.159Z", "modified": "2026-03-24T09:15:33.835Z"}, {"entity": "publication", "iuid": "f48f131387f44524b2e0db88864b0c45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f48f131387f44524b2e0db88864b0c45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f48f131387f44524b2e0db88864b0c45"}}, "title": "Using Historic and Contemporary Genomes to Assess the Genetic Consequences of a Population Decline in an Endangered Tern Population.", "authors": [{"family": "Schnelle", "given": "Anna", "initials": "A", "orcid": "0000-0002-5403-8421", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a663ebd957425293ede7c37c1a2a34.json"}}, {"family": "Rollins", "given": "Robert E", "initials": "RE", "orcid": "0000-0002-5779-7001", "researcher": {"href": "https://publications.scilifelab.se/researcher/ceba437696254c37b039fa4631200a74.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Cecere", "given": "Jacopo G", "initials": "JG"}, {"family": "Serra", "given": "Lorenzo", "initials": "L", "orcid": "0000-0002-8911-8050", "researcher": {"href": "https://publications.scilifelab.se/researcher/de52abed5b814b7c82d985c448cafa7e.json"}}, {"family": "Guti\u00e9rrez", "given": "Jorge S", "initials": "JS"}, {"family": "Masero", "given": "Jose A", "initials": "JA"}, {"family": "Risch", "given": "Markus", "initials": "M"}, {"family": "Bouwhuis", "given": "Sandra", "initials": "S", "orcid": "0000-0003-4023-1578", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f1fb8d7e1e4b0a94aac306ba67006a.json"}}, {"family": "Liedvogel", "given": "Miriam", "initials": "M"}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "19", "issue": "1", "pages": "e70192", "issn-l": "1752-4571"}, "abstract": "Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (Gelochelidon nilotica) has declined from 500 breeding pairs in the 1940s to 52 in 2025, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data among the declining population, two thriving populations and the ancestors of the declining population. We find comparable nucleotide diversity, but lower observed heterozygosity in the Central European population compared to the Mediterranean populations. The contemporary samples show some population structure as well, although admixture analyses and low genetic differentiation (F ST) still suggest potential population connectivity. Museum specimens from the historic population reveal an increased level of genetic diversity compared to the contemporary population, with effective population size estimates suggesting two past population declines. While inbreeding coefficients (F ROH) in the current Central European population are significantly higher than in the historic population, they are similar to those in the Mediterranean populations. These results suggest that population structure may be emerging, and that although inbreeding is not yet at worrisome levels in the last Central European population of gull-billed terns, it may be on the rise. If this endangered population remains small and isolation manifests, the effects of inbreeding depression may become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.", "doi": "10.1111/eva.70192", "pmid": "41488439", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12759046"}, {"db": "pii", "key": "EVA70192"}], "notes": [], "created": "2026-01-07T10:52:49.278Z", "modified": "2026-01-07T10:52:49.806Z"}, {"entity": "publication", "iuid": "9e497d987d264f8bade35c9d92a568de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e497d987d264f8bade35c9d92a568de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e497d987d264f8bade35c9d92a568de"}}, "title": "Long-term heating differently impacts diversity and seasonal dynamics of prokaryotes and micro-eukaryotes in Baltic Sea coastal biofilm communities.", "authors": [{"family": "Svendsen", "given": "Ida Krogsgaard", "initials": "IK", "orcid": "0000-0003-3265-6234", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d420e1d66fa445e89f9cc0fc4432a3a.json"}}, {"family": "Rula", "given": "Iryna", "initials": "I", "orcid": "0000-0003-0906-0301", "researcher": {"href": "https://publications.scilifelab.se/researcher/e235bf754668420cb161059fe6d49dc0.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Sunde", "given": "Johanna", "initials": "J", "orcid": "0000-0002-3145-1475", "researcher": {"href": "https://publications.scilifelab.se/researcher/972ff747b7044a6096583673286e9443.json"}}, {"family": "Li", "given": "Songjun", "initials": "S", "orcid": "0009-0008-4816-2451", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0c5a7e34da45c2aca6f8de83af14b5.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}, {"family": "Salis", "given": "Romana Katerina", "initials": "RK", "orcid": "0000-0001-7724-4984", "researcher": {"href": "https://publications.scilifelab.se/researcher/04732c60ef2040289f7a5664aa697a7d.json"}}], "type": "journal article", "published": "2026-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "6", "issue": "1", "pages": "ycag101", "issn-l": null}, "abstract": "Warming temperatures, heat waves, and altered conditions associated with climate change affect biodiversity and ecological processes across environments, with coastal zones being particularly vulnerable. Biofilm-forming organisms in shallow coastal areas are taxonomically diverse and include bacteria, fungi, and algae that contribute to energy and nutrient cycling along with providing habitats and food for species at the base of the food web. To understand how biofilm-forming organisms respond differently to spatiotemporally changing environmental conditions, seasonal sampling was performed in a Baltic Sea bay that has undergone 50 years of thermal heating, an unaffected nearby control bay, and a temperature gradient along an exposed coastline between the bays. The diversity, composition, and seasonal dynamics of the biofilm communities differed between the three environments largely due to temperature and water chemistry, with biofilms in the heated bay being more similar across seasons compared with the control bay and the gradient, and with prokaryotes exhibiting stronger spatial heterogeneity and seasonal dynamics compared to micro-eukaryotes. In the gradient, the dominating taxonomic groups were distinct, community composition was primarily influenced by seasonal turnover and wave exposure, and alpha diversity of prokaryotes decreased with increasing temperature. Seasonal shifts in the composition of micro-eukaryotic heterotrophs, phototrophs, and mixotrophs differed between environments, with heterotrophs being more dominant at higher temperatures. In conclusion, these contrasting responses indicated that climate warming may disproportionately impact different components of coastal biofilm communities, potentially decoupling key ecological processes and reducing community resilience in Baltic Sea coastal habitats.", "doi": "10.1093/ismeco/ycag101", "pmid": "42147142", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13174331"}, {"db": "pii", "key": "ycag101"}], "notes": [], "created": "2026-06-08T17:26:27.957Z", "modified": "2026-06-08T17:26:28.388Z"}, {"entity": "publication", "iuid": "936c13b506f14b1f90ff1ab6d0359b4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/936c13b506f14b1f90ff1ab6d0359b4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/936c13b506f14b1f90ff1ab6d0359b4f"}}, "title": "Benchmarking of single nuclei RNA-seq methods on human post-mortem brain tissue", "authors": [{"family": "Nikouei", "given": "Kasra", "initials": "K"}, {"family": "Gruyters", "given": "Elin", "initials": "E"}, {"family": "Memic", "given": "Fatima", "initials": "F", "orcid": "0000-0002-8876-1212", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5dcdcbf16f4caab9cea24133389afb.json"}}, {"family": "Stockmeier", "given": "Craig A", "initials": "CA", "orcid": "0000-0003-1861-1013", "researcher": {"href": "https://publications.scilifelab.se/researcher/89ebb5b73b9a42498192d35aea2d92c5.json"}}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J", "orcid": "0000-0002-4539-1776", "researcher": {"href": "https://publications.scilifelab.se/researcher/51675f0ff9aa47d89d6b2eb84a14820a.json"}}], "type": "journal-article", "published": "2026-01-00", "journal": {"title": "Genomics", "issn": "0888-7543", "issn-l": null, "volume": "118", "issue": "1", "pages": "111184"}, "abstract": "Molecular analysis of human post-mortem brain tissue holds the promise to identify disease associated mechanisms. Single nuclei RNA-sequencing (snRNA-seq) is a powerful tool for molecular-level investigations of human brain tissue with cell type resolution. In the fast-developing field of post-mortem snRNA-seq, the samples sizes of case/control studies have drastically increased over the last years. Still, to overcome genetic variability across individuals and to investigate the many relevant brain regions that have not yet been sampled, even larger cohorts are necessary. It is thus important to benchmark snRNA-seq methods against each other on relevant tissue. We compared five such methods, 10\u00d7 Genomics v3.1, 10\u00d7 Genomics Flex Gene Expression, Parse Biosciences Evercode v2, PIPseq v5.0 from Fluent Biosciences (now acquired by Illumina) and Smart-seq3xpress, using fresh frozen post-mortem human forebrain tissue samples. Using tissue samples from the same three donors for all methods, our investigation revealed comparable overall technical performance among the five methods but suggests that biological variability was better captured with Smart-seq3xpress. We could not model the effect of sample quality, which limits the generalizability of our results. Thus, our study suggests that the selection of snRNA-seq method should mainly be informed by the need of specific data and practical experimental considerations such as hardware requirements, ability to multiplex, tissue quantity input requirements, and transportation of samples/tissues.", "doi": "10.1016/j.ygeno.2025.111184", "pmid": "41453581", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null}, "xrefs": [{"db": "pii", "key": "S0888-7543(25)00200-9"}], "notes": [], "created": "2026-01-13T10:27:04.485Z", "modified": "2026-03-24T09:16:35.858Z"}, {"entity": "publication", "iuid": "457495686eaa4727b243b252d2f4e6fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/457495686eaa4727b243b252d2f4e6fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/457495686eaa4727b243b252d2f4e6fe"}}, "title": "Characterization of CTNND2-related neurodevelopmental disease, phenotype-genotype spectrum and WNT dynamics in early neurogenesis.", "authors": [{"family": "Shahsavani", "given": "Mansoureh", "initials": "M"}, {"family": "Wincent", "given": "Josephine", "initials": "J", "orcid": "0000-0002-1698-9605", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9777724444021924229d3fdc8673e.json"}}, {"family": "Reiter", "given": "Ricarda", "initials": "R"}, {"family": "Soltysova", "given": "Andrea", "initials": "A"}, {"family": "Schuy", "given": "Jakob", "initials": "J"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT", "orcid": "0000-0003-4352-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4dc1001c944a9d9dfe4c092cfda497.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Ficek", "given": "Andrej", "initials": "A"}, {"family": "Druschke", "given": "Lotta", "initials": "L"}, {"family": "Kusikova", "given": "Katarina", "initials": "K"}, {"family": "Hsieh", "given": "Tzung-Chien", "initials": "TC"}, {"family": "Krichhoff", "given": "Aron", "initials": "A"}, {"family": "Krawitz", "given": "Peter", "initials": "P"}, {"family": "Li", "given": "Jing-Mei", "initials": "JM"}, {"family": "Webersinke", "given": "Gerald", "initials": "G"}, {"family": "Gorokhova", "given": "Svetlana", "initials": "S"}, {"family": "Missirian", "given": "Chantal", "initials": "C"}, {"family": "Riccardi", "given": "Florence", "initials": "F"}, {"family": "Pavinato", "given": "Lisa", "initials": "L"}, {"family": "Brusco", "given": "Alfredo", "initials": "A", "orcid": "0000-0002-8318-7231", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fa6038bda54597ac495d278d106511.json"}}, {"family": "Mandrile", "given": "Giorgia", "initials": "G"}, {"family": "Trajkova", "given": "Slavica", "initials": "S"}, {"family": "Pintus", "given": "Francesco", "initials": "F"}, {"family": "Gagachovska", "given": "Biljana", "initials": "B"}, {"family": "Waisfisz", "given": "Quinten", "initials": "Q"}, {"family": "van Hagen", "given": "Annet", "initials": "A"}, {"family": "Bedoukian", "given": "Emma", "initials": "E"}, {"family": "Izumi", "given": "Kosuke", "initials": "K"}, {"family": "Granger", "given": "Leslie", "initials": "L"}, {"family": "Petersen", "given": "Andrea", "initials": "A", "orcid": "0000-0003-3882-0867", "researcher": {"href": "https://publications.scilifelab.se/researcher/69701b12d455487a9dd1ab55f9904327.json"}}, {"family": "Oegema", "given": "Renske", "initials": "R", "orcid": "0000-0002-7146-617X", "researcher": {"href": "https://publications.scilifelab.se/researcher/246eec36818e410296fd2d6ea502483f.json"}}, {"family": "Huibers", "given": "Manon", "initials": "M"}, {"family": "Demurger", "given": "Florence", "initials": "F"}, {"family": "Brischoux-Boucher", "given": "Elise", "initials": "E"}, {"family": "Julia", "given": "Sophie", "initials": "S"}, {"family": "Banneau", "given": "Guillaume", "initials": "G"}, {"family": "Zavala", "given": "M Jesus", "initials": "MJ"}, {"family": "Lagos", "given": "Catalina", "initials": "C"}, {"family": "Repetto", "given": "Gabriela M", "initials": "GM"}, {"family": "Jouret", "given": "Guillaume", "initials": "G"}, {"family": "Kentros", "given": "Catherine", "initials": "C"}, {"family": "Ganapathi", "given": "Mythily", "initials": "M"}, {"family": "Chung", "given": "Wendy K", "initials": "WK"}, {"family": "May", "given": "Halie", "initials": "H"}, {"family": "Hiatt", "given": "Susan M", "initials": "SM"}, {"family": "Kelley", "given": "Whitley V", "initials": "WV"}, {"family": "F\u00f6rster", "given": "Alisa", "initials": "A"}, {"family": "Olfe", "given": "Lisa", "initials": "L"}, {"family": "Shillington", "given": "Amelle", "initials": "A"}, {"family": "Dauriat", "given": "Benjamin", "initials": "B"}, {"family": "Mercier", "given": "Sandra", "initials": "S"}, {"family": "Cogn\u00e9", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-5503-6292", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f0dea78166143c38c60c12206444207.json"}}, {"family": "Engel", "given": "Camille", "initials": "C"}, {"family": "Dahlen", "given": "Eric", "initials": "E"}, {"family": "Rosenberger", "given": "Georg", "initials": "G"}, {"family": "Sauvigny", "given": "Thomas", "initials": "T"}, {"family": "Abdallah", "given": "Hamza Hadj", "initials": "HH"}, {"family": "Courtin", "given": "Thomas", "initials": "T"}, {"family": "Stray-Pedersen", "given": "Asbj\u00f8rg", "initials": "A"}, {"family": "Bernat", "given": "John A", "initials": "JA"}, {"family": "Paolillo", "given": "Vitoria K", "initials": "VK"}, {"family": "Viso", "given": "Florencia Del", "initials": "FD"}, {"family": "Alaimo", "given": "Joseph T", "initials": "JT"}, {"family": "Thiffault", "given": "Isabelle", "initials": "I"}, {"family": "Farrow", "given": "Emily G", "initials": "EG"}, {"family": "Cohen", "given": "Ana S A", "initials": "ASA"}, {"family": "Weis", "given": "Serge", "initials": "S"}, {"family": "Duba", "given": "Hans-Christoph", "initials": "HC"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Falk", "given": "Anna", "initials": "A", "orcid": "0000-0003-1634-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b708dfb7f0548589bdee53d6e6b536e.json"}}, {"family": "Weis", "given": "Denisa", "initials": "D"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2025-12-30", "journal": {"title": "Res Sq", "issn": "2693-5015", "issn-l": null}, "abstract": "Heterozygous variants in CTNND2, encoding the brain-specific protein \u03b4-catenin, are associated with a broad spectrum of neurodevelopmental disorders, including dyslexia, attention deficit hyperactivity disorder, intellectual disability, and autism. Despite its clinical significance, the full phenotypic spectrum of CTNND2-associated disorders and the neurodevelopmental role of \u03b4-catenin, a key component of the cadherin-catenin cell adhesion complex, remain poorly defined.\n\nThrough international collaboration, we assembled the phenotypic and molecular information for 57 individuals, 42 previously unpublished, carrying heterozygous CTNND2 variants. All individuals were evaluated by local clinicians, and the variants were identified through exome or genome sequencing, clinical microarray, or karyotyping. To investigate the effects of \u03b4-catenin loss on early neurogenesis, we performed neural differentiation and transcriptomic profiling in three patient-derived neural stem cell lines and three CRISPR-Cas9-generated CTNND2 knockout lines. In one patient-derived line, we further analyzed cerebral organoid development and performed pathway modulation to assess phenotypic rescue.\n\nThe 41 CTNND2 variants included 12 previously reported loss-of-function- and one missense variant, and 28 novel variants comprising 10 missense and 18 predicted loss-of-function changes. Eight of the novel variants occurred de novo, and 12 were inherited from a parent with a neurodevelopmental phenotype. The most common clinical features were developmental delay (90%), intellectual disability (74%), and behavioral abnormalities (79%). Functional studies revealed impaired early neurogenesis in one patient-derived line, characterized by aberrant neural rosette formation. Transcriptome analysis showed dysregulated WNT signaling, and partial rescue of these defects was achieved by modulating the WNT pathway, highlighting \u03b4-catenin's role in early neural development.\n\nThis study defines the clinical symptoms of CTNND2-related neurodevelopmental disorders, outlining a recognizable yet variable phenotype that overlaps with other forms of intellectual disability and autism. Our findings provide preliminary evidence of genotype-phenotype correlations and highlight \u03b4-catenin's critical role in modulating WNT signaling during early neural development. These insights advance our understanding of CTNND2-associated disorders and support the importance of mechanistic studies to inform personalized diagnostics and therapies.", "doi": "10.21203/rs.3.rs-8224288/v1", "pmid": "41502569", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12772691"}, {"db": "pii", "key": "rs.3.rs-8224288"}], "notes": [], "created": "2026-01-13T10:29:57.427Z", "modified": "2026-01-25T08:39:21.323Z"}, {"entity": "publication", "iuid": "96f3d22ca79f4d718217e5f0af6a3865", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96f3d22ca79f4d718217e5f0af6a3865.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96f3d22ca79f4d718217e5f0af6a3865"}}, "title": "A north-south hemispheric migratory divide in the butterfly Vanessa cardui.", "authors": [{"family": "Garc\u00eda-Berro", "given": "Aurora", "initials": "A", "orcid": "0000-0002-2419-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fdb6dd337074a89bf36e3b06458f042.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Suchan", "given": "Tomasz", "initials": "T", "orcid": "0000-0002-0811-8754", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b3c7df2089e4060a8ad426a5570654c.json"}}, {"family": "Palah\u00ed", "given": "Aleix", "initials": "A", "orcid": "0000-0002-1373-4949", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee01ff0f2c3746939dbf64a7fca04439.json"}}, {"family": "Collins", "given": "Steve C", "initials": "SC"}, {"family": "Martins", "given": "Dino J", "initials": "DJ"}, {"family": "Pierce", "given": "Naomi E", "initials": "NE", "orcid": "0000-0003-3366-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1e6c94b58244ada2442e0541168252.json"}}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}], "type": "journal article", "published": "2025-12-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "11341", "issn-l": "2041-1723"}, "abstract": "Reversed seasonality and distinct navigation cues in the Earth's two hemispheres may shape the evolution of migratory behaviour in animals. Migratory divides-contact zones where populations have evolved alternative migratory strategies-are well-documented in birds and typically occur longitudinally. We hypothesise that insect migratory divides are less likely to emerge longitudinally, but may exist latitudinally, driven by hemisphere-specific sensory adaptations that lead to spatial and temporal isolation. Here, we examine this hypothesis in the cosmopolitan painted lady butterfly (Vanessa cardui), whose Southern Hemisphere dynamics remain unexplored. Investigating the genomes of 300 individuals across Africa and Europe, we identify a 9 Mb chromosomal inversion on chromosome 8, which exhibits strong haplotype structure aligned with hemispheric origin, with a few potential heterozygotes near the equator. The inversion harbours 336 genes, including several directly relevant to migration. Notably, one inversion breakpoint intersects the gene encoding the GABA-B receptor, which responds to the neuropeptide \u03b3-aminobutyric acid (GABA), crucial for insect navigation. Our findings provide genomic evidence of a migratory divide in insects and highlight the role of inverted seasonality in the two hemispheres and genomic rearrangements as isolating barriers for highly mobile species.", "doi": "10.1038/s41467-025-67185-7", "pmid": "41469375", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12753642"}, {"db": "pii", "key": "10.1038/s41467-025-67185-7"}], "notes": [], "created": "2026-01-07T11:02:45.340Z", "modified": "2026-01-07T11:02:45.758Z"}, {"entity": "publication", "iuid": "eede36ef32fd4a6aac7dd2a2b9baa667", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eede36ef32fd4a6aac7dd2a2b9baa667.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eede36ef32fd4a6aac7dd2a2b9baa667"}}, "title": "The splicing genes SmEa and SmEb regulate plant development during vegetative growth in poplar.", "authors": [{"family": "Goretti", "given": "Daniela", "initials": "D", "orcid": "0000-0003-3996-0204", "researcher": {"href": "https://publications.scilifelab.se/researcher/cabe11cdf08446bda52aa5d2b62ea239.json"}}, {"family": "Collani", "given": "Silvio", "initials": "S", "orcid": "0000-0002-9603-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/0896530185b54e16824cd26658ccdfc8.json"}}, {"family": "Marcon", "given": "Alice", "initials": "A", "orcid": "0009-0006-9957-6115", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb0b7d67e464160bda5a6acfdf96d95.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Schmid", "given": "Markus", "initials": "M", "orcid": "0000-0002-0068-2967", "researcher": {"href": "https://publications.scilifelab.se/researcher/8705d242aa8f4f92b930c2cdc23254f0.json"}}], "type": "journal article", "published": "2025-12-23", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "25", "issue": "1", "pages": "1723", "issn-l": "1471-2229"}, "abstract": "Spliceosomes are large evolutionary conserved ribonucleoprotein complexes containing at their core heptameric rings of Sm (or LSm) proteins and U-rich snRNAs. The role of Sm proteins in animal development is well established, and recent research has begun to link mutations in these genes to growth defects in plants. One of the most studied Sm genes is SmE1/PCP, mutants of which display a temperature-dependent phenotype in Arabidopsis thaliana.\n\nThis study provides a first glimpse into the function of a core splicing protein in the regulation of growth in a perennial species. Phylogenetic analysis identified two paralogous SmE genes in poplar, named SmEa and SmEb, that encode identical proteins and are orthologs of SmEs from Arabidopsis, as suggested by Y2H and in vivo experiments. CRISPR/Cas9 mutagenesis in hybrid aspen identified a role for SmEs in development in plants grown in an environment simulating seasonal photoperiod and temperature changes. Unlike in Arabidopsis, low temperatures had no or only a very minor effect on the development of sme mutants in aspen.\n\nWe identified specific aspects of SmE in poplar, highlighting the importance of examining the physiological and evolutionary differences that define this gene family in woody compared to herbaceous plants.\n\nThe online version contains supplementary material available at 10.1186/s12870-025-07676-3.", "doi": "10.1186/s12870-025-07676-3", "pmid": "41436944", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12729064"}, {"db": "pii", "key": "10.1186/s12870-025-07676-3"}], "notes": [], "created": "2026-01-07T11:04:57.648Z", "modified": "2026-01-07T11:04:57.822Z"}, {"entity": "publication", "iuid": "5717b69dac574afaa6ebf045b297c89b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5717b69dac574afaa6ebf045b297c89b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5717b69dac574afaa6ebf045b297c89b"}}, "title": "Comparative assessment of SNP genotyping assays for challenging forensic samples utilizing ancient DNA methods", "authors": [{"family": "Staadig", "given": "Adam", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Sidstedt", "given": "Maja", "initials": "M"}, {"family": "Kling", "given": "Daniel", "initials": "D"}, {"family": "Fagerholm", "given": "Siri Aili", "initials": "SA"}, {"family": "Ansell", "given": "Ricky", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Tillmar", "given": "Andreas", "initials": "A"}], "type": "journal-article", "published": "2025-12-23", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "433", "issn-l": "1474-7596"}, "abstract": "The fields of ancient DNA research and forensic genetics share both methodological similarities and common challenges, particularly in the analysis of degraded DNA. Leveraging these overlaps, this study evaluates three single nucleotide polymorphisms (SNP)-based genotyping assays for analyzing challenging forensic samples: the FORCE-QIAseq SNP panel, the Twist ancient DNA hybridization capture panel, and whole-genome sequencing.\n\nWe analyze twenty skeletal bone and tooth samples from authentic missing person cases, where almost all samples are severely degraded and contain exceptionally low amounts of endogenous DNA, reflected by both reduced quantifiable DNA concentrations and lower proportions of human DNA reads than typically obtained from high-quality forensic samples. Despite these challenging sample characteristics, both the FORCE and Twist assays successfully generate a substantial number of genotypes across many samples, while whole-genome sequencing yields fewer SNP calls. However, techniques like probabilistic genotyping, increase sequencing depth or genotype imputation can further enhance the utility of WGS for forensic use.\n\nThis study highlights the effectiveness of incorporating ancient DNA methods into forensic genetics for the analysis of degraded samples. The findings are broadly applicable to both forensic and ancient DNA research disciplines, offering valuable insights into assay selection based on sample condition and investigative goals.", "doi": "10.1186/s13059-025-03912-z", "pmid": "41430704", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12723910"}, {"db": "pii", "key": "10.1186/s13059-025-03912-z"}], "notes": [], "created": "2026-01-07T11:00:22.743Z", "modified": "2026-01-09T07:55:19.944Z"}, {"entity": "publication", "iuid": "c70282615a154262b20d3bfd207d2419", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c70282615a154262b20d3bfd207d2419.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c70282615a154262b20d3bfd207d2419"}}, "title": "ZEB1, a novel junctional adhesion molecule A regulator, impacts sensitivity of pancreatic cancer-associated fibroblasts to reovirus.", "authors": [{"family": "Dam", "given": "Nicole", "initials": "N"}, {"family": "Harryvan", "given": "Tom J", "initials": "TJ"}, {"family": "Dang", "given": "Hao", "initials": "H"}, {"family": "Ioannidis", "given": "Gavriil", "initials": "G"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B"}, {"family": "Hawinkels", "given": "Lukas J A C", "initials": "LJAC"}, {"family": "Kemp", "given": "Vera", "initials": "V"}], "type": "journal article", "published": "2025-12-18", "journal": {"title": "Mol Ther Oncol", "issn": "2950-3299", "issn-l": null, "volume": "33", "issue": "4", "pages": "201071"}, "abstract": "Oncolytic virus (OV) therapy is a promising treatment for various tumors. However, in pancreatic ductal adenocarcinoma (PDAC), the high abundance of cancer-associated fibroblasts (CAFs) can limit OV therapy efficacy by impairing viral spread and anti-tumor immunity. We have previously shown that oncolytic reovirus infection of CAFs depends on the expression of the reovirus entry receptor junctional adhesion molecule A (JAM-A), which is not or lowly expressed in most PDAC CAFs. We propose that increasing JAM-A expression on CAFs will boost viral spread in a tumor. However, there are currently no known regulators of JAM-A expression. Therefore, we performed a genome-wide CRISPR-Cas9 knockout screen to identify novel regulators of JAM-A expression. Ablation of the top negative regulator, zinc finger E-box binding homeobox 1 (ZEB1), in pancreatic fibroblasts led to strong JAM-A upregulation. We show that ZEB1 directly regulates JAM-A expression by binding to the enhancer-box (E-box) regions located within the JAM-A promoter. Importantly, ZEB1 ablation increased the sensitivity of fibroblasts to reovirus infection and subsequent cell death. Our work provides a novel overview of genes regulating JAM-A expression and provides a rational approach of combining ZEB1 inhibition with reovirus therapy to target both CAFs and tumor cells in stroma-rich tumors such as PDAC.", "doi": "10.1016/j.omton.2025.201071", "pmid": "41244268", "labels": {"CRISPR Functional Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12617759"}, {"db": "pii", "key": "S2950-3299(25)00140-7"}], "notes": [], "created": "2025-11-25T08:36:19.443Z", "modified": "2025-12-19T13:03:44.572Z"}, {"entity": "publication", "iuid": "2f040ec2230c4d4294c4dd7d17bf0d45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f040ec2230c4d4294c4dd7d17bf0d45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f040ec2230c4d4294c4dd7d17bf0d45"}}, "title": "Necessity of individual VDJ-databases for annotating antibody heavy chain characteristics in non-human primates.", "authors": [{"family": "Aartse", "given": "Aafke", "initials": "A"}, {"family": "Bakx", "given": "Jacco G J", "initials": "JGJ"}, {"family": "Mortier", "given": "Daniella", "initials": "D"}, {"family": "Hofman", "given": "Sam", "initials": "S"}, {"family": "Mooij", "given": "Petra", "initials": "P"}, {"family": "Claireaux", "given": "Mathieu", "initials": "M"}, {"family": "Eggink", "given": "Dirk", "initials": "D"}, {"family": "Bogers", "given": "Willy M", "initials": "WM"}, {"family": "Remarque", "given": "Edmond J", "initials": "EJ"}, {"family": "Corcoran", "given": "Martin M", "initials": "MM"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "Bontrop", "given": "Ronald E", "initials": "RE"}, {"family": "van Gils", "given": "Marit J", "initials": "MJ"}, {"family": "Koopman", "given": "Gerrit", "initials": "G"}], "type": "journal article", "published": "2025-12-15", "journal": {"title": "Immunogenetics", "issn": "1432-1211", "volume": "77", "issue": "1", "pages": "35", "issn-l": "0093-7711"}, "abstract": "Non-human primates are important for preclinical vaccine evaluation. In depth characterization of the antibody response requires representative immunoglobulin (IG) germline gene databases for correct gene and allele assignments and assessment of affinity maturation of antigen-specific antibodies. Current IG-reference databases do not cover the genetic diversity observed in frequently used macaque species and it is unclear to what extent closely related animals express shared alleles at similar levels. Here, IG-germline alleles of sixteen cynomolgus macaques (CynoSet), some of which were related, were characterized and compared with previously described Mauritian and Indonesian origin cynomolgus macaque datasets. Although the CynoSet showed more overlap with the Mauritian origin dataset, compared to an Indonesian origin dataset, there were clear differences in allelic expression patterns, independent of family relationship. Calculation of somatic hypermutation levels in post-infection influenza hemagglutinin-specific B cells demonstrated the need for individualized IG-genotyping for accurate evaluation of the antigen-specific B cell response.", "doi": "10.1007/s00251-025-01392-w", "pmid": "41392054", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12702801"}, {"db": "pii", "key": "10.1007/s00251-025-01392-w"}], "notes": [], "created": "2026-01-22T13:22:00.965Z", "modified": "2026-01-22T13:22:00.976Z"}, {"entity": "publication", "iuid": "e42f9cac44624ea49439d8938a4dd87b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e42f9cac44624ea49439d8938a4dd87b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e42f9cac44624ea49439d8938a4dd87b"}}, "title": "Human oligodendrocyte progenitor cells mediate synapse elimination through TAM receptor activation.", "authors": [{"family": "Gkogka", "given": "Asimenia", "initials": "A", "orcid": "0009-0001-7892-0769", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f6c80990684a2cb715a05e5dc6e830.json"}}, {"family": "Malwade", "given": "Susmita", "initials": "S", "orcid": "0000-0002-6756-018X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d254484412d4fcab1b65858d2d1d5bb.json"}}, {"family": "Koskuvi", "given": "Marja", "initials": "M"}, {"family": "Ohtonen", "given": "Sohvi", "initials": "S"}, {"family": "Molnar", "given": "Ellinor", "initials": "E"}, {"family": "Bose", "given": "Raj", "initials": "R", "orcid": "0009-0008-4039-862X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dfa265d83834453be680aed87c0f667.json"}}, {"family": "Ceccatelli", "given": "Sandra", "initials": "S", "orcid": "0000-0002-9367-8480", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee421983d86b46ac8b36dd0766c1f90d.json"}}, {"family": "Koistinaho", "given": "Jari", "initials": "J", "orcid": "0000-0001-6559-1153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e92f575e61b244ec9a9f96190f0df35b.json"}}, {"family": "Tiihonen", "given": "Jari", "initials": "J", "orcid": "0000-0002-0400-6798", "researcher": {"href": "https://publications.scilifelab.se/researcher/d55a02bf2b1340878d23f0d594e778f2.json"}}, {"family": "Schalling", "given": "Martin", "initials": "M", "orcid": "0000-0001-5011-2922", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe1154f55d34051a41554d328bc8be3.json"}}, {"family": "Samudyata", "given": "Samudyata", "initials": "S", "orcid": "0000-0002-1062-2626", "researcher": {"href": "https://publications.scilifelab.se/researcher/4856a75f064f4e0f8726bfd4a6658ac6.json"}}, {"family": "Sellgren", "given": "Carl M", "initials": "CM", "orcid": "0000-0001-9103-2785", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c0740ddfd6d4c98988b2a19096a9814.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10612", "issn-l": "2041-1723"}, "abstract": "Oligodendrocyte progenitor cells (OPCs) have been implicated in synaptic remodelling in animal models, but the underlying mechanisms and their relevance to human brain development remain unclear. Here, we generate a human multi-lineage forebrain organoid model in which OPCs, together with microglia, form close contacts with synapses and spontaneously internalize synaptic material. Single-nucleus transcriptomic profiling with unbiased cell-cell communication analysis identifies the growth arrest-specific gene 6 (GAS6)-TYRO3, AXL, and MERTK (TAM) receptor axis as a key signalling pathway, with neurons and microglia expressing GAS6 and a subset of OPCs expressing AXL. Further, dose-dependent pharmacological inhibition of TAM receptors demonstrates the importance of AXL, and targeted reduction of AXL expression in OPCs impairs synaptic uptake. These findings reveal a role for GAS6-AXL signalling in driving synaptic internalisation by AXL+ OPCs during early human brain development.", "doi": "10.1038/s41467-025-66521-1", "pmid": "41350273", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12680777"}, {"db": "pii", "key": "10.1038/s41467-025-66521-1"}], "notes": [], "created": "2026-01-07T15:28:15.485Z", "modified": "2026-01-07T15:28:16.609Z"}, {"entity": "publication", "iuid": "148bff77b6a7405ba3d7dadd0c170a4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/148bff77b6a7405ba3d7dadd0c170a4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/148bff77b6a7405ba3d7dadd0c170a4a"}}, "title": "Gray wolves in an anthropogenic context on a small island in prehistoric Scandinavia.", "authors": [{"family": "Girdland-Flink", "given": "Linus", "initials": "L", "orcid": "0000-0001-6499-8728", "researcher": {"href": "https://publications.scilifelab.se/researcher/74574daaa4e340bca662b3e3bf4899e9.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Apel", "given": "Jan", "initials": "J", "orcid": "0000-0002-8894-1985", "researcher": {"href": "https://publications.scilifelab.se/researcher/60265a0624a74b7aa01f278b7d53c608.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}], "type": "journal article", "published": "2025-12-02", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "122", "issue": "48", "pages": "e2421759122"}, "abstract": "Dogs were domesticated at least once from a yet-unidentified wolf population at least ~15,000 y ago. However, how domestication took place is a topic of ongoing debate, and the ability of human groups to manage wolves in their communities during early stages of domestication is poorly understood. Here, we report multiproxy data from two canids excavated from Late Neolithic and Bronze Age contexts in the Stora F\u00f6rvar cave on the island of Stora Karls\u00f6 in the Baltic Sea. The island is small (2.5 sq km) and, like the neighboring island of Gotland, carries no endemic populations of terrestrial mammals. Instead, the current consensus is that human introductions account for some mammal fauna on Gotland, and for the majority of that on Stora Karls\u00f6. Genome-wide data show that the two canids have ancestry indistinguishable from Eurasian wolves, with no shared ancestry with domestic dogs of the Canis familiaris lineage. Their genome-wide heterozygosity is lower than that observed in 72 previously published ancient wolf genomes, and instead comparable to dogs. Stable isotope data (\u03b413C and \u03b415N) reveals a diet rich in marine protein, which is consistent with habitation alongside the human groups who used Stora Karls\u00f6 as a seal-hunting, fowling, and sea fishing station, and in the Bronze Age probably also for grazing. Skeletal size is at the lower end of wolf variability, and one individual shows advanced pathology consistent with reduced mobility. While other scenarios are possible, a parsimonious explanation is that these wolves were brought to the island by humans and were possibly under human control.", "doi": "10.1073/pnas.2421759122", "pmid": "41284891", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-04T08:42:12.711Z", "modified": "2025-12-05T10:18:48.574Z"}, {"entity": "publication", "iuid": "39d27f777a814e6eb3ad7aa9db9e0df5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39d27f777a814e6eb3ad7aa9db9e0df5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39d27f777a814e6eb3ad7aa9db9e0df5"}}, "title": "Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets.", "authors": [{"family": "Hamsikova", "given": "Marie", "initials": "M"}, {"family": "Hurdalek", "given": "Jan", "initials": "J"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Ptacek", "given": "Jakub", "initials": "J"}, {"family": "Vydra Bousova", "given": "Kristyna", "initials": "K"}, {"family": "Vondrasek", "given": "Jiri", "initials": "J"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}, {"family": "Zemanova", "given": "Lucie", "initials": "L"}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Arch. Biochem. Biophys.", "issn": "1096-0384", "volume": "774", "pages": "110634", "issn-l": "0003-9861"}, "abstract": "PDZ domains play key roles in mediating protein-protein interactions by recognizing short PDZ-binding motifs, typically at the C-termini of target proteins. Zonula occludens 1 (ZO-1) is a scaffolding protein that links tight junction proteins to the actin cytoskeleton, and contains three PDZ domains. Here, we focus on its third PDZ (PDZ3_ZO-1) domain, which interacts with the C-terminus of junctional adhesion protein A as well as connexin 45. To investigate how the domain context of the PDZ3_ZO-1 domain affects its folding and function, we previously established two distinct fusions of PDZ3_ZO-1 and a Trp-cage mini-protein. These fusions with swapped domain order result in FD3A with Trp-cage fused C-terminally and FD4A with Trp-cage fused N-terminally. This study aims to explore the extent to which the distinct Trp-cage fusions affect the function of PDZ3_ZO-1 domain in peptide binding. We find that PDZ3_ZO-1 retains its function, interaction with the connexin 45 peptide, also as part of the fusion proteins. Furthermore, using a phage display approach, we identified a new PDZ3_ZO-1 binding peptide derived from the C-terminal region of methylcytosine dioxygenase TET3. Subsequent validation revealed a significantly higher affinity of PDZ3_ZO-1 for the TET3 peptide as compared to the connexin 45 peptide. Thermodynamic analyses revealed that the swapped domain order conferred distinct effects on the thermodynamic parameters. These results provide insights into the structural and functional adaptability of PDZ domains in engineered proteins, and offer useful principles for the rational design of functional fusion proteins.", "doi": "10.1016/j.abb.2025.110634", "pmid": "41047091", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-9861(25)00348-0"}], "notes": [], "created": "2025-11-19T09:52:22.470Z", "modified": "2025-11-19T09:52:22.474Z"}, {"entity": "publication", "iuid": "a77133b5c6e1485c8c39308492347e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a77133b5c6e1485c8c39308492347e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a77133b5c6e1485c8c39308492347e7f"}}, "title": "Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.", "authors": [{"family": "Clasen", "given": "Frederick", "initials": "F"}, {"family": "Yildirim", "given": "Suleyman", "initials": "S"}, {"family": "Ar\u0131kan", "given": "Muzaffer", "initials": "M"}, {"family": "Garcia-Guevara", "given": "Fernando", "initials": "F"}, {"family": "Hano\u011flu", "given": "L\u0171tf\u0171", "initials": "L"}, {"family": "Y\u0131lmaz", "given": "Nesrin H", "initials": "NH"}, {"family": "\u015een", "given": "Aysu", "initials": "A"}, {"family": "Celik", "given": "Handan Kaya", "initials": "HK"}, {"family": "Neslihan", "given": "Alagoz Aybala", "initials": "AA"}, {"family": "Demir", "given": "Tu\u01e7\u00e7e Kahraman", "initials": "TK"}, {"family": "Temel", "given": "Zeynep", "initials": "Z"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Moyes", "given": "David L", "initials": "DL"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S", "orcid": "0000-0001-5834-4533", "researcher": {"href": "https://publications.scilifelab.se/researcher/90fcd41a9a3645c3b733564c99a97aea.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Gut Microbes", "issn": "1949-0984", "volume": "17", "issue": "1", "pages": "2506843", "issn-l": null}, "abstract": "The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.", "doi": "10.1080/19490976.2025.2506843", "pmid": "40420833", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12118390"}], "notes": [], "created": "2025-11-21T15:28:41.143Z", "modified": "2025-11-21T15:28:41.197Z"}, {"entity": "publication", "iuid": "a1a66eb9378f48bcbb9c32923b5503e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3"}}, "title": "Genome Variation in Three Anthophora Bee Species Reflects Divergent Demographic Histories", "authors": [{"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/2270d42b20f6456a8db81f41503b0063.json"}}, {"family": "Dias", "given": "Guilherme", "initials": "G", "orcid": "0000-0002-1459-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/73778a1096e04b5d94f8d5c6f3584d99.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A", "orcid": "0000-0002-5438-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/57ec91022afd4c1390433d6383a06fc0.json"}}, {"family": "Mosbech", "given": "Mai\u2010Britt", "initials": "M", "orcid": "0000-0002-6068-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/efde81e53e6e48cba694e82e6fa8d38c.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Lager", "given": "Nina", "initials": "N"}, {"family": "Strand", "given": "Anna\u2010Sofi", "initials": "A"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lindblad\u2010Toh", "given": "Kerstin", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Mol Ecol", "issn": "0962-1083", "pages": "e70204", "volume": "34", "issue": "24", "issn-l": "0962-1083"}, "abstract": "Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.", "doi": "10.1111/mec.70204", "pmid": "41387163", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-17T11:40:16.625Z", "modified": "2025-12-21T19:08:10.173Z"}, {"entity": "publication", "iuid": "cf1b91a85bc74e92ad44a2a472bf97b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf1b91a85bc74e92ad44a2a472bf97b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf1b91a85bc74e92ad44a2a472bf97b8"}}, "title": "Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis.", "authors": [{"family": "Zheng", "given": "Chao", "initials": "C"}, {"family": "Herv\u00e9", "given": "Bastien", "initials": "B", "orcid": "0000-0002-2610-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd3c5f38fbf64b30828c15839db38448.json"}}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Rubio Rodr\u00edguez-Kirby", "given": "Leslie Ann", "initials": "LA"}, {"family": "Guerreiro Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Kukanja", "given": "Petra", "initials": "P", "orcid": "0000-0003-1228-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/082ef6e681214c14b8ca36cd0188722b.json"}}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Jimenez-Beristain", "given": "Tony", "initials": "T", "orcid": "0009-0005-3756-3354", "researcher": {"href": "https://publications.scilifelab.se/researcher/9717ea6f895441649166ea40aa34d2c3.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Agirre", "given": "Eneritz", "initials": "E", "orcid": "0000-0002-5012-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/a507b19745c64c3bb8ef5dce800c8687.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "28", "issue": "12", "pages": "2612-2627", "issn-l": "1097-6256"}, "abstract": "Multiple sclerosis (MS) is a chronic autoimmune disease that targets mature oligodendrocytes (MOLs) and their myelin. MOLs are heterogeneous and can transition to immune-like states in MS. However, the dynamics of this process remain unclear. Here, we used single-cell multiome assay for transposase-accessible chromatin and RNA sequencing targeting oligodendroglia (OLG) from the experimental autoimmune encephalomyelitis (EAE) MS mouse model at multiple disease stages. We found that immune OLG states appear at early disease stages and persist to late stages, which can be consistent with epigenetic memory of previous neuroinflammation. Transcription factor activity suggested immunosuppression in OLG at early disease stages. Different MOLs exhibit differential responsiveness to EAE, with MOL2 exhibiting a stronger transcriptional immune response than MOL5/MOL6, and showed divergent responses at the epigenetic level during disease evolution. Our single-cell multiomic resource highlights dynamic and subtype-specific responses of OLG to EAE, which might be amenable to modulation in MS.", "doi": "10.1038/s41593-025-02100-3", "pmid": "41249698", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-025-02100-3"}], "notes": [], "created": "2025-12-04T08:40:54.011Z", "modified": "2025-12-04T08:40:54.919Z"}, {"entity": "publication", "iuid": "4aa787602e4e4678988c48ce41e25ce7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4aa787602e4e4678988c48ce41e25ce7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4aa787602e4e4678988c48ce41e25ce7"}}, "title": "Ancient RNA expression profiles from the extinct woolly mammoth.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E"}, {"family": "Fromm", "given": "Bastian", "initials": "B"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Bozlak", "given": "Elif", "initials": "E"}, {"family": "Brown", "given": "Katherine", "initials": "K"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Furug\u00e5rd", "given": "Cecilia", "initials": "C"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Peterson", "given": "Kevin J", "initials": "KJ"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": null, "issue": null, "pages": null}, "abstract": "Ancient DNA has revolutionized the study of extinct and extant organisms that lived up to 2 million years ago, enabling the reconstruction of genomes from multiple extinct species, as well as the ecosystems where they once thrived. However, current DNA sequencing techniques alone cannot directly provide insights into tissue identity, gene expression dynamics, or transcriptional regulation, as these are encoded in the RNA fraction. Here, we report transcriptional profiles from 10 Late Pleistocene woolly mammoths. One of these, dated to be \u223c39,000 years old, yielded sufficient detail to recover tissue-specific regulatory mechanisms and biological functions essential for skeletal muscle metabolism, representing the oldest ancient RNA sequences recorded to date. We showcase the potential to study ancient RNA molecules beyond preconceived limitations, providing an analytical framework for validating and decoding preserved transcriptomes through time. With our findings, we anticipate the emergence of integrative paleo-studies combining genomics, proteomics, and transcriptomics.", "doi": "10.1016/j.cell.2025.10.025", "pmid": "41240910", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)01231-0"}], "notes": [], "created": "2025-11-17T15:01:06.080Z", "modified": "2025-11-19T07:44:17.391Z"}, {"entity": "publication", "iuid": "22942ea7e4604351ab779e9dac5bcad1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22942ea7e4604351ab779e9dac5bcad1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22942ea7e4604351ab779e9dac5bcad1"}}, "title": "That's So Last Season: Unraveling the Genomic Consequences of Fur Farming in Arctic Foxes (Vulpes lagopus).", "authors": [{"family": "Cockerill", "given": "Christopher A", "initials": "CA", "orcid": "0000-0001-9776-3183", "researcher": {"href": "https://publications.scilifelab.se/researcher/43a0788d687045f7b0257996a55327b0.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Bj\u00f6rklund", "given": "Gabriella", "initials": "G"}, {"family": "Hasselgren", "given": "Malin", "initials": "M", "orcid": "0000-0002-4875-4413", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e7f1368a98040f4a683c3d082483079.json"}}, {"family": "Wall\u00e9n", "given": "Johan", "initials": "J"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Fuglei", "given": "Eva", "initials": "E"}, {"family": "Unnsteinsdottir", "given": "Ester Rut", "initials": "ER"}, {"family": "White", "given": "Paula", "initials": "P"}, {"family": "Samelius", "given": "Gustaf", "initials": "G"}, {"family": "Alisauskas", "given": "Ray", "initials": "R"}, {"family": "Berteaux", "given": "Dominique", "initials": "D"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Landa", "given": "Arild", "initials": "A"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "P\u00e1lsson", "given": "Sn\u00e6bj\u00f6rn", "initials": "S", "orcid": "0000-0002-4297-3500", "researcher": {"href": "https://publications.scilifelab.se/researcher/44a3d48564f04b5ea53d14f19bb623cc.json"}}, {"family": "Magn\u00fasson", "given": "Kristinn P\u00e9tur", "initials": "KP"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9707-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/40450a7e8cda45ba8292b9a677b3fb29.json"}}], "type": "journal article", "published": "2025-11-13", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": null, "issue": null, "pages": "e70166"}, "abstract": "Humans have relied on animal fur for centuries, yet fur farming only began recently during the mid-19th Century. Little is known about this incipient domestication or the genomic processes involved. Domestication may involve founder effects, population bottlenecks and low population size, which, when combined with intense artificial selection, lead to inbreeding, a limited gene pool and reduced fitness. The arctic fox (Vulpes lagopus) has been farmed intensively since the early 1900s and has been artificially selected for economic phenotypes. We investigated the origin of these lineages and the genomic consequences of intensive farming by comparing the genomes of farmed and wild arctic foxes from across their range. Our research indicates recent inbreeding through long Runs of Homozygosity and reduced genomic variation in farmed foxes relative to their respective wild populations. We identified a coastal ecotype origin for all Fennoscandian farmed arctic foxes, aligning them phylogenetically with the wild Icelandic population, a geographically isolated and phenotypically distinct coastal lineage. The depleted genome-wide heterozygosity and increased recent inbreeding in farmed fox lineages is consistent with a heavy consequence of domestication, shedding light on the demographic history and genomic consequences of human manipulation. We highlight the need for increased genomic investigations into fur farm populations to understand the incipient domestication process and uncover the cost of intense farming. The genomic consequences of domestication must be considered in the management of fur farms, with actionable steps needed to prevent descendants of escaped farmed foxes from polluting the gene pool in the wild through introgression.", "doi": "10.1111/mec.70166", "pmid": "41229383", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-16T14:58:28.536Z", "modified": "2025-11-19T07:43:38.634Z"}, {"entity": "publication", "iuid": "558da5213cd248b6a7ab633e36fd8c6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/558da5213cd248b6a7ab633e36fd8c6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/558da5213cd248b6a7ab633e36fd8c6e"}}, "title": "Ancient host-associated microbes obtained from mammoth remains.", "authors": [{"family": "Guinet", "given": "Benjamin", "initials": "B"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Moreland", "given": "Kelsey", "initials": "K"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Danilov", "given": "Gleb", "initials": "G"}, {"family": "Kanellidou", "given": "Foteini", "initials": "F"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Muller", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Plotnikov", "given": "Valerii", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Termes", "given": "Laura", "initials": "L"}, {"family": "Zazula", "given": "Grant", "initials": "G"}, {"family": "Mortensen", "given": "Peter", "initials": "P"}, {"family": "Grigorieva", "given": "Lena", "initials": "L"}, {"family": "Richards", "given": "Michael", "initials": "M"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2025-11-13", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "188", "issue": "23", "pages": "6606-6619.e24"}, "abstract": "Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.", "doi": "10.1016/j.cell.2025.08.003", "pmid": "40902595", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(25)00917-1"}], "notes": [], "created": "2025-09-30T13:54:45.200Z", "modified": "2025-11-28T10:42:10.971Z"}, {"entity": "publication", "iuid": "e962bd7ef8824c55975d40adb2d41799", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e962bd7ef8824c55975d40adb2d41799.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e962bd7ef8824c55975d40adb2d41799"}}, "title": "Oligodendroglia as functional effectors of Multiple Sclerosis risk variants", "authors": [{"family": "Carlstr\u00f6m", "given": "Karl E", "initials": "KE", "orcid": "0000-0002-3001-2403", "researcher": {"href": "https://publications.scilifelab.se/researcher/3aa5f65acad34b5790a2b9f607521825.json"}}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Sun", "given": "Ting", "initials": "T", "orcid": "0000-0002-7104-7215", "researcher": {"href": "https://publications.scilifelab.se/researcher/521fca43267242fca06da0f5fc823e6a.json"}}, {"family": "Dumral", "given": "\u00d6zge", "initials": "\u00d6"}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Mahmud", "given": "Neemat", "initials": "N"}, {"family": "Kit Lor", "given": "Yuk", "initials": "Y"}, {"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Goldman", "given": "Steve A", "initials": "SA", "orcid": "0000-0002-5498-4303", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a78fe500aa54369b3716c70792dee90.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "posted-content", "published": "2025-11-12", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.11.11.687640", "pmid": null, "labels": {"CRISPR Functional Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-19T09:35:53.525Z", "modified": "2025-12-18T18:35:03.301Z"}, {"entity": "publication", "iuid": "05f686d75d0343e0a27bd5e6fb686ba1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05f686d75d0343e0a27bd5e6fb686ba1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05f686d75d0343e0a27bd5e6fb686ba1"}}, "title": "Stable clonal contribution of lineage-restricted stem cells to human hematopoiesis.", "authors": [{"family": "Yoshizato", "given": "Tetsuichi", "initials": "T", "orcid": "0000-0003-4283-2983", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6f499e339d2444b817a81ab2712b9e5.json"}}, {"family": "Nilsson", "given": "Christer", "initials": "C", "orcid": "0000-0003-0695-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f78180b33fa48cd86474d5c3cdaa852.json"}}, {"family": "Grasso", "given": "Francesca", "initials": "F"}, {"family": "H\u00f6gstrand", "given": "Kari", "initials": "K"}, {"family": "Mazzi", "given": "Stefania", "initials": "S", "orcid": "0009-0009-2676-5232", "researcher": {"href": "https://publications.scilifelab.se/researcher/83dc55ff218049b287e650588772cbfd.json"}}, {"family": "Winroth", "given": "Axel", "initials": "A", "orcid": "0009-0002-3314-7781", "researcher": {"href": "https://publications.scilifelab.se/researcher/63fae66620a04a79bb642b29703a5aaf.json"}}, {"family": "Lehander", "given": "Madeleine", "initials": "M"}, {"family": "Barbosa", "given": "Indira", "initials": "I", "orcid": "0009-0004-1171-2932", "researcher": {"href": "https://publications.scilifelab.se/researcher/20efd8770db84811a240a8bb70c43939.json"}}, {"family": "Waldin", "given": "Gunilla", "initials": "G"}, {"family": "Mortera-Blanco", "given": "Teresa", "initials": "T"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Widfeldt", "given": "Mikaela Hillberg", "initials": "MH"}, {"family": "Aliouat", "given": "Affaf", "initials": "A"}, {"family": "Brennan", "given": "Margs S", "initials": "MS", "orcid": "0000-0002-8864-4147", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b684863566a420bb894bbd7265d938e.json"}}, {"family": "Markljung", "given": "Ellen", "initials": "E"}, {"family": "Hillen", "given": "Amy", "initials": "A", "orcid": "0000-0002-8567-1545", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba7f6c5a2f04d71816a8381ede8a615.json"}}, {"family": "Chari", "given": "Edwin", "initials": "E"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW", "orcid": "0000-0002-2575-0807", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67389ef276a47cfacec7cbe50da37a7.json"}}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ae0c1d2cf5461894c6d0d80ed42f68.json"}}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fc5e4f49e4330b095c26cd965cc98.json"}}], "type": "journal article", "published": "2025-11-11", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "issn-l": "1061-4036"}, "abstract": "Dynamic steady-state lineage contribution of human hematopoietic stem cell (HSC) clones needs to be assessed over time. However, clonal contribution of HSCs has only been investigated at single time points and without assessing the critical erythroid and platelet lineages. Here we screened for somatic mutations in healthy aged individuals, identifying expanded HSC clones accessible for lineage tracing of all major blood cell lineages. In addition to HSC clones with balanced contribution to all lineages, we identified clones with all myeloid lineages but no or few B and T lymphocytes or all myeloid lineages and B cells but no T cells. No other lineage restriction patterns were reproducibly observed. Retrospective phylogenetic inferences uncovered a 'hierarchical' pattern of descendant subclones more lineage biased than their ancestral clone and a more common 'stable' pattern with descendant subclones showing highly concordant lineage contributions with their ancestral clone, despite decades of separation. Prospective lineage tracing confirmed remarkable stability over years of HSC clones with distinct lineage replenishment patterns.", "doi": "10.1038/s41588-025-02405-w", "pmid": "41219528", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41588-025-02405-w"}], "notes": [], "created": "2025-11-21T14:18:19.115Z", "modified": "2025-11-21T14:18:20.018Z"}, {"entity": "publication", "iuid": "6176a29337eb4648a2c736c7849ce6b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6176a29337eb4648a2c736c7849ce6b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6176a29337eb4648a2c736c7849ce6b6"}}, "title": "Linking nutrient availability and community size to stochasticity in microbial community assembly.", "authors": [{"family": "Bick", "given": "Berenike", "initials": "B", "orcid": "0000-0001-9445-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/58373f9528d04f4bbcceebb2d14f4b20.json"}}, {"family": "Lumpi", "given": "Theresa", "initials": "T"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S"}], "type": "journal article", "published": "2025-11-11", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "12", "issn-l": "0168-6496"}, "abstract": "Both deterministic (e.g. species-environment interactions) and stochastic processes (e.g. random birth and death events) shape communities, but it remains poorly understood, which environmental conditions promote stochasticity. Here, we investigated interactive effects of nutrient availability and community size on stochasticity in order to predict how eutrophication and biomass loss shift the balance between predictable and random community dynamics. For this, we used freshwater bacterial communities in a microcosm experiment, where communities were diluted to varying sizes and exposed to low, intermediate, and high nutrient concentrations. Stochasticity was estimated with null modelling and as beta-diversity among replicate communities. At low nutrient concentrations, deterministic processes dominated, especially in smaller communities, which had the lowest diversity and abundance. Whereas, higher nutrient concentrations increased stochasticity. In contrast to theoretical predictions, this was particularly the case in larger communities with the highest diversity and abundance, likely due to stochastic initial growth. The findings underline how nutrient availability and community size jointly influence stochastic assembly processes, with important consequences for bacterial diversity and ecosystem functioning under environmental change.", "doi": "10.1093/femsec/fiaf110", "pmid": "41147699", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12603558"}, {"db": "pii", "key": "8305078"}], "notes": [], "created": "2025-12-05T11:46:56.250Z", "modified": "2025-12-05T11:46:56.438Z"}, {"entity": "publication", "iuid": "383fc2f557f74c5ca9961f9823a9c2e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/383fc2f557f74c5ca9961f9823a9c2e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/383fc2f557f74c5ca9961f9823a9c2e0"}}, "title": "Parallel clines of chromosomal inversion frequencies in seaweed flies are associated with thermal variation.", "authors": [{"family": "Nicolas", "given": "L\u00e9a A", "initials": "LA", "orcid": "0009-0007-2292-8431", "researcher": {"href": "https://publications.scilifelab.se/researcher/400196db3fb04ab0911f28029b922598.json"}}, {"family": "Berdan", "given": "Emma L", "initials": "EL", "orcid": "0000-0002-6435-4604", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f65066e9a744b95b25ec0597b4b8e23.json"}}, {"family": "Wellenreuther", "given": "Maren", "initials": "M", "orcid": "0000-0002-2764-8291", "researcher": {"href": "https://publications.scilifelab.se/researcher/82e9b593bf0f4535a7b9231608b1e27d.json"}}, {"family": "Colinet", "given": "Herv\u00e9", "initials": "H"}, {"family": "Clouard", "given": "Andr\u00e9a", "initials": "A"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "M\u00e9rot", "given": "Claire", "initials": "C"}], "type": "journal article", "published": "2025-11-05", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X"}, "abstract": "Chromosomal inversion supergenes, which form blocks of linked genes, are increasingly recognized for their role in maintaining intra-specific diversity. They are predicted to be relevant genetic architectures for local adaptation in the face of gene flow. However, pinpointing the underlying traits and functional mechanisms under selection remains challenging. The seaweed fly Coelopa frigida harbors several large polymorphic inversions, of which the Cf-Inv(4.1) inversion displays a latitudinal cline of frequencies along the North American Atlantic Coast, suggesting a putative role in adaptation along the eco-climatic gradient. To investigate this hypothesis, we designed a molecular marker for karyotyping and studied natural and experimental populations from North America and Europe. We confirmed that this inversion is also polymorphic in Europe, and displays parallel latitudinal clines across continents, providing strong indirect support that Cf-Inv(4.1) is under natural selection along similar environmental gradients. We found that Cf-Inv(4.1) had a significant impact on egg-to-adult survival and fecundity under different thermal conditions. However, no effect on cold tolerance could be determined using supercooling point and chill coma recovery time. We speculate that fitness associated with Cf-Inv(4.1) is shaped by subtle life-history differences whose relative advantage depends on climate. While our experimental approaches provided insights into genotype-phenotype associations, it is worth noting that selection acts on the overall fitness, involving complex sets of traits. This is especially relevant for inversions linking hundreds of genes. This multi-gene property also explains why inversions are frequently involved in repeated parallel adaptation to environmental gradients, as demonstrated here in the seaweed fly.", "doi": "10.1038/s41437-025-00808-3", "pmid": "41193615", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-025-00808-3"}], "notes": [], "created": "2025-11-19T07:41:34.155Z", "modified": "2025-11-19T07:41:34.300Z"}, {"entity": "publication", "iuid": "ff23b886460946f8b866e1a1db68e6a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff23b886460946f8b866e1a1db68e6a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff23b886460946f8b866e1a1db68e6a3"}}, "title": "Ancient DNA and dating evidence for the dispersal of hippos into central Europe during the last glacial.", "authors": [{"family": "Arnold", "given": "Patrick", "initials": "P"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "F\u00fcglistaler", "given": "Andreas", "initials": "A"}, {"family": "Lindauer", "given": "Susanne", "initials": "S"}, {"family": "Hoselmann", "given": "Christian", "initials": "C"}, {"family": "Friedrich", "given": "Ronny", "initials": "R"}, {"family": "Hajdas", "given": "Irka", "initials": "I"}, {"family": "Dickinson", "given": "Marc", "initials": "M"}, {"family": "Menger", "given": "Frank", "initials": "F"}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Wegmann", "given": "Daniel", "initials": "D"}, {"family": "Penkman", "given": "Kirsty E H", "initials": "KEH"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2025-11-03", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "35", "issue": "21", "pages": "5363-5371.e6", "issn-l": "0960-9822"}, "abstract": "Late Pleistocene hippo fossils (Hippopotamus amphibius) from Europe have generally been associated with the last interglacial period (Eemian, 129-115 thousand years ago [kya]).1,2,3,4 As a widely accepted indicator species for temperate climate conditions, it was assumed they went extinct with the onset of the last glacial (Weichselian) around 115 kya.2,5 Their origin and relationships to extant African common hippos and the exact age of their extinction in central Europe, however, remain unclear. Here, we address these questions using an integrated approach applied to hippos from the Upper Rhine Graben in central Europe. By sequencing the paleogenome of a European hippo, we reveal its close genetic links to modern hippos from Africa. Six additional partial mitochondrial genomes confirm that European representatives were part of the same, once widespread species that is today restricted to sub-Saharan Africa. Surprisingly, radiocarbon dating shows that hippos were present in central Europe during the middle Weichselian (a period spanning from earlier than 47 kya until \u223c31 kya), i.e., well into the last glacial. Similar radiocarbon dates for woolly mammoth and woolly rhino fossils from the same sites imply the presence of both faunas during this period. Despite the paleogenome's low coverage, we are able to confidently estimate its genome-wide diversity by recalibrating the sequencing quality scores and assessing post-mortem damage. The low genome-wide diversity recovered suggests that it belonged to a small, isolated population. Overall, our combined data imply that hippos inhabited the Upper Rhine Graben refugium during temperate phases of the middle Weichselian.", "doi": "10.1016/j.cub.2025.09.035", "pmid": "41067227", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(25)01205-9"}], "notes": [], "created": "2025-11-19T09:56:40.454Z", "modified": "2025-11-19T09:56:40.458Z"}, {"entity": "publication", "iuid": "2b2c9cd55b354c8c805f7b3f3749f406", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b2c9cd55b354c8c805f7b3f3749f406.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b2c9cd55b354c8c805f7b3f3749f406"}}, "title": "Warming-Induced Effects on Microbial Communities and Nitrogen Cycling Capacity in Tundra Litter Are Modulated by Herb Abundance and Litter Quality.", "authors": [{"family": "Jeanbille", "given": "Mathilde", "initials": "M", "orcid": "0000-0002-7758-8928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aec9e57ba006483381b852b505728277.json"}}, {"family": "Clemmensen", "given": "Karina E", "initials": "KE", "orcid": "0000-0002-9627-6428", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a4e19bdfc1431c9dd1c3f1cd58c766.json"}}, {"family": "Juhanson", "given": "Jaanis", "initials": "J", "orcid": "0000-0003-3799-2819", "researcher": {"href": "https://publications.scilifelab.se/researcher/43736fc1dba8405285b1143f5ba3f170.json"}}, {"family": "Michelsen", "given": "Anders", "initials": "A", "orcid": "0000-0002-9541-8658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1ae80fdcd1949869986ad85c68a5586.json"}}, {"family": "Alatalo", "given": "Juha", "initials": "J", "orcid": "0000-0001-5084-850X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e31e5ef78cd941ffb26abd000ea418c1.json"}}, {"family": "Cooper", "given": "Elisabeth J", "initials": "EJ", "orcid": "0000-0002-0634-1282", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e24fe660b0540ea9b977e022b22a82d.json"}}, {"family": "Henry", "given": "Greg H R", "initials": "GHR", "orcid": "0000-0002-2606-9650", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec146a7b05534922b90d3205f12b5716.json"}}, {"family": "Hofgaard", "given": "Annika", "initials": "A", "orcid": "0000-0001-6919-5537", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cb3c8abbf684418a75b41492e83ad5c.json"}}, {"family": "Hollister", "given": "Robert D", "initials": "RD", "orcid": "0000-0002-4764-7691", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e541fcf014f49e38fccb53eeb989b64.json"}}, {"family": "J\u00f3nsd\u00f3ttir", "given": "Ingibj\u00f6rg S", "initials": "IS", "orcid": "0000-0003-3804-7077", "researcher": {"href": "https://publications.scilifelab.se/researcher/89fc1fd6b2b84dba86483c9e25d2a214.json"}}, {"family": "Klanderud", "given": "Kari", "initials": "K", "orcid": "0000-0003-1049-7025", "researcher": {"href": "https://publications.scilifelab.se/researcher/11f070d4cdfa40e3addf23592be1c840.json"}}, {"family": "Tolvanen", "given": "Anne", "initials": "A", "orcid": "0000-0002-5304-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea61db4d29d428091e2bce0ae8d00a9.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Glob Chang Biol", "issn": "1365-2486", "issn-l": "1354-1013", "volume": "31", "issue": "11", "pages": "e70582"}, "abstract": "Climate warming is changing tundra vegetation in the Arctic, with implications for plant litter properties. Warming may thus modify bacterial and fungal communities and their nitrogen (N) cycling capacity in the litter layer, which in turn can affect plant N availability. To address potential warming effects, we characterized the responses of bacterial and fungal communities and their genetically encoded capacity for inorganic N-transformations in the litter layer, as well as 15N natural abundance in the underlying soil layer as an integrated measure of N processes in the soil, in 16 long-term alpine and Arctic tundra warming experiments distributed across 12 circumpolar locations. Although abundance, diversity, and composition of microbial communities were structured by the local conditions rather than experimental warming, warming indirectly modified microbial communities and their capacity for N transformations through changes in litter quality. Specifically, experimental warming resulted in stronger connections between the capacity for nitrification, denitrification and N-fixation in the litter and the \u03b415N signature in the soil. These warming-induced connections were mainly mediated by increased dominance of herbs but also increased litter mass. These findings suggest accelerated inorganic N cycling in the litter layer with warming, particularly coupled to local abundance of herbs, which can create positive feedback on plant growth as well as ecosystem respiration. Thus, microbial communities in the litter may contribute to an intensification of ongoing vegetation shifts across the tundra biome.", "doi": "10.1111/gcb.70582", "pmid": "41221642", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC12606403"}], "notes": [], "created": "2025-11-16T14:52:02.241Z", "modified": "2025-11-21T14:19:43.976Z"}, {"entity": "publication", "iuid": "fdfce138b5554e72a4f6cf82097b08e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdfce138b5554e72a4f6cf82097b08e2"}}, "title": "Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo-Pacific Species Complex of Whistlers (Aves: Pachycephala).", "authors": [{"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Guinet", "given": "Benjamin", "initials": "B"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "21", "pages": "e70018", "issn-l": "0962-1083"}, "abstract": "Genomic studies have revealed introgressive hybridisation as a common phenomenon across the tree of life, particularly among young radiations. As incipient speciation tends to be induced by vicariance events, it is assumed that introgressive hybridisation is more frequent in young radiations in which allopatrically distributed species have a high probability of coming into secondary contact. In this study, we use whole genomic data to investigate spatio-temporal introgression patterns in a songbird radiation that has colonised a highly dynamic island region in the Indo-Pacific. Some taxa within this radiation have colonised remote oceanic islands whereas others occur on landmasses and islands in the Sahul region that were periodically connected during Pleistocene periods of lower sea levels. Our results show that introgressive hybridisation has been pervasive within this young radiation, despite prominent plumage differences between taxa. Geographical proximity has been an important factor for hybridisation and we further find that species occupying islands in the environmentally unstable Sahul region exhibit particularly high signatures of introgressive hybridisation. Yet, one species appears to have been shielded from hybridisation, perhaps due to specific ecological specialisations. Finally, we identify a hybrid species on an island where two oceanic radiations meet. Our results also caution against relying solely on analyses that only detect asymmetric introgression when examining systems with complex introgression histories. Collectively, our results support a growing body of literature that suggests that reticulate speciation is more common than previously thought. This has implications for our understanding of species formation and their persistence through time.", "doi": "10.1111/mec.70018", "pmid": "40650490", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573736"}], "notes": [], "created": "2025-11-19T08:33:24.398Z", "modified": "2025-11-19T08:33:24.490Z"}, {"entity": "publication", "iuid": "7f52e3a6678e478fa8713a395977ad99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f52e3a6678e478fa8713a395977ad99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f52e3a6678e478fa8713a395977ad99"}}, "title": "Reproductive Isolation due to Divergent Ecological Selection Is Accompanied by Vast Genomic Instability in Experimentally Evolved Yeast Populations.", "authors": [{"family": "Bendixsen", "given": "Devin P", "initials": "DP", "orcid": "0000-0003-0831-7646", "researcher": {"href": "https://publications.scilifelab.se/researcher/533f0c534a214ee68a037b243a63a028.json"}}, {"family": "Gilchrist", "given": "Ciaran", "initials": "C", "orcid": "0000-0002-7639-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/44917102032e428998899b3e63e5c4df.json"}}, {"family": "Haberkorn", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-7371-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/099838e4d3b94ee1af5cdfbf8ffea5d2.json"}}, {"family": "Persson", "given": "Karl", "initials": "K", "orcid": "0000-0002-2173-8165", "researcher": {"href": "https://publications.scilifelab.se/researcher/e13a27bed91340bf997f179e1c2c6c3b.json"}}, {"family": "Geijer", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-4158-2938", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad8eab8b087d47c4bce77ee2661628fb.json"}}, {"family": "Warringer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-6144-2740", "researcher": {"href": "https://publications.scilifelab.se/researcher/864cb0fde85a4aaeb68627f67e97d283.json"}}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "22", "pages": "e70110", "issn-l": "0962-1083"}, "abstract": "Populations evolving independently in divergent environments accumulate genetic differences and potentially evolve reproductive isolation as a by-product of divergence. The speed and mechanisms underlying this process are difficult to investigate because we rarely get the opportunity to witness them in natural settings, and histories of selection and gene flow between populations are often unknown. Here, we experimentally evolved yeast for 1000 generations of evolution in both divergent and parallel environments. At regular time points during experimental evolution, we made crosses between parallel- and divergent-evolving populations to measure postzygotic reproductive isolation (gamete viability). We used whole genome population sequencing to determine the mutational load, the number and types of structural variation, and other genomic features of the parent, F1 and F2 intraspecific hybrids. We found evidence for large-scale phenotypic and genome-wide differentiation in response to divergent laboratory selection. Divergent-selected populations produced hybrids with reduced gamete viability-a classic signature of postzygotic reproductive isolation in the form of hybrid breakdown. Parallel-selected populations, on the other hand, remained more reproductively compatible (with exceptions). We found that F2 hybrid genomes contained vast genomic instability, that is, new structural variants (especially insertions, deletions and interchromosomal translocations) that were not observed in parent and F1 genomes, which is likely a result of chromosome missegregation and recombination errors in hybrid meiosis. Our results provide phenotypic and genomic evidence that partial reproductive isolation evolved due to adaptation to divergent environments, consistent with predictions of ecological speciation theory.", "doi": "10.1111/mec.70110", "pmid": "40960070", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12617035"}], "notes": [], "created": "2025-11-19T09:48:26.950Z", "modified": "2025-11-19T09:48:27.465Z"}, {"entity": "publication", "iuid": "696f138df66747158e7f0f9a47bbd9ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/696f138df66747158e7f0f9a47bbd9ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/696f138df66747158e7f0f9a47bbd9ae"}}, "title": "Paleogenomic evidence on the temporal continuity of indigenous goat exploitation in the Canary Islands", "authors": [{"family": "D\u00edaz-P\u00e9rez", "given": "Clara", "initials": "C"}, {"family": "Santana", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9615-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a4f0fc23b847b98e0d57d22a8a756d.json"}}, {"family": "Daly", "given": "Kevin G", "initials": "KG"}, {"family": "Ord\u00f3\u00f1ez", "given": "Alejandra C", "initials": "AC"}, {"family": "Serrano", "given": "Javier G", "initials": "JG"}, {"family": "Armas-Quintana", "given": "Sara B", "initials": "SB"}, {"family": "Vacas-Fumero", "given": "Emilio", "initials": "E"}, {"family": "Brito-Mayor", "given": "Aitor", "initials": "A"}, {"family": "Gilson", "given": "Simon Pierre", "initials": "SP"}, {"family": "Morales", "given": "Jacob", "initials": "J"}, {"family": "Marrero Salas", "given": "Efra\u00edn", "initials": "E"}, {"family": "Hern\u00e1ndez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Alberto", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Moreno", "given": "Marco", "initials": "M"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Hern\u00e1ndez", "given": "Mariano", "initials": "M"}, {"family": "Arnay", "given": "Matilde", "initials": "M"}, {"family": "Fregel", "given": "Rosa", "initials": "R", "orcid": "0000-0002-2951-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/abfbfec4ddea49f8b4eedcf1e04e01c2.json"}}], "type": "journal-article", "published": "2025-11-00", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "28", "issue": "11", "pages": "113771"}, "abstract": null, "doi": "10.1016/j.isci.2025.113771", "pmid": null, "labels": {"Ancient DNA": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2025-11-05T07:40:52.150Z", "modified": "2025-11-19T07:57:42.304Z"}, {"entity": "publication", "iuid": "394d345f587e4a8fa382227d3718c80e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/394d345f587e4a8fa382227d3718c80e"}}, "title": "HAPP: High-accuracy pipeline for processing deep metabarcoding data.", "authors": [{"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Granqvist", "given": "Emma", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Godeiro", "given": "Nerivania N", "initials": "NN", "orcid": "0000-0002-1669-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/990e5c3362f94d76af29742ab5876a8a.json"}}, {"family": "Bellini", "given": "Bruno C", "initials": "BC"}, {"family": "Orsholm", "given": "Johanna", "initials": "J"}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Comput. Biol.", "issn": "1553-7358", "issn-l": "1553-734X", "volume": "21", "issue": "11", "pages": "e1013558"}, "abstract": "Deep metabarcoding offers an efficient and reproducible approach to biodiversity monitoring, but noisy data and incomplete reference databases challenge accurate diversity estimation and taxonomic annotation. Here, we introduce a novel algorithm, NEEAT, for removing spurious operational taxonomic units (OTUs) originating from nuclear-embedded mitochondrial DNA sequences (NUMTs) or sequencing errors. It integrates 'echo' signals across samples with the identification of unusual evolutionary patterns among similar DNA sequences. We also extensively benchmark current tools for chimera removal, taxonomic annotation and OTU clustering of deep metabarcoding data. The best performing tools/parameter settings are integrated into HAPP, a high-accuracy pipeline for processing deep metabarcoding data. Tests using CO1 data from BOLD and large-scale metabarcoding data on insects demonstrate that HAPP significantly outperforms existing methods, while enabling efficient analysis of extensive datasets by parallelizing computations across taxonomic groups.", "doi": "10.1371/journal.pcbi.1013558", "pmid": "41202092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12622834"}, {"db": "pii", "key": "PCOMPBIOL-D-25-00687"}], "notes": [], "created": "2025-11-21T11:45:11.315Z", "modified": "2025-11-21T12:27:09.804Z"}, {"entity": "publication", "iuid": "ee9a4f95a65047b6b653d5c9247a378c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee9a4f95a65047b6b653d5c9247a378c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee9a4f95a65047b6b653d5c9247a378c"}}, "title": "Genomic Landscape of Divergence in Ballan Wrasse (Labrus bergylta).", "authors": [{"family": "Jansson", "given": "Eeva", "initials": "E", "orcid": "0000-0002-7840-7201", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d9b75e0780c43f8ac26d9a7a0418555.json"}}, {"family": "Ayllon", "given": "Fernando", "initials": "F", "orcid": "0009-0005-6051-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/beb3c127a1fe47ec874dca9fe6f3ffd4.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Casas", "given": "Laura", "initials": "L", "orcid": "0000-0001-6617-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5189f1f7c74aad9b8a2af7f47ad4f3.json"}}, {"family": "Saborido-Rey", "given": "Fran", "initials": "F", "orcid": "0000-0002-2760-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/74db5d050f844f6a944e2393d83728b9.json"}}, {"family": "Furmanek", "given": "Tomasz", "initials": "T"}, {"family": "Brieuc", "given": "Marine S O", "initials": "MSO", "orcid": "0000-0001-8601-2122", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef26450b493a412faac6b9b0b4a1a857.json"}}, {"family": "Villegas-Rios", "given": "David", "initials": "D", "orcid": "0000-0001-5660-5322", "researcher": {"href": "https://publications.scilifelab.se/researcher/0038fd6eb1234894a0b1938c0e862a36.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M", "orcid": "0000-0003-4762-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b95d1205db043108756e235bcb25c84.json"}}, {"family": "Edvardsen", "given": "Rolf B", "initials": "RB", "orcid": "0000-0001-8430-8042", "researcher": {"href": "https://publications.scilifelab.se/researcher/07efd6f7e7b04bbd8af5221f78e982c7.json"}}, {"family": "Lille-Lang\u00f8y", "given": "Roger", "initials": "R", "orcid": "0000-0002-8010-8542", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea677d3afed44519b9a3e5406c721735.json"}}, {"family": "Glover", "given": "Kevin A", "initials": "KA"}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e17732"}, "abstract": "The architecture underpinning genomic divergence is still a largely uncharted territory and likely case-dependent. Here, we investigated genome-wide variation in Ballan wrasse, a northeastern Atlantic fish species that displays two sympatric colour morphs, spotty and plain, that have been suggested to represent subspecies. We produced a chromosome-level reference genome and thereafter investigated genomic divergence among 152 individuals including both morphs, from two localities in Spain and Norway each and one in France. Differences between morphs dominated in Spain in accordance with sympatric divergence, whereas in Norway allopatric differentiation was prominent and repeated genomic signals of local divergence were found. Chromosomes had large low-recombining areas shared across all populations. Within the Spanish morphs, these areas contained large islands of divergence, totalling ~11% of the genome, and showed high morph specificity and strong selection. The same regions showed frequent admixture in the French morphs and no differentiation in Norway. In contrast, divergent regions observed between sampling localities in Norway were shorter and found throughout the genome. High inbreeding and lower diversity were observed in the Norwegian samples, consistent with the proposed recolonisation bottleneck and subsequent drift. Several genomic regions were significantly associated with morphs and contained tens of genes of diverse functions, suggesting that colouration is unlikely to be the sole driver of divergence. Our results do not support the hypothesis of shared larger genomic features underlying intraspecific colour divergence. Instead, we observe gradual accumulation of differences into low-recombining regions, likely when additional factors like assortative mating and/or lack of gene flow favour their development.", "doi": "10.1111/mec.17732", "pmid": "40095420", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "NGI Other": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573741"}], "notes": [], "created": "2025-08-19T13:31:21.967Z", "modified": "2025-11-28T10:51:26.963Z"}, {"entity": "publication", "iuid": "4454335dc4504444ac7197bda2a143ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4454335dc4504444ac7197bda2a143ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4454335dc4504444ac7197bda2a143ad"}}, "title": "Genetic mapping in the red mason bee implicates ANTSR as an ancient sex-determining locus in bees and ants.", "authors": [{"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Magnusson", "given": "Sara", "initials": "S"}, {"family": "Huser", "given": "Linn", "initials": "L"}, {"family": "Nor Fuad", "given": "Muhammad Nafiz Ikhwan Bin", "initials": "MNIB"}, {"family": "Everitt", "given": "Turid", "initials": "T"}, {"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC"}, {"family": "Theodorou", "given": "Panagiotis", "initials": "P"}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Paxton", "given": "Robert J", "initials": "RJ"}, {"family": "Seidelmann", "given": "Karsten", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "volume": "23", "issue": "11", "pages": "e3003458", "issn-l": "1544-9173"}, "abstract": "Haplodiploid inheritance, in which females are diploid and males are haploid, is found in all species of Hymenoptera. Sex in haplodiploids is commonly determined by the alleles present at a complementary sex determination (CSD) locus, with heterozygosity triggering the female developmental pathway. The identity of this locus differs among taxa and is only known in a few species. Here, we map a single CSD locus to a 2 kbp region in the genome of the red mason bee Osmia bicornis. It overlaps the long noncoding RNA ANTSR, which has been identified as the sex-determining gene in the invasive ant Linepithema humile. This locus is homozygous in diploid males and exhibits extremely high levels of haplotype diversity, consistent with the action of frequency-dependent selection. The elevated levels of heterozygosity in the CSD locus enable us to fine-map potentially functional genetic variation within it. We also identify elevated levels of genetic diversity in the ortholog of the CSD locus in five other bee and ant genera, suggesting that it may govern sex determination widely in Hymenoptera. Our data are consistent with the hypothesis that ANTSR evolved a role in sex determination over 150 million years ago and is the ancestral sex-determination locus of bees and ants.", "doi": "10.1371/journal.pbio.3003458", "pmid": "41183133", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12594375"}, {"db": "pii", "key": "PBIOLOGY-D-25-02082"}], "notes": [], "created": "2025-11-21T13:19:56.177Z", "modified": "2025-11-21T13:19:56.233Z"}, {"entity": "publication", "iuid": "72cefc191b884104801e8e6a814331a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72cefc191b884104801e8e6a814331a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72cefc191b884104801e8e6a814331a3"}}, "title": "Epigenetic alterations facilitate transcriptional and translational programs in hypoxia.", "authors": [{"family": "Watt", "given": "Kathleen", "initials": "K"}, {"family": "Dauber", "given": "Bianca", "initials": "B", "orcid": "0009-0006-6755-3840", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd42e74de22e49a4a1b279ba43048c9a.json"}}, {"family": "Szkop", "given": "Krzysztof J", "initials": "KJ"}, {"family": "Lee", "given": "Laura", "initials": "L"}, {"family": "Jovanovic", "given": "Predrag", "initials": "P", "orcid": "0000-0002-0090-0047", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9428a0025a74362a8ada196e0a9292d.json"}}, {"family": "Chen", "given": "Shan", "initials": "S"}, {"family": "Palia", "given": "Ranveer", "initials": "R"}, {"family": "Vassalakis", "given": "Julia A", "initials": "JA"}, {"family": "Cooper", "given": "Tyler T", "initials": "TT"}, {"family": "Papadopoli", "given": "David", "initials": "D"}, {"family": "Masvidal", "given": "La\u00eca", "initials": "L"}, {"family": "Jewer", "given": "Michael", "initials": "M"}, {"family": "Tandoc", "given": "Kristofferson", "initials": "K"}, {"family": "Plummer", "given": "Hannah", "initials": "H"}, {"family": "Lajoie", "given": "Gilles A", "initials": "GA"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I", "orcid": "0000-0002-5510-9762", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cc0d0d273054042b1ef202ea6174f0d.json"}}, {"family": "Larsson", "given": "Ola", "initials": "O", "orcid": "0000-0003-1412-1308", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8d18c6429ac46d094a81a3049b7f478.json"}}, {"family": "Postovit", "given": "Lynne-Marie", "initials": "LM", "orcid": "0000-0002-8088-4197", "researcher": {"href": "https://publications.scilifelab.se/researcher/21ec312efc1846938b6f3c62e493c307.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "volume": "27", "issue": "11", "pages": "1965-1981", "issn-l": null}, "abstract": "Adaptation to cellular stresses entails an incompletely understood coordination of transcriptional and post-transcriptional gene expression programs. Here, by quantifying hypoxia-dependent transcriptomes, epigenomes and translatomes in T47D breast cancer cells and H9 human embryonic stem cells, we show pervasive changes in transcription start site (TSS) selection associated with nucleosome repositioning and alterations in H3K4me3 distribution. Notably, hypoxia-associated TSS switching was induced or reversed via pharmacological modulation of H3K4me3 in the absence of hypoxia, defining a role for H3K4me3 in TSS selection independent of HIF1-transcriptional programs. By remodelling 5'UTRs, TSS switching selectively alters protein synthesis, including enhanced translation of messenger RNAs encoding pyruvate dehydrogenase kinase 1, which is essential for metabolic adaptation to hypoxia. These results demonstrate a previously unappreciated mechanism of translational regulation during hypoxia driven by epigenetic reprogramming of the 5'UTRome.", "doi": "10.1038/s41556-025-01786-8", "pmid": "41102449", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12611764"}, {"db": "pii", "key": "10.1038/s41556-025-01786-8"}], "notes": [], "created": "2025-10-29T10:04:31.556Z", "modified": "2025-11-28T10:46:16.259Z"}, {"entity": "publication", "iuid": "0577c5369a1d4893bc7f6fb121420f6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0577c5369a1d4893bc7f6fb121420f6f"}}, "title": "Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes).", "authors": [{"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Smith", "given": "Brian Tilston", "initials": "BT"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e17760"}, "abstract": "Speciation is a fundamental concept in evolutionary biology, and understanding the mechanisms driving speciation remains the foremost research topic within this field. Hybridisation is often involved in speciation and can influence its rates, potentially accelerating, decelerating or even reversing the process. This study investigates the evolutionary history of the New Guinean bird genus Melidectes, consisting of six species that inhabit various montane regions at different elevations. While most Melidectes species have allopatric distributions, two species overlap in the central mountain range and hybridise. However, plumage differences and elevational adaptations are assumed to maintain the species' boundaries. Utilising specimens from natural history collections and comprehensive genomic analyses, including a de novo genome assembly, we characterise allopatric speciation patterns within the genus and highlight how future speciation could potentially be driven by climate change. Contrary to previous hypotheses, our findings suggest that in the two distributionally overlapping species, phenotypic differences do not prevent gene flow. We find limited acoustic differentiation and extensive admixture across most of their distributions. Divergence and admixture levels conform poorly to the current taxonomy and follow a geographical pattern in which the most isolated populations at the ends of the distributions are most divergent and show least admixture. However, in contrast, their mitochondrial genomes do group in accordance with species identity, namely, into two deeply divergent lineages. We propose that this system demonstrates the ephemeral nature of speciation, in which two incipient species have started mixing extensively as they came into secondary contact, resulting in nearly complete fusion into a single lineage.", "doi": "10.1111/mec.17760", "pmid": "40219608", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573753"}], "notes": [], "created": "2025-11-19T08:27:00.806Z", "modified": "2025-11-19T09:18:52.732Z"}, {"entity": "publication", "iuid": "e3a0b036f1a64129a355aafe11a904e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e3a0b036f1a64129a355aafe11a904e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e3a0b036f1a64129a355aafe11a904e8"}}, "title": "Disease-specific epigenetic deregulation of enhancers, transposons, and polycomb targets in acute promyelocytic leukemia.", "authors": [{"family": "Zhong", "given": "Xiangfu", "initials": "X"}, {"family": "Cordeddu", "given": "Lina", "initials": "L"}, {"family": "Gamboa-Cedeno", "given": "Angelica", "initials": "A"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Genome Med", "issn": "1756-994X", "issn-l": "1756-994X", "volume": "17", "issue": "1", "pages": "135"}, "abstract": "Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML), characterized by a fusion between the PML and RARA genes and by a block in the myeloid maturation at the promyelocytic stage.\r\n\r\nThis study investigates the epigenetic landscape of APL by integrating ChIP-seq data on eight histone modifications and RNA-seq in APL as well as non-APL AML. APL showed a distinct chromatin profile that differed from non-APL AML.\r\n\r\nWe describe APL-specific changes in H3K27ac, H3K9me3, and H3K27me3 with impact on enhancer activity, repression of transposable elements, and Polycomb regulated gene repression. The APL-specific H3K27ac pattern identifies APL-specific enhancer and super-enhancer regions, including a subset of enhancers that are bound by the PML-RARA fusion protein. While chromatin bound specifically by PML-RARA were dominantly active, APL was also characterized by gain of APL-specific heterochromatin states with significant gains of H3K9me3 enriched lamina-associated domains and the transposable elements LINE, LTR, and SINE.\r\n\r\nThese findings suggest a unique enhancer and heterochromatin profile in APL, with implications for transcription regulation and treatment response. These findings offer novel insights into the pathogenesis of APL.", "doi": "10.1186/s13073-025-01565-y", "pmid": "41168841", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573822"}, {"db": "pii", "key": "10.1186/s13073-025-01565-y"}], "notes": [], "created": "2025-11-28T10:53:15.320Z", "modified": "2026-07-15T07:14:00.504Z"}, {"entity": "publication", "iuid": "ea181adcfb564b289434e673fccd07a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea181adcfb564b289434e673fccd07a3"}}, "title": "Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years.", "authors": [{"family": "Gilardet", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4851-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f507b07ed934c73988dfd0537254485.json"}}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-7973-6173", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b1165126184cb980f8bc7e9b9c0fdd.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G", "orcid": "0000-0002-0957-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/62bbfad753a943ea94eb9a0384713a17.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6929-4869", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d428a542d44a829e17924e94a3f6dc.json"}}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Southon", "given": "John", "initials": "J"}, {"family": "Vasiliev", "given": "Sergey K", "initials": "SK"}, {"family": "Shunkov", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-1388-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/c43a1135a5804441b6ab9680f7cbd2b3.json"}}, {"family": "Kozlikin", "given": "Maxim B", "initials": "MB", "orcid": "0000-0001-5082-3345", "researcher": {"href": "https://publications.scilifelab.se/researcher/da2a8523fc1c42178159bbd3e8b64ecc.json"}}, {"family": "Douka", "given": "Katerina", "initials": "K", "orcid": "0000-0002-0558-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a6efe4f6db44f6b85ed2653d2a3342f.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "17", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Bovines have a complex yet poorly understood evolutionary history that is characterized by admixture and diversity loss during the Late Pleistocene. Unraveling this history is challenging in part because deep-time and geographically widespread genetic data are currently limited. In mid-latitude Asia, Denisova Cave, located in the Altai, Siberia, and nearby paleontological sites have yielded a large collection of remains spanning the Middle to Late Pleistocene, many of which are identifiable as bovines via morphology or paleoproteomics. In this study, we screened these bovine bones for ancient DNA and generated mitogenomes, to refine knowledge of Pleistocene bovine diversity in the region. We found that bovines carrying a yak-like mitogenome were common residents of the Altai mountains, along with bison belonging to the clade X mitochondrial lineage and, more rarely, aurochs. The yak-like mitochondrial lineage identified in this study represents a previously unknown lineage sister to present-day yak mitogenome diversity. This yak-like mitochondrial lineage, termed yak X, was identified at several sites, and survived in mid-latitude Asia across climatic transitions for around 200,000 years. Our findings suggest that all three bovine taxa harbored diversity no longer present in extant populations, thus mirroring archaic hominin findings at Denisova Cave. The Altai mountains therefore appear to have been a hotspot of both bovine and hominin diversity.", "doi": "10.1093/gbe/evaf206", "pmid": "41206445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12628791"}, {"db": "pii", "key": "8315343"}], "notes": [], "created": "2025-11-21T17:51:54.435Z", "modified": "2025-11-21T17:51:56.168Z"}, {"entity": "publication", "iuid": "3f18e5c79db74984ba3dfc82d76eecf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f18e5c79db74984ba3dfc82d76eecf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f18e5c79db74984ba3dfc82d76eecf3"}}, "title": "A pangenome and pantranscriptome of hexaploid oat.", "authors": [{"family": "Avni", "given": "Raz", "initials": "R", "orcid": "0000-0002-0801-5093", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e818aced4e14e529c60a7dd5d396de0.json"}}, {"family": "Kamal", "given": "Nadia", "initials": "N", "orcid": "0000-0002-3258-4130", "researcher": {"href": "https://publications.scilifelab.se/researcher/da83072939d347778c03424c656d1bae.json"}}, {"family": "Bitz", "given": "Lidija", "initials": "L"}, {"family": "Jellen", "given": "Eric N", "initials": "EN", "orcid": "0000-0002-7906-4845", "researcher": {"href": "https://publications.scilifelab.se/researcher/83594761835445f9a5c92cad770ca372.json"}}, {"family": "Bekele", "given": "Wubishet A", "initials": "WA", "orcid": "0000-0002-6463-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ea58d9ecc7a45c58a19fd0a36bed3ff.json"}}, {"family": "Angessa", "given": "Tefera T", "initials": "TT"}, {"family": "Auvinen", "given": "Petri", "initials": "P", "orcid": "0000-0002-3947-4778", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b998007ca8b412c8dac49230d5cea94.json"}}, {"family": "Bitz", "given": "Oliver", "initials": "O"}, {"family": "Boyle", "given": "Brian", "initials": "B", "orcid": "0000-0002-0158-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/de076e7c690542cfbc5b2da120521e29.json"}}, {"family": "Canales", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0001-7911-856X", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd058ce520fc48de81a2c4f2762659b4.json"}}, {"family": "Carlson", "given": "Craig H", "initials": "CH", "orcid": "0000-0003-2050-5455", "researcher": {"href": "https://publications.scilifelab.se/researcher/f856003d4ec44935812545685e22fe41.json"}}, {"family": "Chapman", "given": "Brett", "initials": "B", "orcid": "0000-0003-4484-2253", "researcher": {"href": "https://publications.scilifelab.se/researcher/4410e6ff3a7d489e84b05dc81edf53ce.json"}}, {"family": "Chawla", "given": "Harmeet Singh", "initials": "HS"}, {"family": "Chen", "given": "Yutang", "initials": "Y", "orcid": "0000-0001-8128-8728", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d3e1845423c4e0389ee86c0986a294d.json"}}, {"family": "Copetti", "given": "Dario", "initials": "D"}, {"family": "Correia de Lemos", "given": "Samara", "initials": "S", "orcid": "0000-0003-3484-1943", "researcher": {"href": "https://publications.scilifelab.se/researcher/4105d0322d0c478e8c3758d2d353c3e2.json"}}, {"family": "Dang", "given": "Viet", "initials": "V", "orcid": "0000-0001-6408-6323", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dc432298db04432b1285e4530d566de.json"}}, {"family": "Eichten", "given": "Steven R", "initials": "SR", "orcid": "0000-0003-2268-395X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c014d8bcd56b4240a3b8ed3219fac6f2.json"}}, {"family": "Klos", "given": "Kathy Esvelt", "initials": "KE"}, {"family": "Fenn", "given": "Amit M", "initials": "AM", "orcid": "0000-0003-2203-3922", "researcher": {"href": "https://publications.scilifelab.se/researcher/b27d342e880f4692bc1224c520b78dae.json"}}, {"family": "Fiebig", "given": "Anne", "initials": "A", "orcid": "0000-0003-3159-3593", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af17bbf24b34f20a9f433583ff00c05.json"}}, {"family": "Fu", "given": "Yong-Bi", "initials": "YB", "orcid": "0000-0003-3106-1247", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f089f51863447cf88cdb4ec23e009bc.json"}}, {"family": "Gundlach", "given": "Heidrun", "initials": "H", "orcid": "0000-0002-6757-0943", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e6d69126dd4a9a9a99827c672b5fa5.json"}}, {"family": "Gupta", "given": "Rajeev", "initials": "R", "orcid": "0000-0002-1451-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd2a62988238458e9ab17d4d7f60f2bb.json"}}, {"family": "Haberer", "given": "Georg", "initials": "G", "orcid": "0000-0002-6612-6939", "researcher": {"href": "https://publications.scilifelab.se/researcher/5313eb519bd24ee3b92a090746ad93a3.json"}}, {"family": "He", "given": "Tianhua", "initials": "T"}, {"family": "Herrmann", "given": "Matthias H", "initials": "MH", "orcid": "0000-0003-1760-6167", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1be02f0c5024c29aa810cb1dcc63c3f.json"}}, {"family": "Himmelbach", "given": "Axel", "initials": "A", "orcid": "0000-0001-7338-0946", "researcher": {"href": "https://publications.scilifelab.se/researcher/473928fe106248bdba303b0455faa930.json"}}, {"family": "Howarth", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0001-9364-0880", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ec8235c6e6348d3a4e1f84f0759348b.json"}}, {"family": "Hu", "given": "Haifei", "initials": "H", "orcid": "0000-0003-1070-213X", "researcher": {"href": "https://publications.scilifelab.se/researcher/573e418a00344b0192db99e0c8a4707a.json"}}, {"family": "Isidro Y S\u00e1nchez", "given": "Julio", "initials": "J", "orcid": "0000-0002-9044-3221", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef581d9a44994c798decadb0531b313c.json"}}, {"family": "Itaya", "given": "Asuka", "initials": "A", "orcid": "0000-0003-4132-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfab79c8f493415e9d86932559a40663.json"}}, {"family": "Jannink", "given": "Jean-Luc", "initials": "JL", "orcid": "0000-0003-4849-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df52f0eac0e4649adf4b87e2a702abe.json"}}, {"family": "Jia", "given": "Yong", "initials": "Y", "orcid": "0000-0002-0394-3966", "researcher": {"href": "https://publications.scilifelab.se/researcher/078c829a8fc2442da58be531b08381ee.json"}}, {"family": "Kaur", "given": "Rajvinder", "initials": "R"}, {"family": "Knauft", "given": "Manuela", "initials": "M"}, {"family": "Langdon", "given": "Tim", "initials": "T"}, {"family": "Lux", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5543-1911", "researcher": {"href": "https://publications.scilifelab.se/researcher/076281817e274a45819ff2f53f9047cf.json"}}, {"family": "Marmon", "given": "Sofia", "initials": "S", "orcid": "0000-0001-6929-7859", "researcher": {"href": "https://publications.scilifelab.se/researcher/0105355f5c26423f98f7e4429318bb2c.json"}}, {"family": "Marosi", "given": "Vanda", "initials": "V"}, {"family": "Mayer", "given": "Klaus F X", "initials": "KFX", "orcid": "0000-0001-6484-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd32d600030146e9891b324e80708362.json"}}, {"family": "Michel", "given": "Steve", "initials": "S"}, {"family": "Nandety", "given": "Raja Sekhar", "initials": "RS", "orcid": "0000-0002-1129-0790", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6834d990f14f578a96a7b57e06dbf8.json"}}, {"family": "Nilsen", "given": "Kirby T", "initials": "KT"}, {"family": "Paczos-Grz\u0119da", "given": "Edyta", "initials": "E", "orcid": "0000-0001-6273-0322", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a271331d534543a3907db410616d4b.json"}}, {"family": "Pasha", "given": "Asher", "initials": "A", "orcid": "0000-0002-9315-0520", "researcher": {"href": "https://publications.scilifelab.se/researcher/dea77d66f7a040f680e391da2b46ce24.json"}}, {"family": "Prats", "given": "Elena", "initials": "E"}, {"family": "Provart", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0001-5551-7232", "researcher": {"href": "https://publications.scilifelab.se/researcher/23c3f4e8ce0c44e3a74c8c0ad1aa7554.json"}}, {"family": "Ravagnani", "given": "Adriana", "initials": "A"}, {"family": "Reid", "given": "Robert W", "initials": "RW"}, {"family": "Schlueter", "given": "Jessica A", "initials": "JA"}, {"family": "Schulman", "given": "Alan H", "initials": "AH"}, {"family": "Sen", "given": "Taner Z", "initials": "TZ"}, {"family": "Singh", "given": "Jaswinder", "initials": "J", "orcid": "0000-0002-1139-9251", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e830c055e2542d6a2e6388ec3cad25c.json"}}, {"family": "Singh", "given": "Mehtab", "initials": "M", "orcid": "0000-0003-4550-9858", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2c9ff04964e42f08b8e906b51bf0b0d.json"}}, {"family": "Sirijovski", "given": "Nick", "initials": "N", "orcid": "0000-0002-6191-3845", "researcher": {"href": "https://publications.scilifelab.se/researcher/040fc49df77d4171bf2695ae420f2302.json"}}, {"family": "Stein", "given": "Nils", "initials": "N", "orcid": "0000-0003-3011-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/11ef5173e1214a9f920bcadad30afc70.json"}}, {"family": "Studer", "given": "Bruno", "initials": "B"}, {"family": "Viitala", "given": "Sirja", "initials": "S"}, {"family": "Vronces", "given": "Shauna", "initials": "S"}, {"family": "Walkowiak", "given": "Sean", "initials": "S", "orcid": "0000-0002-3866-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acd3a3bf11144baa35b773b921e23c9.json"}}, {"family": "Wang", "given": "Penghao", "initials": "P", "orcid": "0000-0002-3751-3921", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd3893272754899abcdb06dabaf195e.json"}}, {"family": "Waters", "given": "Amanda J", "initials": "AJ"}, {"family": "Wight", "given": "Charlene P", "initials": "CP", "orcid": "0000-0003-1410-5631", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bffc6376bf8453da9d6ac3b962805b6.json"}}, {"family": "Yan", "given": "Weikai", "initials": "W"}, {"family": "Yao", "given": "Eric", "initials": "E"}, {"family": "Zhang", "given": "Xiao-Qi", "initials": "XQ"}, {"family": "Zhou", "given": "Gaofeng", "initials": "G"}, {"family": "Zhou", "given": "Zhou", "initials": "Z"}, {"family": "Tinker", "given": "Nicholas A", "initials": "NA", "orcid": "0000-0002-2452-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef54eb854d47488f88ffc97360bfef59.json"}}, {"family": "Fiedler", "given": "Jason D", "initials": "JD", "orcid": "0000-0001-7736-4484", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e65e63fd07a4543a61a30ea653254d7.json"}}, {"family": "Li", "given": "Chengdao", "initials": "C", "orcid": "0000-0002-9653-2700", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3e4736c749c4b07b76e1ae98c4c9bbe.json"}}, {"family": "Maughan", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-3714-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a.json"}}, {"family": "Spannagl", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0701-7035", "researcher": {"href": "https://publications.scilifelab.se/researcher/88a57f18a3794d1aaf7af7c579697860.json"}}, {"family": "Mascher", "given": "Martin", "initials": "M", "orcid": "0000-0001-6373-6013", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2d033b05734d53a888db3e03edee0a.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836"}, "abstract": "Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.", "doi": "10.1038/s41586-025-09676-7", "pmid": "41162711", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09676-7"}], "notes": [], "created": "2025-11-19T07:39:59.482Z", "modified": "2025-11-28T10:46:37.749Z"}, {"entity": "publication", "iuid": "20bf7f8602df4703bfd5057606fcaa7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20bf7f8602df4703bfd5057606fcaa7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20bf7f8602df4703bfd5057606fcaa7b"}}, "title": "A Novel Supergene Controls Queen Size and Colony Social Organization in the Ant Myrmica ruginodis.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Sepp\u00e4", "given": "Perttu", "initials": "P", "orcid": "0000-0001-5393-6943", "researcher": {"href": "https://publications.scilifelab.se/researcher/700fa3a2724f442884d886463b1cf95c.json"}}, {"family": "Downing", "given": "Philip A", "initials": "PA", "orcid": "0000-0002-5286-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e004ff0660ee411cb310ab108f29c171.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Helanter\u00e4", "given": "Heikki", "initials": "H", "orcid": "0000-0002-6468-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/3947ff78ae914e6785fb081458619533.json"}}, {"family": "Viljakainen", "given": "Lumi", "initials": "L", "orcid": "0000-0002-6587-6156", "researcher": {"href": "https://publications.scilifelab.se/researcher/462f8aece21843458fa4e3f99a5c5449.json"}}], "type": "journal article", "published": "2025-10-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "11", "issn-l": "0737-4038"}, "abstract": "Large independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Their independent origins, as well as the similarities of the associated phenotypes, make ant supergenes a promising system for studying the parallel evolution of genome organization and adaptability. However, the genetic basis of differences in social organization and queen phenotypes remains unknown in many ant species, limiting the potential power of this system for comparative studies. We investigated the genetic basis of colony social organization in the queen-size dimorphic ant Myrmica ruginodis by sampling 95 queens from 31 colonies in southern Finland. Whole-genome sequencing revealed a novel 9 Mb supergene associated with both queen size and social organization. Queens homozygous for the AA haplotype were larger and found only in single-queen colonies, while queens in multiple-queen colonies were smaller and carried only AB and BB genotypes. This supergene is not homologous to previously identified supergenes in ants, suggesting it arose through a distinct evolutionary pathway.", "doi": "10.1093/molbev/msaf255", "pmid": "41077914", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12572780"}, {"db": "pii", "key": "8284624"}], "notes": [], "created": "2025-11-21T14:49:16.789Z", "modified": "2025-11-21T14:49:17.100Z"}, {"entity": "publication", "iuid": "1938da5a9fb54644b9fd03953d33a22d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1938da5a9fb54644b9fd03953d33a22d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1938da5a9fb54644b9fd03953d33a22d"}}, "title": "Autoreactive T cells identified in patients with anti-Jo1+ antisynthetase syndrome recognise a new epitope on histidyl t-RNA synthetase.", "authors": [{"family": "Galindo-Feria", "given": "Angeles S", "initials": "AS"}, {"family": "Sharma", "given": "Ravi Kumar", "initials": "RK"}, {"family": "Dubnovitsky", "given": "Anatoly", "initials": "A"}, {"family": "Gerstner", "given": "Christina", "initials": "C"}, {"family": "Kozhukh", "given": "Genadiy", "initials": "G"}, {"family": "Van Vollenhoven", "given": "Annika", "initials": "A"}, {"family": "Boada", "given": "Juan Sebastian Diaz", "initials": "JSD"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2892-673X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc367f2adb7c4379b7dc441be34e7ded.json"}}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Dastmalchi", "given": "Maryam", "initials": "M"}, {"family": "Reid", "given": "Hugh H", "initials": "HH"}, {"family": "Sandalova", "given": "Tatyana", "initials": "T"}, {"family": "Rossjohn", "given": "Jamie", "initials": "J"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "Horuluoglu", "given": "Begum", "initials": "B", "orcid": "0000-0003-2241-5170", "researcher": {"href": "https://publications.scilifelab.se/researcher/19120340af6c42bd8a359ce39d4a8b99.json"}}], "type": "journal article", "published": "2025-10-25", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967"}, "abstract": "Anti-Jo1+ antisynthetase syndrome (ASyS) is characterised by autoantibodies targeting histidyl t-RNA synthetase (HisRS), association with HLA-DRB1*03:01 and a distinct clinical phenotype including interstitial lung disease, myositis, arthritis, and mechanic's hands. Previous studies of autoreactive HisRS-specific CD4+T cells point to yet undiscovered T cell epitopes. We aimed to identify new epitopes on HisRS to investigate the presence of autoreactive T cells and their corresponding T-cell receptor (TCR) repertoire from patients with ASyS.\n\nPeptides from HisRS N-terminal region with appropriate major histocompatibility complex (MHC) anchor residues were selected for in vitro binding assays. The peptide (HisRS41-55) with the highest HLA-DRB1*03:01 binding affinity was selected for studies with HLA-class II tetramers. Peripheral blood mononuclear cells (PBMCs) from patients with ASyS with HLA-DRB1*03:01 (n = 12) were stimulated in vitro with peptide and peptide-HLA-DRB1*03:01 tetramers were used to detect HisRS+CD4+T cells. Single TCR sequencing of captured T cells allowed analyses of the underlying TCR repertoire.\n\nWe identified a new T cell epitope on HisRS with high affinity for HLA-DRB1*03:01. Autoreactive HisRS+CD4+T cells were detected in PBMCs of patients (n = 6/12). TCR repertoire analysis of HisRS+CD4+T cells revealed shared gene V-alpha and beta usages. Moreover, HisRS+CD4+T cells persisted after treatment in 2 patients (P2 and P4) and 2 identical T cell clones were detected between the initial and follow-up time points in 1 patient (P2).\n\nAutoreactive T-cells targeting a new HisRS epitope were identified indicating T cell reactivity to diverse epitopes of the HisRS protein in patients with anti-Jo1 autoantibodies. Furthermore, we demonstrated the TCR repertoire of autoreactive HisRS+CD4+T cells in patients. Persistence of these T-cells and specific clones may be contributing to disease.", "doi": "10.1016/j.ard.2025.09.015", "pmid": "41139557", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-4967(25)04429-2"}], "notes": [], "created": "2025-10-29T10:08:57.216Z", "modified": "2025-11-11T13:53:36.238Z"}, {"entity": "publication", "iuid": "eaf9b454889b42e98966f350d0a69e84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84"}}, "title": "A mosaic of modular variation at a single gene underpins convergent plumage coloration.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Kakhki", "given": "Niloofar Alaei", "initials": "NA"}, {"family": "Lammers", "given": "Fritjof", "initials": "F", "orcid": "0000-0002-3110-8220", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a13a19d3594543a30c5146011aaa3a.json"}}, {"family": "de Souza", "given": "Stacey G", "initials": "SG", "orcid": "0000-0001-6596-5522", "researcher": {"href": "https://publications.scilifelab.se/researcher/63b19ded18de4742b8b0e63408500bc7.json"}}, {"family": "Ducrest", "given": "Anne-Lyse", "initials": "AL", "orcid": "0000-0001-6412-2769", "researcher": {"href": "https://publications.scilifelab.se/researcher/020a4c63ac834ff1a09234094ff552d2.json"}}, {"family": "Burri", "given": "Marta", "initials": "M"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Lukhele", "given": "Sifiso M", "initials": "SM", "orcid": "0000-0003-0638-0641", "researcher": {"href": "https://publications.scilifelab.se/researcher/67a4a265644e452898bd89600ca081d8.json"}}, {"family": "Moysi", "given": "Michaella", "initials": "M"}, {"family": "Yohannes", "given": "Elizabeth", "initials": "E"}, {"family": "Abbasov", "given": "Abdin", "initials": "A", "orcid": "0009-0002-6370-9167", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8b1ae2193849cc956e9750bfc47ead.json"}}, {"family": "Albayrak", "given": "Tamer", "initials": "T", "orcid": "0000-0003-4115-3946", "researcher": {"href": "https://publications.scilifelab.se/researcher/36f1ec59f0da42d89af256efda6c7db5.json"}}, {"family": "Aliabadian", "given": "Mansour", "initials": "M", "orcid": "0000-0002-3200-4853", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf133d36d2ec42bba680538cd5e69151.json"}}, {"family": "Auchli", "given": "Nicolas", "initials": "N"}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Christoforou", "given": "Ioulios", "initials": "I"}, {"family": "Copete", "given": "Jos\u00e9 Luis", "initials": "JL", "orcid": "0000-0001-8542-0351", "researcher": {"href": "https://publications.scilifelab.se/researcher/e18b36757e804e0fb00a2f13015e79b6.json"}}, {"family": "Fulco", "given": "Egidio", "initials": "E"}, {"family": "Garcia", "given": "Jesus T", "initials": "JT"}, {"family": "Javakhishvili", "given": "Zura", "initials": "Z", "orcid": "0000-0001-7587-4974", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15c16f36f8d407d8b3c69723f6470e2.json"}}, {"family": "Kazazou", "given": "Anna", "initials": "A", "orcid": "0009-0003-6518-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdef2602fe44fd98f1b36f83acde23a.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Paposhvili", "given": "Nika", "initials": "N"}, {"family": "Patchett", "given": "Robert", "initials": "R", "orcid": "0000-0003-4105-3136", "researcher": {"href": "https://publications.scilifelab.se/researcher/787404ed66114f6ca1df945d9110ca8a.json"}}, {"family": "P\u00e9ter", "given": "\u00c1ron", "initials": "\u00c1", "orcid": "0000-0003-3219-9344", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b840805e45a4e0e95ade7ce7d0bdb99.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R", "orcid": "0009-0000-3060-1622", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b0db805e7214250b7df8d01e0803641.json"}}, {"family": "S\u00e1ndor", "given": "Attila D", "initials": "AD", "orcid": "0000-0001-8852-8341", "researcher": {"href": "https://publications.scilifelab.se/researcher/6db813f6be6943cc93dfbb9222bd112f.json"}}, {"family": "Schneider", "given": "Fabian", "initials": "F"}, {"family": "Shurulinkov", "given": "Petar", "initials": "P"}, {"family": "Sklyarenko", "given": "Sergey", "initials": "S", "orcid": "0000-0002-7443-347X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0de4c8591f1b4929ae73d3ea81ca2c17.json"}}, {"family": "Stumberger", "given": "Borut", "initials": "B"}, {"family": "Tagiyev", "given": "Abulfaz", "initials": "A"}, {"family": "Uboldi", "given": "Alessia", "initials": "A", "orcid": "0009-0001-3940-3697", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c73538105e441eb6a5402ad0883799.json"}}, {"family": "Vogiatzis", "given": "Nikitas", "initials": "N", "orcid": "0009-0008-9592-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be0f74759fd4d429c3cb891c51d6e83.json"}}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Yao", "given": "Liqun", "initials": "L"}, {"family": "Peichel", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-7731-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4d7c680f69458dbde56257ff4820c5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Gagnaire", "given": "Pierre-Alexandre", "initials": "PA", "orcid": "0000-0002-1908-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f9487cea1d40938b3f9f00f72e6433.json"}}, {"family": "Kirschel", "given": "Alexander N G", "initials": "ANG", "orcid": "0000-0003-4379-7956", "researcher": {"href": "https://publications.scilifelab.se/researcher/d533e6378c094ef7bf44e570bcbb1145.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Science", "issn": "1095-9203", "volume": "390", "issue": "6770", "pages": "eado8005", "issn-l": "0036-8075"}, "abstract": "The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and their interplay with genetic architecture remain scarce. We show that convergent plumage color evolution in wheatears involves a monogenic architecture with modular variation introgressed at the agouti signaling protein (ASIP) locus. Introgression of a new transposable element insertion and linked protein-coding variation underpin a transspecific throat color polymorphism, which stable isotopes suggest is associated with alternative foraging niches. Cointrogression of linked regulatory ASIP variation resulted in mantle color convergence in one species, whereas convergent color evolution at the genus level required new variation. Our results demonstrate evolutionary trajectories from introgressed variation realized within the constraints of a monogenic architecture.", "doi": "10.1126/science.ado8005", "pmid": "41100596", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-26T14:53:27.788Z", "modified": "2026-01-26T14:53:31.469Z"}, {"entity": "publication", "iuid": "a303b58b4fa1409b9589100fef20ee82", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a303b58b4fa1409b9589100fef20ee82.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a303b58b4fa1409b9589100fef20ee82"}}, "title": "Postnatal sustentacular cells as chromaffin progenitors and tumor cells of origin in VHL-related paragangliomas.", "authors": [{"family": "Bullova", "given": "Petra", "initials": "P"}, {"family": "Cui", "given": "Peng", "initials": "P"}, {"family": "Arceo", "given": "Maria", "initials": "M"}, {"family": "Zhu", "given": "Jiacheng", "initials": "J"}, {"family": "Li", "given": "Wenyu", "initials": "W"}, {"family": "Plescher", "given": "Monika", "initials": "M"}, {"family": "Poltorachenko", "given": "Valentin", "initials": "V"}, {"family": "Stripling", "given": "Katerina", "initials": "K"}, {"family": "Santangeli", "given": "Christian", "initials": "C"}, {"family": "Mykhaylechko", "given": "Lidiya", "initials": "L"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC"}, {"family": "Mints", "given": "Michael", "initials": "M"}, {"family": "Schlisio", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "324", "issn-l": null}, "abstract": "The cellular source of chromaffin cell regeneration after birth and its relationship to paraganglioma tumorigenesis remains incompletely defined. Here, we identify a postnatal population of SOX2/SOX10-expressing sustentacular glia-like cells in the organ of Zuckerkandl (OZ) and adrenal gland that give rise to chromaffin cells in vivo. These cells differ transcriptionally from embryonic chromaffin progenitors known as Schwann cell precursors and exhibit a unique progenitor signature. Genetic lineage tracing confirms their postnatal contribution to chromaffin cells, and SOX2+PHOX2B+ transitional cells were observed in both human and mouse OZ and adrenal tissues. Single-nuclei RNA-seq and inferCNA analysis of pheochromocytoma and paraganglioma (PPGL) revealed that while most sustentacular cells exhibit a stromal profile, a subset in VHL-mutated PPGLs harbor the hallmark 3p chromosomal loss shared with chief tumor cells, suggesting a clonal origin. In an additional PPGL, widespread SOX2 expression in PHOX2B+ tumor cells supports this hypothesis. Finally, DLK1-NOTCH signaling was predicted as a central regulator of chromaffin-sustentacular communication, suggesting DLK1 fine-tunes chromaffin regeneration via NOTCH inhibition and may represent a therapeutic target in PPGL.", "doi": "10.1038/s41698-025-01145-8", "pmid": "41093965", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12528426"}, {"db": "pii", "key": "10.1038/s41698-025-01145-8"}], "notes": [], "created": "2025-11-21T13:44:18.484Z", "modified": "2025-11-28T10:47:30.359Z"}, {"entity": "publication", "iuid": "62196b2aeaf64cffbdc15583c03cd12a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62196b2aeaf64cffbdc15583c03cd12a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62196b2aeaf64cffbdc15583c03cd12a"}}, "title": "Deciphering the determinants of recombinant protein expression across the human secretome.", "authors": [{"family": "Masson", "given": "Helen O", "initials": "HO"}, {"family": "Di Giusto", "given": "Pablo", "initials": "P", "orcid": "0000-0003-1024-1222", "researcher": {"href": "https://publications.scilifelab.se/researcher/443c70edc8054e5c972eea27e8e71883.json"}}, {"family": "Kuo", "given": "Chih-Chung", "initials": "CC"}, {"family": "Malm", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-1763-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c4c6c276dd64fe2abe27da888cd0925.json"}}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Sievertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Grassi", "given": "Luigi", "initials": "L", "orcid": "0000-0002-6308-7540", "researcher": {"href": "https://publications.scilifelab.se/researcher/c006b891dedd483e8f01756f73fd6fb0.json"}}, {"family": "Robasky", "given": "Kimberly", "initials": "K", "orcid": "0000-0002-0090-8698", "researcher": {"href": "https://publications.scilifelab.se/researcher/16439af864534d3bb025acbb1edb933b.json"}}, {"family": "Hsieh", "given": "Chen-Lin", "initials": "CL", "orcid": "0009-0000-9239-8711", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7175e63f7d84a99ac3a2f0b1c49cf88.json"}}, {"family": "Hatton", "given": "Diane", "initials": "D", "orcid": "0000-0002-6600-021X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a947736bdbe4177a909782cea719df8.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Lewis", "given": "Nathan E", "initials": "NE", "orcid": "0000-0001-7700-3654", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8b8fb6dee874a178dd5c9d10d280982.json"}}], "type": "journal article", "published": "2025-10-14", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "41", "pages": "e2506036122", "issn-l": "0027-8424"}, "abstract": "Protein secretion is an essential process of mammalian cells. In biomanufacturing, this process can be optimized to enhance production yields and biotherapeutic quality. While cell line engineering and bioprocess optimization have yielded high protein titers for some recombinant proteins, many remain difficult to express. Here, we investigated factors influencing protein expression in Chinese hamster ovary (CHO) cells, expressing 2,135 Human Secretome Project proteins. While the abundance of mRNA from recombinant proteins explained less than 1% of observed variation in secretion titers, analysis of 218 biochemical and biophysical descriptors uncovered intrinsic protein features that account for ~15% of secretion variability, pinpointing key drivers such as molecular weight, cysteine content, and N-linked glycosylation, and establishing a roadmap for rational design of difficult-to-express proteins. We subsequently analyzed RNA-Seq data from 95 CHO cell cultures, each expressing a distinct recombinant protein, spanning a wide range of titers. Host cell transcriptomic signatures showed strong correlations with titer, thereby providing insights into cellular processes that covary with expression. Cells failing to produce proteins exhibited increased ubiquitin-mediated proteasomal degradation, including ER-associated degradation; whereas high-producing cells demonstrated enhanced lipid metabolism and a stronger response to oxidative stress, suggesting these factors may support successful recombinant protein productions. Together, using this resource, we quantified the contributions of various protein and cellular factors that correlate with the expression of diverse recombinant human proteins in a heterologous host, thereby providing insights for next-generation CHO cell engineering.", "doi": "10.1073/pnas.2506036122", "pmid": "41055974", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2109099"}, {"db": "pmc", "key": "PMC12541331"}], "notes": [], "created": "2025-11-21T09:55:14.036Z", "modified": "2025-11-21T09:55:15.142Z"}, {"entity": "publication", "iuid": "355af91bf856401ab8f7a654af8b92ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/355af91bf856401ab8f7a654af8b92ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/355af91bf856401ab8f7a654af8b92ad"}}, "title": "Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates.", "authors": [{"family": "Papanicolaou", "given": "Natali", "initials": "N", "orcid": "0000-0002-2931-3241", "researcher": {"href": "https://publications.scilifelab.se/researcher/439a0a25106742c893178f4151d71291.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/e282901d24c64b16a540eff0d57776f4.json"}}, {"family": "Wettersten", "given": "Sebastian", "initials": "S"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Kr\u00fcger", "given": "Annika", "initials": "A", "orcid": "0000-0002-2482-0316", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e46d93b561473189588abecdb96f93.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Coucoravas", "given": "Christos", "initials": "C"}, {"family": "Petrosian", "given": "Ioannis", "initials": "I"}, {"family": "Xin", "given": "Xian", "initials": "X", "orcid": "0000-0003-1460-5978", "researcher": {"href": "https://publications.scilifelab.se/researcher/612e837e68e44339b8a9a110beb38125.json"}}, {"family": "Ceyhan", "given": "Ilhan", "initials": "I", "orcid": "0009-0001-9504-6647", "researcher": {"href": "https://publications.scilifelab.se/researcher/c79c334d1b6747159586eca778e2f2df.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb82c502293d424cb266e1c4e405485f.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9088", "issn-l": "2041-1723"}, "abstract": "Sex-chromosome dosage poses a challenge for heterogametic species in maintaining the proper balance of gene products across chromosomes in each sex. While therian mammals (XX/XY system) achieve near-perfect balance of X-chromosome mRNAs through X-upregulation and X-inactivation, birds (ZW/ZZ system) have been found to lack efficient compensation at RNA level, challenging the necessity of resolving major gene-dosage asymmetries in avian cells. Through comprehensive allele-resolved multiome analyses, we examine dosage compensation in female (ZW), male (ZZ), and rare intersex (ZZW) chicken. Our data reveal that females upregulate their single Z chromosome through increased transcriptional burst frequency, mirroring mammalian X upregulation. Z-protein levels are further balanced in females through enhanced translation efficiency. Additionally, we present a global analysis of promoter elements regulating transcriptional burst kinetics in birds, revealing evolutionary conservation of the genomic encoding of burst kinetics between birds and mammals. Our study provides insights into the regulation of avian dosage compensation, and when considering all regulatory layers collectively, an unexpected similarity between avian and mammalian dosage compensation becomes apparent.", "doi": "10.1038/s41467-025-64817-w", "pmid": "41083481", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12518621"}, {"db": "pii", "key": "10.1038/s41467-025-64817-w"}], "notes": [], "created": "2025-12-08T12:39:47.612Z", "modified": "2025-12-08T12:39:48.467Z"}, {"entity": "publication", "iuid": "e79753171cfe4a2a9fd9b888316e8540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e79753171cfe4a2a9fd9b888316e8540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e79753171cfe4a2a9fd9b888316e8540"}}, "title": "Exposure to marine contaminant mixtures with different toxicity drivers reduces microzooplankton diversity.", "authors": [{"family": "J\u00f6nander", "given": "Christina", "initials": "C"}, {"family": "Egardt", "given": "Jenny", "initials": "J"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Spilsbury", "given": "Francis", "initials": "F"}, {"family": "Carmona", "given": "Eric", "initials": "E"}, {"family": "Inostroza", "given": "Pedro A", "initials": "PA"}, {"family": "Brack", "given": "Werner", "initials": "W"}, {"family": "Dahll\u00f6f", "given": "Ingela", "initials": "I", "orcid": "0000-0002-0777-5971", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c6230703491493eb35a7610d0299d8d.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "11", "issn-l": "0168-6496"}, "abstract": "Marine surface waters contain complex mixtures of chemicals that can adversely affect microzooplankton. There is a lack of toxicity data for this organism group, and we used two different methodologies to fill this gap. We tested the toxicity of three chemical mixtures of polar organic chemicals extracted from marine surface water, using a component-based and a whole-mixture approach. The component-based approach estimates cumulative toxic units for each mixture based on concentrations of individual compounds. The observed hazard data for zooplankton was supplemented with ECOSAR-generated QSAR daphnid LC50s when observed data was missing. ECOSAR performance was evaluated for zooplankton, where 65% of the observed hazard data for zooplankton was predicted within a factor of 10. This approach suggested that none of the mixtures should be toxic to zooplankton at their respective measured environmental concentrations. We found contrasting results using the whole-mixture approach with a reduction in ciliates and dinoflagellates, and change in microzooplankton diversity, at the measured environmental concentrations. We suggest an assessment factor of at least 1000 when using additive toxic units in a component-based risk assessment approach to cover for the extrapolation from acute to chronic toxicity data and for the range of sensitivities among microzooplankton species.", "doi": "10.1093/femsec/fiaf102", "pmid": "41070938", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12551639"}, {"db": "pii", "key": "8280373"}], "notes": [], "created": "2025-11-28T10:48:55.458Z", "modified": "2025-12-05T12:21:44.926Z"}, {"entity": "publication", "iuid": "2df9d60e4f3b4842ab27975ddc213a7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2df9d60e4f3b4842ab27975ddc213a7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2df9d60e4f3b4842ab27975ddc213a7e"}}, "title": "Evolution of female ornamentation in dance flies: valuable gifts are worth dressing up for.", "authors": [{"family": "P\u00e4rssinen", "given": "Varpu", "initials": "V", "orcid": "0000-0002-9189-9765", "researcher": {"href": "https://publications.scilifelab.se/researcher/84abea496e734734a215964cf9e27782.json"}}, {"family": "Bussi\u00e8re", "given": "Luc F", "initials": "LF"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Wahlberg", "given": "Emma", "initials": "E"}, {"family": "LeBas", "given": "Natasha R", "initials": "NR"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Kvarnemo", "given": "Charlotta", "initials": "C", "orcid": "0000-0001-8983-2900", "researcher": {"href": "https://publications.scilifelab.se/researcher/914d1337967942d8a3790e47e5b5d86b.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "Evolution", "issn": "1558-5646", "issn-l": "0014-3820"}, "abstract": "Elaborate female ornaments are rare in nature. One explanation for this is that female investment in ornamentation may take away crucial resources from other costly life history traits, such as fecundity, for which there is likely to be a higher fitness return. However, this trade-off between ornaments and fecundity may be less severe in species where the males offer the female an edible nuptial gift during mating. The nutrition gained from mating may make attracting mates with elaborate ornaments more cost-effective for the female. We investigated this link in dance flies in which there is large variation in nuptial gifts, as well as female ornaments. Our phylogenetic analysis showed that nuptial gift value is positively associated with the evolution of female ornaments. We found that species which lack nuptial gifts have no ornaments, and high levels of female ornamentation has evolved most frequently in species with a reliable access to an edible nuptial gift with each mating. Our results also suggest that female ornaments have most likely evolved following the evolution of nuptial gifts. We argue that the added benefits from each mating have helped the females to overcome the costs associated with the development and maintenance of ornaments.", "doi": "10.1093/evolut/qpaf212", "pmid": "41081749", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8284989"}], "notes": [], "created": "2025-12-05T11:34:02.049Z", "modified": "2025-12-05T11:34:02.317Z"}, {"entity": "publication", "iuid": "cbf0674bfb9641a5b13df8dc2fc4a132", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbf0674bfb9641a5b13df8dc2fc4a132.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbf0674bfb9641a5b13df8dc2fc4a132"}}, "title": "Long-term warming raises risks of seasonal seafloor methane release in the coastal Baltic Sea.", "authors": [{"family": "Li", "given": "Songjun", "initials": "S"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "Chang", "given": "Cheng", "initials": "C"}, {"family": "Rula", "given": "Iryna", "initials": "I"}, {"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Svendsen", "given": "Ida Krogsgaard", "initials": "IK"}, {"family": "Forsman", "given": "Anders", "initials": "A"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1636301", "issn-l": "1664-302X"}, "abstract": "Climate change driven ocean warming is a worldwide environmental issue that can impact cycling of greenhouse gases. However, how methane production in marine sediments as a potential contributor to atmospheric greenhouse gases versus its consumption at the sulfate-methane transition zone will be affected by climate change related warming is still not well constrained. In this study, sediments from two Baltic Sea bays with long-term temperature differences were collected during summer and winter. The primary difference between the two bays was that one had been heated by a nearby power plant for 50 years, resulting in a 5.1 \u00b0C increase in annual average temperature compared to an unheated control bay. The results showed that near-seafloor sediment methane concentrations were 50 times higher compared to present-day conditions. Furthermore, the sediment fluxes along with microbial community composition changes suggested that long-term warming may thin the sulfate reduction zone, such that methanotrophic archaea and sulfate reducing bacteria peaked at shallower sediment depths in the heated bay. Overall, the results from long-term warming in natural sediment environment indicated that future climate change warming may increase the risk of methane release to the water and eventually the atmosphere.", "doi": "10.3389/fmicb.2025.1636301", "pmid": "41127623", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12537722"}], "notes": [], "created": "2025-11-21T15:33:15.108Z", "modified": "2025-11-28T10:54:29.001Z"}, {"entity": "publication", "iuid": "c783ffc03b364c5c97b3c8c519bf55a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c783ffc03b364c5c97b3c8c519bf55a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c783ffc03b364c5c97b3c8c519bf55a7"}}, "title": "Autoimmunity-associated DIORA1 binds the MRCK family of serine/threonine kinases and controls cell motility.", "authors": [{"family": "Tr\u0161eli\u010d", "given": "Tilen", "initials": "T", "orcid": "0009-0006-0316-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d50c0b7e88d4033b14afdc5ea254801.json"}}, {"family": "Pelo", "given": "Nathalie", "initials": "N"}, {"family": "Martin de Fremont", "given": "Gregoire", "initials": "G", "orcid": "0000-0003-3393-3969", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e1b9b6db64f4fdb9ab8b6eab5eb59ba.json"}}, {"family": "Iyer", "given": "Vaishnavi S", "initials": "VS"}, {"family": "Richardsdotter Andersson", "given": "Elina", "initials": "E", "orcid": "0009-0003-7008-529X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ff0a7a67ed4fdfb5135c2e33c429ab.json"}}, {"family": "Ottosson", "given": "Vijole", "initials": "V", "orcid": "0009-0003-6530-9033", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f0ee7dd68e3411db6975ec7aac67b16.json"}}, {"family": "Frei", "given": "David Alexander", "initials": "DA"}, {"family": "Baas", "given": "Elisa", "initials": "E", "orcid": "0009-0002-0587-7242", "researcher": {"href": "https://publications.scilifelab.se/researcher/a658fbfac5c74616ac5797b2330ae50a.json"}}, {"family": "Nyberg", "given": "William A", "initials": "WA"}, {"family": "Thorlacius", "given": "Gu\u00f0n\u00fd Ella", "initials": "GE"}, {"family": "Mentlein", "given": "Lara", "initials": "L"}, {"family": "Boddul", "given": "Sanjaykumar V", "initials": "SV", "orcid": "0000-0002-0711-1147", "researcher": {"href": "https://publications.scilifelab.se/researcher/312d8252d0c24f0583512c950504afa9.json"}}, {"family": "Sandu", "given": "Ioana", "initials": "I"}, {"family": "Velasquez Pulgarin", "given": "Diego", "initials": "D"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Gerlach", "given": "Carmen", "initials": "C", "orcid": "0000-0001-7889-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/893fad4751a6411392488c5e37c0aa13.json"}}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}, {"family": "Sunnerhagen", "given": "Maria", "initials": "M"}, {"family": "Wallner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Espinosa", "given": "Alexander", "initials": "A"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}], "type": "journal article", "published": "2025-10-07", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "40", "pages": "e2426917122", "issn-l": "0027-8424"}, "abstract": "Genetic association links disordered autoimmunity 1 (DIORA1) to numerous autoimmune rheumatic diseases, including systemic lupus erythematosus, Sj\u00f6gren's disease, rheumatoid arthritis, polymyositis, and systemic sclerosis. However, its cellular function has remained unknown. Here, we identify the Myotonic Dystrophy Kinase-Related Cdc42-Binding Kinases (MRCK kinases) family of serine/threonine kinases-key regulators of actomyosin contractility and cell motility-as direct interactors of DIORA1. Through interaction mapping, we show that DIORA1 binds three distinct modules of MRCK kinases, including the conserved kinase inhibitory motif, C1-PH, and citron homology domains. DIORA1 knockdown in human cells altered cellular phosphorylation patterns and reduced phosphorylation of known MRCK targets. RNA-sequencing and proteomic analyses revealed upregulation of epithelial-mesenchymal transition genes and proteins, and functional analyses confirmed increased cell invasion, following knockdown of DIORA1. Together, these findings identify the autoimmunity-associated DIORA1 protein as an interactor of MRCK kinases and a regulator of cell motility.", "doi": "10.1073/pnas.2426917122", "pmid": "41042840", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12519202"}], "notes": [], "created": "2025-11-21T17:57:08.724Z", "modified": "2025-11-21T17:57:09.957Z"}, {"entity": "publication", "iuid": "379697221e864158b23905f98efc1f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/379697221e864158b23905f98efc1f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/379697221e864158b23905f98efc1f8a"}}, "title": "Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A"}, {"family": "Pacheco-Valenciana", "given": "Armando", "initials": "A"}, {"family": "Milke", "given": "Felix", "initials": "F"}, {"family": "Dharamshi", "given": "Jennah E", "initials": "JE"}, {"family": "Hampel", "given": "Justyna J", "initials": "JJ"}, {"family": "Damashek", "given": "Julian", "initials": "J"}, {"family": "Wienhausen", "given": "Gerrit", "initials": "G"}, {"family": "Rodriguez-R", "given": "Luis Miguel", "initials": "LM"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "34482", "issn-l": "2045-2322"}, "abstract": "Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.", "doi": "10.1038/s41598-025-22383-7", "pmid": "41044404", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12495000"}, {"db": "pii", "key": "10.1038/s41598-025-22383-7"}], "notes": [], "created": "2025-11-19T07:34:55.667Z", "modified": "2025-11-28T10:47:04.484Z"}, {"entity": "publication", "iuid": "107c7b3b512c45f686868f13aff2dfd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/107c7b3b512c45f686868f13aff2dfd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/107c7b3b512c45f686868f13aff2dfd8"}}, "title": "Innate immune cell subsets are enriched in synovial fluid of ACPA-negative rheumatoid arthritis and characterized by distinct type I IFN gene signatures.", "authors": [{"family": "Argyriou", "given": "Alexandra", "initials": "A"}, {"family": "Wadsworth", "given": "Marc H", "initials": "MH"}, {"family": "Fienman", "given": "Joshua", "initials": "J"}, {"family": "Gonzalez-Sanchez", "given": "Ana Cristina", "initials": "AC"}, {"family": "Ghannoum", "given": "Salim", "initials": "S"}, {"family": "Krishna", "given": "Chirag", "initials": "C"}, {"family": "Gerstner", "given": "Christina", "initials": "C"}, {"family": "Horuluoglu", "given": "Begum", "initials": "B"}, {"family": "Sijbranda", "given": "Merel", "initials": "M"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Hensvold", "given": "Aase", "initials": "A"}, {"family": "Turcinov", "given": "Sara", "initials": "S"}, {"family": "Winkler", "given": "Aaron", "initials": "A"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Chemin", "given": "Karine", "initials": "K"}], "type": "journal article", "published": "2025-10-03", "journal": {"title": "Ann. Rheum. Dis.", "issn": "1468-2060", "issn-l": "0003-4967"}, "abstract": "Around 30% of patients with rheumatoid arthritis (RA) lack rheumatoid factor and anti-citrullinated protein antibodies (ACPA) complicating diagnosis and potentially delaying treatment. We hypothesised that innate immune mechanisms might be more prominent in ACPA- RA.\n\nWe performed single-cell RNA sequencing of mononuclear cells from peripheral blood (PBMC) and synovial fluid (SFMC) of patients with ACPA- and ACPA+ RA (n = 4 per group: discovery cohort; n = 8 per group: validation cohort). Dendritic cells and proinflammatory cytokine production were analysed by flow cytometry on SFMC from patients with ACPA- RA, ACPA+ RA, and psoriatic arthritis. Interferon (IFN) levels in synovial fluid (SF) and serum were measured in these groups.\n\nSeveral macrophage subsets and cDC2 were enriched in ACPA- RA SF whereas the frequency of Tph and B cells was increased in ACPA+ RA SF. Type I IFN-stimulated genes were detected in SFMC, but not PBMC, of patients with ACPA- RA. A type I IFN signature was also observed in synovial tissue from two patients with ACPA- RA in an independent dataset. IFN levels were higher in SF than serum but IFN-\u03b1/\u03b2 production did not differ between ACPA+ and ACPA- RA.\n\nThis study identifies a distinct innate cell composition and type I IFN gene response in synovial joints, but not in peripheral blood, of patients with ACPA- RA. Similar IFN levels across groups suggest the IFN signature may have been primed before the cells entered the joints. These findings provide a foundation for future research on type I IFN responses in ACPA- RA.", "doi": "10.1016/j.ard.2025.07.029", "pmid": "41046204", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pii", "key": "S0003-4967(25)04299-2"}], "notes": [], "created": "2025-11-19T07:45:45.847Z", "modified": "2025-11-19T07:45:45.871Z"}, {"entity": "publication", "iuid": "dda4cd13d28c4f27989bed1cf9560b63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dda4cd13d28c4f27989bed1cf9560b63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dda4cd13d28c4f27989bed1cf9560b63"}}, "title": "Decoding the genetic drivers of marine bacterial blooms through comparative genomics.", "authors": [{"family": "Rey-Velasco", "given": "Xavier", "initials": "X"}, {"family": "Auladell", "given": "Adri\u00e0", "initials": "A"}, {"family": "Deulofeu-Capo", "given": "Ona", "initials": "O"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Ferrera", "given": "Isabel", "initials": "I"}, {"family": "S\u00e1nchez", "given": "Olga", "initials": "O"}, {"family": "Gasol", "given": "Josep M", "initials": "JM"}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "Microbiome", "issn": "2049-2618", "volume": "13", "issue": "1", "pages": "198", "issn-l": "2049-2618"}, "abstract": "While oligotrophic bacteria are known to dominate most marine microbial habitats, under certain conditions, such as during phytoplankton blooms, copiotrophs can dramatically increase in abundance and reach towering proportions of the bacterial communities. We are uncertain whether the bacteria exhibiting this capacity, which we denote as \"bloomers,\" have specific functional characteristics or if, instead, they are randomly selected from the broader pool of copiotrophs. To explore the genomic determinants of this ecological trait, we conducted a comparative genomic analysis of bacterial genomes from microcosm experiments where grazer and viral presence was reduced and nutrient availability was increased, conditions that triggered bacterial blooms.\n\nWe tested which functional genes were overrepresented in the bacteria that responded to the treatments, examining a total of 305 genomes from isolates and metagenome-assembled genomes (MAGs) that were categorized as copiotrophs or oligotrophs according to their codon usage bias (CUB). The responsive bacteria were enriched in genes related to transcriptional regulation in response to stimuli (mostly via two-component systems), transport, secretion, cell protection, catabolism of sugars and amino acids, and membrane/cell wall biosynthesis. These genes confer on them capabilities for adhesion, biofilm formation, resistance to stress, quorum sensing, chemotaxis, nutrient uptake, and fast replication. They were overrepresented mainly in copiotrophic genomes from the families Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, Sphingomonadaceae, and Flavobacteriaceae. Additionally, we found that these responsive bacteria, when abundant, could affect biogeochemical cycling, particularly the phosphorus cycle.\n\nIn this study, we provide insights into the functional characteristics that enable certain bacteria to rapidly respond to changes in the environment and bloom. We also hint at the ecological meaning and implications of these phenomena that could affect biogeochemical cycles in the oceans. Video Abstract.", "doi": "10.1186/s40168-025-02182-y", "pmid": "41029845", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12487129"}, {"db": "pii", "key": "10.1186/s40168-025-02182-y"}], "notes": [], "created": "2025-11-21T13:50:47.554Z", "modified": "2025-11-21T13:53:54.255Z"}, {"entity": "publication", "iuid": "04e9d7eb6fd041648cef2ac003bdaae7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e9d7eb6fd041648cef2ac003bdaae7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e9d7eb6fd041648cef2ac003bdaae7"}}, "title": "Chromosome-level assembly of the club-legged grasshopper (Gomphocerus sibiricus) genome.", "authors": [{"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Varma", "given": "Mahendra", "initials": "M"}, {"family": "Cheng", "given": "Xinyi", "initials": "X"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}], "type": "journal article", "published": "2025-10-01", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836"}, "abstract": "Grasshoppers represent true outliers in genome sizes, both within insects and within animals in general. Their genomes are large and generally variable in sizes and feature a high abundance of repetitive DNA sequences. This has hampered the assembly of grasshopper genomes to chromosome level. Here we present a chromosome-level reference genome for the club-legged grasshopper (Gomphocerus sibiricus, Acrididae: Gomphocerinae) using PacBio HiFi long-read and Hi-C sequencing technologies. In male haploid cells, the species has a chromosome set of n = 9 with an X0 sex-determination system, characterized by an absence of a Y chromosome. Our assembly spans 9.57 Gb in total, with 8.87 Gb organized into nine chromosomes-eight autosomes and the X chromosome. The final assembly has a scaffold N50 value of 1.58 Gb, covers 96.7% single copy Insecta orthologs, and contains 42,665 predicted protein-coding genes and 43,385 mRNA transcripts. We compiled a curated, non-redundant, species-specific repeat library and used it to annotate repetitive DNA, covering 81.69% of the genome, mostly DNA transposons, LINE and LTR retrotransposons. The genome of the club-legged grasshopper shows high degree of synteny with the locusts Schistocerca gregaria and Locusta migratoria, and the analysis strongly indicates three autosome-autosome centric fusions in Gomphocerinae. The genome offers a valuable resource for grasshopper genomics and for exploring the genetic basis of a transspecies color polymorphism.", "doi": "10.1093/g3journal/jkaf231", "pmid": "41029998", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "8269502"}], "notes": [], "created": "2025-10-03T08:05:05.113Z", "modified": "2025-11-14T11:07:48.365Z"}, {"entity": "publication", "iuid": "c9fda46a5deb4048a04ccbe376a95bed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9fda46a5deb4048a04ccbe376a95bed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9fda46a5deb4048a04ccbe376a95bed"}}, "title": "Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals.", "authors": [{"family": "More", "given": "Kuldeep D", "initials": "KD", "orcid": "0000-0002-8278-8086", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b7cfdaad6614e6986ddd3a9c25434c4.json"}}, {"family": "Lebrasseur", "given": "Oph\u00e9lie", "initials": "O", "orcid": "0000-0003-0687-8538", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f100bd635446739f54bcabbf1840bc.json"}}, {"family": "Garrido", "given": "Jaime Lira", "initials": "JL", "orcid": "0000-0002-0702-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/03c72a8c91e04eb5bd580f999435809e.json"}}, {"family": "Seguin-Orlando", "given": "Andaine", "initials": "A", "orcid": "0000-0002-8265-3229", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f62251e48e34acdb3bea43f1f88c415.json"}}, {"family": "Discamps", "given": "Emmanuel", "initials": "E", "orcid": "0000-0002-2464-0761", "researcher": {"href": "https://publications.scilifelab.se/researcher/d53686becfbd4e919aac22195bbc80c0.json"}}, {"family": "Estrada", "given": "Oscar", "initials": "O"}, {"family": "Tonasso-Calvi\u00e8re", "given": "Laure", "initials": "L"}, {"family": "Chauvey", "given": "Lorele\u00ef", "initials": "L"}, {"family": "Tressi\u00e8res", "given": "Ga\u00ebtan", "initials": "G"}, {"family": "Schiavinato", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Gibert", "given": "Morgane", "initials": "M"}, {"family": "Padula", "given": "Horacio", "initials": "H"}, {"family": "Chiavazza", "given": "Horacio", "initials": "H"}, {"family": "Fern\u00e1ndez", "given": "Pablo M", "initials": "PM"}, {"family": "Guardia", "given": "Nicol\u00e1s M", "initials": "NM"}, {"family": "Borges", "given": "Caroline", "initials": "C"}, {"family": "Bertani", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0002-0398-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3e67c04c53c4dc49da8cfb7d77d1492.json"}}, {"family": "Contreras-Mancilla", "given": "Juan", "initials": "J"}, {"family": "Allccarima-Cris\u00f3stomo", "given": "Diana", "initials": "D"}, {"family": "Fhon", "given": "Miguel", "initials": "M"}, {"family": "Barrey", "given": "Eric", "initials": "E", "orcid": "0000-0001-7691-8705", "researcher": {"href": "https://publications.scilifelab.se/researcher/80fc1e75ebc848bd855bab192930fc5d.json"}}, {"family": "Charliquart", "given": "L\u00e9a", "initials": "L"}, {"family": "Robbe", "given": "Emilie", "initials": "E"}, {"family": "de Noblet", "given": "Thibault", "initials": "T"}, {"family": "Zhumatayev", "given": "Rinat", "initials": "R"}, {"family": "Shakenov", "given": "Samat", "initials": "S"}, {"family": "Vila", "given": "Emmanuelle", "initials": "E", "orcid": "0000-0002-2238-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb48894d055d4413a26c6f196f35497e.json"}}, {"family": "Berthon", "given": "R\u00e9mi", "initials": "R"}, {"family": "Mashkour", "given": "Marjan", "initials": "M", "orcid": "0000-0003-3630-9459", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d45bd37c43f4f7fba2c62c9a26e18c7.json"}}, {"family": "Khazaeli", "given": "Roya", "initials": "R"}, {"family": "Nikgoftar", "given": "Ahmad", "initials": "A"}, {"family": "Vahdati", "given": "Ali A", "initials": "AA"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Houle", "given": "Jean-Luc", "initials": "JL", "orcid": "0000-0001-6711-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4700112eee4f10b7175311f42e5f6b.json"}}, {"family": "Bayarsaikhan", "given": "Jamsranjav", "initials": "J"}, {"family": "Wilczynski", "given": "Jaroslaw", "initials": "J"}, {"family": "Moskal-Del Hoyo", "given": "Magdalena", "initials": "M"}, {"family": "Nowak", "given": "Marek", "initials": "M"}, {"family": "Taylor", "given": "William", "initials": "W"}, {"family": "B\u0103l\u0103\u0219escu", "given": "Adrian", "initials": "A"}, {"family": "Dobrescu", "given": "Roxana", "initials": "R"}, {"family": "Benecke", "given": "Norbert", "initials": "N"}, {"family": "Arbuckle", "given": "Benjamin", "initials": "B"}, {"family": "Steadman", "given": "Sharon", "initials": "S"}, {"family": "McMahon", "given": "Gregory", "initials": "G"}, {"family": "\u0160ikanji\u0107", "given": "Petra Raji\u0107", "initials": "PR"}, {"family": "Buric", "given": "Marcel", "initials": "M"}, {"family": "Vuki\u010devi\u0107", "given": "Tajana Trbojevi\u0107", "initials": "TT"}, {"family": "Alvarez", "given": "Nadir", "initials": "N", "orcid": "0000-0002-0729-166X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b080976b224f75a61355bdefebe911.json"}}, {"family": "Castel", "given": "Jean-Christophe", "initials": "JC", "orcid": "0000-0002-2366-5596", "researcher": {"href": "https://publications.scilifelab.se/researcher/a75c23a0ef934486b6fa1d7015445d55.json"}}, {"family": "Boudadi-Maligne", "given": "Myriam", "initials": "M", "orcid": "0000-0003-0583-7419", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9a675a1af44c3481db66d66656f472.json"}}, {"family": "Star", "given": "Bastiaan", "initials": "B", "orcid": "0000-0003-0235-9810", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4edcdfadd284a8e9b6b474ff34fd424.json"}}, {"family": "Post-Melbye", "given": "Julian Robert", "initials": "JR"}, {"family": "R\u00f8dsrud", "given": "Christian L\u00f8chsen", "initials": "CL"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Charlton", "given": "Sophy", "initials": "S", "orcid": "0000-0001-7487-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/32089b9969b243e8b197a9f37ffd63a3.json"}}, {"family": "Mullin", "given": "Victoria E", "initials": "VE"}, {"family": "Daly", "given": "Kevin G", "initials": "KG", "orcid": "0000-0002-5579-6144", "researcher": {"href": "https://publications.scilifelab.se/researcher/7853932330d3450d892199f99cddc921.json"}}, {"family": "Burgos", "given": "Nohemi Sala", "initials": "NS"}, {"family": "Pablos", "given": "Adrian", "initials": "A"}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bradley", "given": "Daniel G", "initials": "DG", "orcid": "0000-0001-7335-7092", "researcher": {"href": "https://publications.scilifelab.se/researcher/9598208f97ac4a76816859659695e1e3.json"}}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Orlando", "given": "Ludovic", "initials": "L", "orcid": "0000-0003-3936-1850", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca463500fb034711b6200d5b611e4c1d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "25", "issue": "7", "pages": "e14112", "issn-l": "1755-098X"}, "abstract": "In the last three decades, DNA sequencing of ancient animal osteological assemblages has become an important tool complementing standard archaeozoological approaches to reconstruct the history of animal domestication. However, osteological assemblages of key archaeological contexts are not always available or do not necessarily preserve enough ancient DNA for a cost-effective genetic analysis. Here, we develop an in-solution target-enrichment approach, based on 80-mer species-specific RNA probes (ranging from 306 to 1686 per species) to characterise (in single experiments) the mitochondrial genetic variation from eight domesticated animal species of major economic interest: cattle, chickens, dogs, donkeys, goats, horses, pigs and sheep. We also illustrate how our design can be adapted to enrich DNA library content and map the Y-chromosomal diversity within Equus caballus. By applying our target-enrichment assay to an extensive panel of ancient osteological remains, farm soil, and cave sediments spanning the last 43 kyrs, we demonstrate that minimal sequencing efforts are necessary to exhaust the DNA library complexity and to characterise mitogenomes to an average depth-of-coverage of 19.4 to 2003.7-fold. Our assay further retrieved horse mitogenome and Y-chromosome data from Late Pleistocene coprolites, as well as bona fide mitochondrial sequences from species that were not part of the probe design, such as bison and cave hyena. Our methodology will prove especially useful to minimise costs related to the genetic analyses of maternal and paternal lineages of a wide range of domesticated and wild animal species, and for mapping their diversity changes over space and time, including from environmental samples.", "doi": "10.1111/1755-0998.14112", "pmid": "40202701", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12415940"}], "notes": [], "created": "2026-02-26T11:49:10.191Z", "modified": "2026-02-26T11:49:11.976Z"}, {"entity": "publication", "iuid": "6ecf241cbd074ff794e16d5e6386bd62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ecf241cbd074ff794e16d5e6386bd62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ecf241cbd074ff794e16d5e6386bd62"}}, "title": "Spatial transcriptomics exploration of the primary neuroblastoma microenvironment in archived FFPE samples unveils novel paracrine interactions.", "authors": [{"family": "Siaw", "given": "Joachim T", "initials": "JT", "orcid": "0000-0002-1286-4485", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a4ce00b5a4b4ebb9ee746de59e2e943.json"}}, {"family": "Merseburger", "given": "Peter", "initials": "P", "orcid": "0000-0002-5154-8696", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0a5677b41b4ffcb46c4e2ce9303e72.json"}}, {"family": "Boren\u00e4s", "given": "Marcus", "initials": "M", "orcid": "0009-0007-6326-5224", "researcher": {"href": "https://publications.scilifelab.se/researcher/9157baf8e62947f8995c484d3cfb93f1.json"}}, {"family": "Jansson", "given": "Caroline", "initials": "C", "orcid": "0009-0001-4115-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d696fca9d64a9f841c0ad59d454156.json"}}, {"family": "Karlsson", "given": "Jenny", "initials": "J", "orcid": "0000-0001-7681-0059", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2ccecaff1d41bfa863dde6616eeadd.json"}}, {"family": "Claeys", "given": "Arne", "initials": "A", "orcid": "0000-0001-6990-1569", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3e7d3acc40b47bd8c5bc8313499dd61.json"}}, {"family": "Jennische", "given": "Eva", "initials": "E", "orcid": "0000-0002-2147-8412", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bc34c602c73456585a2a5815637ebb3.json"}}, {"family": "Lind", "given": "Dan E", "initials": "DE", "orcid": "0000-0002-8299-5659", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ba0b43eeb64fc28393a871fb507ca2.json"}}, {"family": "Gisselsson Nord", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "Palmer", "given": "Ruth H", "initials": "RH", "orcid": "0000-0002-2735-8470", "researcher": {"href": "https://publications.scilifelab.se/researcher/808281ecc2634b66a274895e58a122bd.json"}}, {"family": "Van den Eynden", "given": "Jimmy", "initials": "J", "orcid": "0000-0003-0002-5614", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b20f02703024987bc9791df1dc80e51.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "J. Pathol.", "issn": "1096-9896", "volume": "267", "issue": "2", "pages": "181-195", "issn-l": "0022-3417"}, "abstract": "High-risk neuroblastomas exhibit a high degree of intratumoral heterogeneity. Single-cell RNA sequencing has greatly improved our understanding of these tumors, but the method lacks cellular tissue context and spatial information about local signaling dynamics. To address this, we profiled untreated and chemotherapy-treated high-risk neuroblastomas from archived, formalin-fixed, paraffin-embedded (FFPE) tissues from two patients using spatial transcriptomics. We confirmed the transcriptional and cellular heterogeneous nature of the neuroblastoma microenvironment and identified several unique spatial niches and patterns. In one of the treated tumors, a spatially constrained cluster of undifferentiated and 11p-gained cancer cells was identified, surrounded by a rim of macrophages. A signaling interaction between the chemokine CCL18 and its receptor PITPNM3 was predicted between these cells. In the other tumor, we identified a stromal cluster with high transcriptional similarity to the adrenal cortex. These adrenocortical-like cells expressed several oncogenic ligand-encoding genes (e.g. ALKAL2 and NRTN), which were predicted to communicate with neighboring cancer cells that expressed the corresponding receptors (e.g. ALK, RET). Several of these interactions were further validated experimentally and were shown to be clinically relevant. Collectively, our spatial analysis identifies multiple previously unrecognized signaling axes that may offer novel therapeutic options in neuroblastoma. \u00a9 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.", "doi": "10.1002/path.6457", "pmid": "40778592", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12438011"}], "notes": [], "created": "2025-08-29T10:01:28.113Z", "modified": "2025-11-28T10:40:36.891Z"}, {"entity": "publication", "iuid": "2277209cfb104c25a0c16a2adf69d785", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2277209cfb104c25a0c16a2adf69d785.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2277209cfb104c25a0c16a2adf69d785"}}, "title": "An injury-associated lobular microniche is associated with the classical tumor cell phenotype in pancreatic cancer.", "authors": [{"family": "S\u00f6derqvist", "given": "Sara", "initials": "S"}, {"family": "Viljamaa", "given": "Annika", "initials": "A", "orcid": "0009-0002-8511-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/7db15c31004649d4b3f7bc965cd2e738.json"}}, {"family": "Geyer", "given": "Natalie", "initials": "N"}, {"family": "Keller", "given": "Anna-Lena", "initials": "A"}, {"family": "Ruksha", "given": "Kseniya", "initials": "K"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Hekmati", "given": "Neda", "initials": "N"}, {"family": "Niculae", "given": "Alexandra", "initials": "A"}, {"family": "Engstrand", "given": "Jennie", "initials": "J", "orcid": "0000-0003-1123-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef6292473b94b3b90e78745841cdeaa.json"}}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Salm\u00e9n", "given": "Caroline", "initials": "C"}, {"family": "Costa", "given": "T\u00e2nia D F", "initials": "TDF", "orcid": "0000-0002-6296-5225", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d1862cdeabd47bcaafcafd47bff7a5c.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Str\u00f6mblad", "given": "Staffan", "initials": "S", "orcid": "0000-0002-1236-6339", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4ef16afaed741f4851f1591d3005882.json"}}, {"family": "Zacharouli", "given": "Argyro", "initials": "A"}, {"family": "Ghorbani", "given": "Poya", "initials": "P"}, {"family": "Harrizi", "given": "Sara", "initials": "S"}, {"family": "Hamidi", "given": "Yousra", "initials": "Y"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O", "orcid": "0009-0001-0786-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ada08b5ada04dfb8e948e0873ccf07d.json"}}, {"family": "Milanova", "given": "Stefina", "initials": "S"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Boz\u00f3ky", "given": "B\u00e9la", "initials": "B"}, {"family": "Fern\u00e1ndez Moro", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6863-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/216d382919954ccfb4b47458bb3d9b08.json"}}, {"family": "Gerling", "given": "Marco", "initials": "M", "orcid": "0000-0002-1810-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f9aa5d37124e379eb160737d657bab.json"}}], "type": "journal article", "published": "2025-09-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "8307"}, "abstract": "Pancreatic cancer is an aggressive disease with a dense fibrotic stroma and is often accompanied by chronic inflammation. Peritumoral inflammation is typically viewed as a reaction to nearby tumor growth. Here, we report that the inflamed pancreatic lobules are frequently invaded by tumor cells, forming a distinct, non-fibrotic tumor niche. Using a semi-supervised machine learning approach for annotations of clinical samples and multiplex protein profiling, we show that tumor cells at the invasion front are closely associated with acinar cells undergoing damage-induced changes, and with activated fibroblasts expressing markers of injury. The invaded lobules are linked to classical tumor phenotypes, in contrast to fibrotic areas where tumor cells display a more basal profile, highlighting microenvironment-dependent tumor subtype differences. In female mice, lobular invasion similarly aligns with the classical tumor phenotype. Together, our data reveal that pancreatic tumors colonize injured lobules, creating a unique niche that shapes tumor characteristics and contributes to disease biology.", "doi": "10.1038/s41467-025-63864-7", "pmid": "41006303", "labels": {"CRISPR Functional Genomics": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12475445"}, {"db": "pii", "key": "10.1038/s41467-025-63864-7"}], "notes": [], "created": "2025-11-13T15:11:41.935Z", "modified": "2026-03-18T09:36:43.639Z"}, {"entity": "publication", "iuid": "ab9d1b96921b4340bf1580058440e585", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9d1b96921b4340bf1580058440e585.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9d1b96921b4340bf1580058440e585"}}, "title": "Effects of Stress Coping Styles and Social Defeat on Zebrafish Behaviour and Brain Transcriptomics.", "authors": [{"family": "Huben\u00e1", "given": "Pavla", "initials": "P", "orcid": "0000-0001-6351-6395", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6289bcd5ca44998a6dfd876a82ba132.json"}}, {"family": "Benrejdal", "given": "Lisa", "initials": "L", "orcid": "0000-0002-0707-1296", "researcher": {"href": "https://publications.scilifelab.se/researcher/21a1aabfa72342179ddd1b334d403d53.json"}}, {"family": "Brodin", "given": "David", "initials": "D", "orcid": "0000-0002-1768-6761", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b8b61f55e9b49529f1bc412e07db318.json"}}, {"family": "Axling", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6753-6457", "researcher": {"href": "https://publications.scilifelab.se/researcher/5857d627e160441196581f048bb800f1.json"}}, {"family": "Sarma", "given": "Oly Sen", "initials": "OS"}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}, {"family": "Winberg", "given": "Svante", "initials": "S", "orcid": "0000-0003-4252-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3f91e307ce54a9385b84784a7c8b107.json"}}], "type": "journal article", "published": "2025-09-22", "journal": {"title": "Neurosci Bull", "issn": "1995-8218", "issn-l": null}, "abstract": "Individuals with divergent personality traits corresponding to stress coping styles have been suggested to differ in behavioural and neural plasticity. We used a model of social defeat stress to assess the coping ability of wild zebrafish selectively bred for boldness/shyness. Behavioural tests were applied to assess parameters such as boldness/exploration, aggressiveness, and displacement behaviour. Gene expression changes in the brain were assessed via RNA sequencing. The main results show a strong effect of shyness and boldness phenotype on behaviour and the brain transcriptome. Fish of the shy line displayed significant behavioural differences, while the number of differentially-expressed genes remained low. In contrast, fish of the bold line exhibited a small effect on behaviour and pronounced changes in brain gene expression. This study highlights the importance of boldness phenotype and its influence on the response to social challenges at the behavioural and transcriptomic levels.", "doi": "10.1007/s12264-025-01506-0", "pmid": "40982127", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s12264-025-01506-0"}], "notes": [], "created": "2025-11-28T10:41:34.101Z", "modified": "2025-11-28T14:59:54.531Z"}, {"entity": "publication", "iuid": "529c1d9b93b7499997f647488acac746", "links": {"self": {"href": "https://publications.scilifelab.se/publication/529c1d9b93b7499997f647488acac746.json"}, "display": {"href": "https://publications.scilifelab.se/publication/529c1d9b93b7499997f647488acac746"}}, "title": "Pronounced seasonal dynamics in transcription of vitamin B1 acquisition strategies diverge among Baltic Sea bacterioplankton.", "authors": [{"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Paerl", "given": "Ryan W", "initials": "RW"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2025-09-16", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "20", "issue": "1", "pages": "115", "issn-l": null}, "abstract": "Vitamin B1 (thiamin) is essential to life; yet little is known of the regulation of its availability in marine environments or how it varies seasonally. Since microbes are the key synthesizers of the vitamin in marine environments, we here used metatranscriptomics to examine the seasonal dynamics of B1 acquisition strategies (including both uptake and synthesis pathways) in Baltic Sea bacterioplankton.\n\nElevated B1-related gene expression was observed in summer, coinciding with increased temperatures and bacterial activity and decreased nutrient availability. Different bacterial taxa exhibited distinct B1 acquisition strategies. We identified filamentous Cyanobacteria of the order Nostocales as critical to sustaining B1 production during summer, potentially compensating for limited synthesis in heterotrophic bacteria, especially for 4-amino-5-hydroxymethylpyrimidine (HMP) synthesis. Also, Pelagibacterales accounted for major portions of the community transcription, primarily taking up and salvaging the B1 precursor HMP during summer. This study highlights the partitioning of B1 synthesis, salvage, and uptake among microbial taxa, underscoring that transcriptional activity was more dynamic over time than changes in the genomic potential.\n\nWe emphasize the influence of environmental conditions on microbial community dynamics and B1 cycling in general, and the potential implications of global change-induced increases in filamentous Cyanobacteria blooms on vitamin food web transfer in particular.", "doi": "10.1186/s40793-025-00780-9", "pmid": "40958120", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12442306"}, {"db": "pii", "key": "10.1186/s40793-025-00780-9"}], "notes": [], "created": "2025-11-21T13:08:52.937Z", "modified": "2025-11-21T13:08:52.943Z"}, {"entity": "publication", "iuid": "71ccdbd2e86142819f626395f6e88614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71ccdbd2e86142819f626395f6e88614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71ccdbd2e86142819f626395f6e88614"}}, "title": "Personality and repeated social defeat affect health condition and gene expression in the skin and intestines in zebrafish.", "authors": [{"family": "Benrejdal", "given": "Lisa", "initials": "L"}, {"family": "Huben\u00e1", "given": "Pavla", "initials": "P"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Morales Castro", "given": "Rodrigo A", "initials": "RA"}, {"family": "Rekha", "given": "Rokeya Sultana", "initials": "RS"}, {"family": "Winberg", "given": "Svante", "initials": "S"}, {"family": "Bergman", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Prog. Neuropsychopharmacol. Biol. Psychiatry", "issn": "1878-4216", "pages": "111487", "issn-l": "0278-5846"}, "abstract": "Personality traits and acquired experience affect the capacity of an individual to cope with environmental and social changes. Behavioural adaptation and physiological alterations are important to prepare the body for these potential challenges. Whether inherited traits or acquired social rank (reflecting stress levels) are more important and how different personality-social rank combinations affect an individual's health is not well understood. One important aspect of health status is the function of biological barriers, as they represent the first line of defence of an organism. In the current study, we used a model of social defeat stress applied to a bold and a shy line of zebrafish. The Fulton's condition factor was determined, and gene expression analysis was performed on skin and intestines. The differences between lines explained a major part of the transcriptional changes observed as compared to differences in social rank. Additionally, shy fish that experienced repeated social defeat presented a poor body condition, accompanied by changes in gene expression suggesting inflammation in the gut. In the skin, shy fish showed a transcriptional enrichment of pathways related to cell division as well as increased expression of the stress response-associated gene crh2r. Together, these results complement our previous work and show that shy loser fish experience important changes not only in behaviour but also in their biological barriers, potentially putting their overall health at higher risk.", "doi": "10.1016/j.pnpbp.2025.111487", "pmid": "40935229", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0278-5846(25)00241-6"}], "notes": [], "created": "2025-09-30T13:55:16.843Z", "modified": "2025-09-30T13:55:16.858Z"}, {"entity": "publication", "iuid": "39cafd188c9e4072bfd89e2955794ce5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39cafd188c9e4072bfd89e2955794ce5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39cafd188c9e4072bfd89e2955794ce5"}}, "title": "Immunogenicity and innate immunity to high-dose and repeated vaccination of modified mRNA versus unmodified mRNA.", "authors": [{"family": "Engstrand", "given": "Olivia", "initials": "O"}, {"family": "Joas", "given": "Gustav", "initials": "G"}, {"family": "Miranda", "given": "Marcos C", "initials": "MC"}, {"family": "Yan", "given": "Xianglei", "initials": "X"}, {"family": "Lenart", "given": "Klara", "initials": "K"}, {"family": "Cerveira", "given": "Rodrigo Arcoverde", "initials": "RA"}, {"family": "Reinhardt", "given": "Annika", "initials": "A"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Mol Ther Nucleic Acids", "issn": "2162-2531", "volume": "36", "issue": "3", "pages": "102588", "issn-l": "2162-2531"}, "abstract": "mRNA vaccines represent a new era with several novel constructs underway. We compared the responses of high doses and multiple repetitive immunizations of a nucleoside-modified mRNA construct to a sequence-codon-optimized unmodified mRNA construct encoding the identical model antigen (HIV-1 gag). Rhesus macaques were immunized five times at 2-week intervals, with a final boost 20 weeks later. At 24 h post-vaccination, both unmodified (160 \u03bcg) and modified (400 \u03bcg and 800 \u03bcg) mRNA constructs elicited clear but transient increase of plasmacytoid dendritic cells, intermediate CD14+ CD16+ monocytes, and neutrophils along with secretion of type I interferon (IFN)-related and inflammatory cytokines. Unmodified mRNA induced higher interleukin-7 (IL-7) and IFN-\u03b1 levels, whereas modified mRNA induced higher IL-6 levels. Transcriptomic profiling showed significant upregulation of genes related to type I IFN signaling, antigen presentation, and innate immune activation induced by both mRNA constructs. The high-dose modified mRNA induced a higher number of differentially expressed genes at prime, which further increased after the fifth immunization. These differences in innate immune activation nonetheless led to similar levels and kinetics of gag-specific antibody and T cell responses. These findings offer insights into the immunogenic and reactogenic potential of different mRNA vaccine modalities, guiding future vaccine and therapy development.", "doi": "10.1016/j.omtn.2025.102588", "pmid": "40612710", "labels": {"Affinity Proteomics Stockholm": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12221724"}, {"db": "pii", "key": "S2162-2531(25)00142-8"}], "notes": [], "created": "2025-09-19T14:41:12.463Z", "modified": "2025-11-28T14:59:07.787Z"}, {"entity": "publication", "iuid": "1da67eaf49c14bdab8a4d24096830778", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1da67eaf49c14bdab8a4d24096830778.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1da67eaf49c14bdab8a4d24096830778"}}, "title": "Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data.", "authors": [{"family": "Li", "given": "Tianyi", "initials": "T"}, {"family": "Yang", "given": "Qiao", "initials": "Q"}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Engblom", "given": "Camilla", "initials": "C"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Lin", "given": "Qirong", "initials": "Q"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Steen", "given": "Sanna", "initials": "S"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Chen", "given": "Xinsong", "initials": "X"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "310", "issn-l": null}, "abstract": "Breast cancer is a highly heterogeneous disease with diverse outcomes, and intra-tumoral heterogeneity plays a significant role in both diagnosis and treatment. Despite its importance, the spatial distribution of intra-tumoral heterogeneity is not fully elucidated. Spatial transcriptomics has emerged as a promising tool to study the molecular mechanisms behind many diseases. It offers accurate measurements of RNA abundance, providing powerful tools to correlate the morphologies of cellular neighborhoods with localized gene expression patterns. However, the spot-based spatial transcriptomic tools, including the most widely used platform, Visium, do not achieve single-cell resolution readouts, which hinders data interpretability. In this study, we present a computational pathology image analysis pipeline (i.e., computational tissue annotation, CTA) that utilizes machine learning algorithms to accurately map tumor, stroma, and immune compartments within Visium-assayed tumor sections. Using a cohort of 23 breast tumor sections from four patients, we demonstrate that CTA can provide high-resolution annotations on the hematoxylin-and-eosin-stained images alongside the paired sequencing data, support the evaluation of deconvolution methods, deepen insights into intra-tumoral heterogeneity by increasing data analysis resolution, assist with spatially resolved intrinsic subtyping, and enhance the visualization of lymphocyte clones at single-cell resolution. The proposed pipeline provides valuable insights into the complex spatial architecture of breast cancer, contributing to more personalized diagnostics and treatment strategies.", "doi": "10.1038/s41698-025-01104-3", "pmid": "40925915", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12420830"}, {"db": "pii", "key": "10.1038/s41698-025-01104-3"}], "notes": [], "created": "2025-11-19T08:43:31.550Z", "modified": "2025-11-28T10:47:25.200Z"}, {"entity": "publication", "iuid": "59aa3bfaa17d4c5f88c7b8cdf0f1a206", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59aa3bfaa17d4c5f88c7b8cdf0f1a206.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59aa3bfaa17d4c5f88c7b8cdf0f1a206"}}, "title": "Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity.", "authors": [{"family": "Xu", "given": "Yunyun", "initials": "Y"}, {"family": "Lou", "given": "Daohua", "initials": "D"}, {"family": "Chen", "given": "Ping", "initials": "P"}, {"family": "Li", "given": "Gang", "initials": "G"}, {"family": "Usoskin", "given": "Dimtry", "initials": "D"}, {"family": "Pan", "given": "Jian", "initials": "J"}, {"family": "Li", "given": "Fang", "initials": "F"}, {"family": "Huang", "given": "Shungen", "initials": "S"}, {"family": "Hess", "given": "Caroline", "initials": "C"}, {"family": "Tang", "given": "Ruze", "initials": "R"}, {"family": "Hu", "given": "Xiaohan", "initials": "X"}, {"family": "Yu", "given": "Juanjuan", "initials": "J"}, {"family": "Arceo", "given": "Maria", "initials": "M"}, {"family": "de Krijger", "given": "Ronald R", "initials": "RR"}, {"family": "Tischler", "given": "Arthur S", "initials": "AS"}, {"family": "Schlisio", "given": "Susanne", "initials": "S"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}, {"family": "Hu", "given": "Yizhou", "initials": "Y"}, {"family": "Wang", "given": "Jian", "initials": "J"}], "type": "journal article", "published": "2025-09-08", "journal": {"title": "Dev. Cell", "issn": "1878-1551", "issn-l": "1534-5807", "volume": "60", "issue": "17", "pages": "2248-2263.e11"}, "abstract": "Neuroblastoma, the most prevalent extracranial pediatric solid tumor, arises from neural crest progeny cells. It exhibits substantial developmental plasticity and intratumoral heterogeneity, leading to survival rates below 50% in high-risk cases. The regulatory mechanisms underlying this plasticity remain largely elusive. In this integrative study, we used single-cell MultiOmics from a mouse spontaneous tumor model and spatial transcriptomics from human patient samples to dissect the transcriptional and epigenetic landscapes that govern developmental states in neuroblastoma. We identified developmental intermediate states in high-risk neuroblastomas critical for malignant transitions and uncovered extensive epigenetic priming with latent capacity for diverse state transitions. Furthermore, we mapped enhancer gene regulatory networks (eGRNs) and tumor microenvironments sustaining these aggressive states. State transitions and malignancy could be interfered with by targeting transcription factors controlling the eGRNs.", "doi": "10.1016/j.devcel.2025.04.013", "pmid": "40347947", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1534-5807(25)00251-5"}], "notes": [], "created": "2025-05-26T07:50:11.913Z", "modified": "2025-11-14T11:05:58.511Z"}, {"entity": "publication", "iuid": "ebe4355205e54bc3b50d10a1a62fb6e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebe4355205e54bc3b50d10a1a62fb6e8"}}, "title": "Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.", "authors": [{"family": "Deng", "given": "Qiaoling", "initials": "Q", "orcid": "0000-0002-3776-1132", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdfda2d3f64742e8a09bbded5f322f96.json"}}, {"family": "Goodall", "given": "Jake", "initials": "J", "orcid": "0000-0003-0960-4241", "researcher": {"href": "https://publications.scilifelab.se/researcher/457d1a2733cc4a569ffeb70750999199.json"}}, {"family": "Bergenius Nord", "given": "Mikaela", "initials": "M"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Delling", "given": "Bo", "initials": "B", "orcid": "0000-0001-9148-9574", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c1c3f7ddf0945d18660ecbaa85303b0.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Palm", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9890-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebffe35bae646eb8a15163b0cb0820f.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A", "orcid": "0000-0002-2184-5534", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad9186f5720d493980b92869fb504cb8.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2025-09-03", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": null, "issue": null, "pages": "e70094"}, "abstract": "How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (Coregonus albula) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring- and autumn-spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high-quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC-directed scaffolding. We generated low-coverage whole-genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring- and autumn-spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome-wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.", "doi": "10.1111/mec.70094", "pmid": "40903929", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": null, "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-09-08T14:16:37.667Z", "modified": "2025-11-21T12:48:41.202Z"}, {"entity": "publication", "iuid": "0c35ae7c18b94e239d19318c61b04c7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c35ae7c18b94e239d19318c61b04c7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c35ae7c18b94e239d19318c61b04c7a"}}, "title": "Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.", "authors": [{"family": "L\u00f3pez Clinton", "given": "Samantha", "initials": "S", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications.scilifelab.se/researcher/46b97ad0ac8541dc807e570724e58c69.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Goodsell", "given": "Robert", "initials": "R"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-3929-251X", "researcher": {"href": "https://publications.scilifelab.se/researcher/440662f277ea4756a08a7f5925b3f485.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "15", "issue": "9", "pages": "e72163"}, "abstract": "Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.", "doi": "10.1002/ece3.72163", "pmid": "40964625", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440566"}, {"db": "pii", "key": "ECE372163"}], "notes": [], "created": "2025-11-19T08:12:39.732Z", "modified": "2025-11-28T10:40:00.285Z"}, {"entity": "publication", "iuid": "df60b381dc4943cdbbccf12206421777", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df60b381dc4943cdbbccf12206421777.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df60b381dc4943cdbbccf12206421777"}}, "title": "Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp.", "authors": [{"family": "Yang", "given": "Xuyue", "initials": "X"}, {"family": "Tunstr\u00f6m", "given": "Kalle", "initials": "K", "orcid": "0000-0002-5285-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd0ddb97d724542b6e7c46f782f3bbd.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "134", "issue": "9", "pages": "567-575", "issn-l": "0018-067X"}, "abstract": "Parasitoid wasps are major causes of mortality of many species, making host immune defences a common target of adaptive evolution, though such targets outside model species are poorly understood. In this study, we used two tests of positive selection to compare across three closely related Galerucella leaf beetles that show substantial differences in their phenotypic response to the shared parasitoid wasp Asecodes parviclava, their main natural enemy. Using a codon-based test, which detects excess amino acid fixations per locus along each species' lineage, we found more evidence of positive selection on parasitoid-relevant immune genes in the species with the strongest immunocompetence (G. pusilla) compared with the species having weaker immunocompetence (G. tenella and G. calmariensis). Moreover, genes coding for the early phases in the immune response cascade were predominantly among the positively selected immune genes, providing targets for future functional genomic study to pin-point connections between genotypic and phenotypic differences in defences towards a parasitoid wasp. In contrast, genome-wide analyses of the haplotype frequency spectrum, which quantify selection over recent evolutionary time scales, revealed similar signatures of positive selection on immune genes across species. These results advance the field of host-parasitoid dynamics by providing novel insights into the tempo and mode of insect host evolutionary dynamics, and offering a framework for making genotype to phenotype connections for immunocompetence phenotypes.", "doi": "10.1038/s41437-025-00794-6", "pmid": "40921792", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12457636"}, {"db": "pii", "key": "10.1038/s41437-025-00794-6"}], "notes": [], "created": "2025-09-29T07:36:03.222Z", "modified": "2025-11-21T09:22:48.226Z"}, {"entity": "publication", "iuid": "c57d8ac1a6904e40856c4f78a2d6803b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c57d8ac1a6904e40856c4f78a2d6803b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c57d8ac1a6904e40856c4f78a2d6803b"}}, "title": "Induced somatic mutation accumulation during skeletal muscle regeneration reduces muscle strength.", "authors": [{"family": "Vrta\u010dnik", "given": "Peter", "initials": "P"}, {"family": "Merino", "given": "Lara G", "initials": "LG", "orcid": "0000-0002-7208-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/afebb85c860744dc8ad5840caa6f06c0.json"}}, {"family": "Subhash", "given": "Santhilal", "initials": "S", "orcid": "0000-0002-0077-4597", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ca22115b7c9444ab2056126a1c9d36d.json"}}, {"family": "Helgad\u00f3ttir", "given": "Hafd\u00eds T", "initials": "HT", "orcid": "0000-0003-4352-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce4dc1001c944a9d9dfe4c092cfda497.json"}}, {"family": "Bardin", "given": "Matthieu", "initials": "M", "orcid": "0000-0001-9755-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4070871377c4fbcabf6e9a299d01277.json"}}, {"family": "Stefani", "given": "Fabiana", "initials": "F", "orcid": "0009-0008-8933-0773", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f3b815508714611a894e9853362b123.json"}}, {"family": "Wang", "given": "Depin", "initials": "D"}, {"family": "Chen", "given": "Ping", "initials": "P"}, {"family": "Franco", "given": "Irene", "initials": "I", "orcid": "0000-0002-4272-239X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eac8823b89543f09e9d2cb141bdb587.json"}}, {"family": "Rev\u00eachon", "given": "Gwladys", "initials": "G", "orcid": "0000-0002-4824-6793", "researcher": {"href": "https://publications.scilifelab.se/researcher/356dd0dbbdaa4d21957e516ce11bbd74.json"}}, {"family": "Eriksson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3233-2862", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8641fd4d16471abf18990610fb89a1.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Nat Aging", "issn": "2662-8465", "volume": "5", "issue": "9", "pages": "1739-1749", "issn-l": null}, "abstract": "Aging is associated with a progressive decline in tissue function and regenerative capacity, partly due to genomic instability, one of the hallmarks of aging1,2. Genomic instability encompasses DNA damage and the accumulation of somatic mutations in post-zygotic cells, yet the specific impact of these mutations on age-related tissue dysfunction remains poorly understood. To address this, we developed a mouse model in which genomic instability was induced specifically in muscle progenitor cells3 through targeted deletion of the Msh2 (ref. 4) and Blm5 genes. This allowed us to assess how elevated DNA damage and somatic mutations, from single-nucleotide variants (SNVs) to structural variants, affect muscle regeneration following injury. These mice exhibited impaired muscle regeneration, characterized by smaller muscle fibers, reduced muscle mass gain and decreased grip strength. Importantly, similar muscle deficits were observed in a second mouse model where somatic mutations were elevated with less substantial DNA damage. These findings provide evidence that the accumulation of somatic mutations can potentially compromise the function of somatic cells, contributing to the aging phenotype in skeletal muscle.", "doi": "10.1038/s43587-025-00941-y", "pmid": "40836125", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12443595"}, {"db": "pii", "key": "10.1038/s43587-025-00941-y"}], "notes": [], "created": "2025-09-08T07:07:06.110Z", "modified": "2025-11-19T08:29:17.738Z"}, {"entity": "publication", "iuid": "d393109fcd1c4ba9be1fc99ed851ad05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d393109fcd1c4ba9be1fc99ed851ad05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d393109fcd1c4ba9be1fc99ed851ad05"}}, "title": "In-depth patient-specific analysis of tumor heterogeneity in melanoma brain metastasis: Insights from spatial transcriptomics and multi-region bulk sequencing.", "authors": [{"family": "Sharma", "given": "Nidhi", "initials": "N", "orcid": "0000-0002-2475-9340", "researcher": {"href": "https://publications.scilifelab.se/researcher/eadc0f3bfb5443e8a14af7d785085324.json"}}, {"family": "R\u00e1jov\u00e1", "given": "Jana", "initials": "J"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Vikstr\u00f6m", "given": "Sofi", "initials": "S"}, {"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications.scilifelab.se/researcher/45a1c5d3d2d34a9e96d112877632784c.json"}}, {"family": "Jensdottir", "given": "Margret", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Eriksson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Transl Oncol", "issn": "1936-5233", "volume": "59", "pages": "102468", "issn-l": null}, "abstract": "Melanoma brain metastases (MBM) exhibit extensive intertumor and intratumor heterogeneity (ITH), driven by a complex tumor microenvironment. The aim of this study was to perform a detailed analysis of individual MBM patient tumors using a multiomics approach, integrating spatial transcriptomics with multi-region bulk exome, proteome, and transcriptome profiling for a small group of four patient samples. We identified significant patient-specific variations in immune cell infiltration, particularly in B/plasma cells, myeloid cells, and cancer-associated fibroblasts (CAFs). Notably, immunotherapy-treated patients showed enriched pathways related to epithelial-mesenchymal transition (EMT), interferon-gamma (IFN-\u03b3) signaling, oxidative phosphorylation, T-cell signaling, inflammation and DNA damage, which aligned with distinct cellular compositions observed in the spatial analysis. We also uncovered considerable ITH, especially at the protein level, revealing differential expression patterns of key tumor and immune-related markers. The correlation between mRNA and protein data highlighted consistent enrichment of critical pathways across multiomics layers. These findings highlight the molecular and cellular landscape of individual patient MBM, underscoring the importance of addressing tumor heterogeneity in the development of effective therapeutic strategies.", "doi": "10.1016/j.tranon.2025.102468", "pmid": "40669378", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12284558"}, {"db": "pii", "key": "S1936-5233(25)00199-8"}], "notes": [], "created": "2025-07-18T10:25:23.220Z", "modified": "2025-11-28T10:44:36.443Z"}, {"entity": "publication", "iuid": "f77da0ef90c647a0af9d18b2b04042f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f77da0ef90c647a0af9d18b2b04042f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f77da0ef90c647a0af9d18b2b04042f0"}}, "title": "Gone With the Wind: Exploring a Vanished Rock Dove, Columba livia, Hybrid Zone in the Sahara Desert.", "authors": [{"family": "Hern\u00e1ndez-Alonso", "given": "Germ\u00e1n", "initials": "G", "orcid": "0000-0001-6065-1428", "researcher": {"href": "https://publications.scilifelab.se/researcher/408d39dcc0c24431816561f71350cb0f.json"}}, {"family": "van Grouw", "given": "Hein", "initials": "H"}, {"family": "Farahani", "given": "Motahare F", "initials": "MF"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "15", "issue": "9", "pages": "e72061"}, "abstract": "Rock doves (Columba livia) are the wild ancestor of domestic and feral pigeons and had a wide distribution across Eurasia and the northern part of Africa. West African rock doves have been identified as genetically distinct from all other populations, possibly representing a distinct species. This divergence is hypothesized to have arisen through cycles of allopatry during the dry and wet Sahara periods. Based on the Refugia Theory and observed admixture patterns, it was proposed that a hybrid zone existed in the Sahara during its last green period, playing a critical role in the speciation of West African rock doves. This project aims to test the existence and location of this vanished hybrid zone by analyzing whole-genome sequences from six historical rock doves from previously unsampled populations in the Central Sahara and West Africa, along with published genomic data. By exploring population structure, genetic diversity, and admixture patterns, our results confirm the existence of the hybrid zone, likely located around the mountainous regions of northwest Africa. To explain the observed genetic differentiation of West African rock doves, we propose a four-step scenario involving speciation by reinforcement. Finally, we support a species-level taxonomic arrangement to designate the West African rock dove as C. gymnocycla.", "doi": "10.1002/ece3.72061", "pmid": "40896089", "labels": {"Ancient DNA": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12391023"}, {"db": "pii", "key": "ECE372061"}, {"db": "figshare", "key": "10.6084/m9.figshare.29267132"}], "notes": [], "created": "2025-11-05T07:40:54.780Z", "modified": "2025-11-19T07:57:17.516Z"}, {"entity": "publication", "iuid": "99d94470f07541c2b23fad1eefd0f74b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99d94470f07541c2b23fad1eefd0f74b"}}, "title": "Genomic studies in Linum shed light on the evolution of the distyly supergene and the molecular basis of convergent floral evolution.", "authors": [{"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "PI", "orcid": "0000-0002-5197-3502", "researcher": {"href": "https://publications.scilifelab.se/researcher/295e9debf36c4641aa6c346e915b64ef.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Losvik", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-7669-9266", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85c35a0abd54a7087c94942290179be.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Sol\u00e9r", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "247", "issue": "6", "pages": "2964-2981"}, "abstract": "Distyly, an example of convergent evolution, is governed by a supergene, the S-locus, in several species. Recent studies highlight similar genomic architectures of independently evolved S-loci, but its mode of origin and whether similar regulatory pathways underlie the convergent evolution of distyly remains unclear. We examined the evolution of supergenes and mechanisms underlying distyly in Linum species that diverged c. 33 million years ago (Ma). Using haplotype-resolved genomes and population genomics, we identified and characterized the S-loci of Linum perenne (distylous) and Linum grandiflorum (style length dimorphic), and compared them to that of Linum tenue (distylous). We then tested for a conserved hormonal mechanism regulating style length polymorphism in Linum. The S-locus supergene was consistently hemizygous in short-styled individuals across all three species, although it showed variation in size, gene content, repeat elements and extent of recombination suppression. Two S-linked candidate genes, TSS1 (style length) and WDR-44 (anther height/pollen self-incompatibility), were conserved. Consistent with a brassinosteroid-dependent role of TSS1, epibrassinolide treatment revealed a conserved, morph-specific effect on style length. S-locus structural polymorphism, candidate distyly genes and mechanisms regulating style length remain conserved > 30 Ma in Linum. In combination with findings from other systems, our results suggest that the brassinosteroid pathway frequently contributes to style length polymorphism.", "doi": "10.1111/nph.70392", "pmid": "40682296", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371154"}], "notes": [], "created": "2025-08-19T13:25:54.698Z", "modified": "2025-11-19T10:24:41.159Z"}, {"entity": "publication", "iuid": "7799feb1743049b29d4ce4b791a4dd02", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7799feb1743049b29d4ce4b791a4dd02.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7799feb1743049b29d4ce4b791a4dd02"}}, "title": "Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.", "authors": [{"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Termes", "given": "Laura", "initials": "L"}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Moots", "given": "Hannah M", "initials": "HM"}, {"family": "Tubbesing", "given": "Florentine", "initials": "F"}, {"family": "Larsdotter", "given": "Juliana", "initials": "J"}, {"family": "Oteo-Garc\u00eda", "given": "Gonzalo", "initials": "G"}, {"family": "Moreland", "given": "Kelsey", "initials": "K"}, {"family": "van Essen", "given": "Hans", "initials": "H"}, {"family": "Arbour", "given": "Victoria", "initials": "V"}, {"family": "Keddie", "given": "Grant", "initials": "G"}, {"family": "Richards", "given": "Michael P", "initials": "MP"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Lister", "given": "Adrian", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "9", "pages": "20250305", "issn-l": "1744-9561"}, "abstract": "Climate changes profoundly impact species distributions and can drastically alter dynamics between formerly isolated taxa. The evolution of mammoths within North America was characterized by repeated cycles of dispersal and putative gene flow between woolly and Columbian mammoths. However, as genome-wide studies on mammoths have predominantly focused on Siberia, the consequences of these North American range shifts remain unclear. Here, we generated genome-wide and morphological data for two Late Pleistocene mammoth molars from British Columbia, Canada (BC), and jointly analysed these with previously published data. Our genome-wide analysis (n = 16) revealed gene flow between woolly and Columbian mammoths that would have gone undiscovered based on morphological (n = 48) and mitochondrial analysis (n = 124) alone. Consistent with their hybrid nature, our analyses suggest that these two BC mammoths had elevated genomic diversity. Our results highlight the importance of combining data types to reconstruct past evolutionary events. These findings demonstrate how the geographical range expansion of woolly mammoths resulted in long-term hybridization with local Columbian mammoths and enhance our understanding of the genomic and morphological consequences of climate-mediated dispersal.", "doi": "10.1098/rsbl.2025.0305", "pmid": "40994021", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12461089"}], "notes": [], "created": "2025-11-19T08:22:48.349Z", "modified": "2025-11-19T08:22:48.432Z"}, {"entity": "publication", "iuid": "663259e242554c7aa13f3a0303e14035", "links": {"self": {"href": "https://publications.scilifelab.se/publication/663259e242554c7aa13f3a0303e14035.json"}, "display": {"href": "https://publications.scilifelab.se/publication/663259e242554c7aa13f3a0303e14035"}}, "title": "Classification of Paediatric Celiac Disease Using RNA Sequencing and Real-Time PCR of Duodenal Biomarkers.", "authors": [{"family": "Bragde", "given": "Hanna Gustafsson", "initials": "HG", "orcid": "0000-0001-9104-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/7192535c27614e7a81122bef9fee9d42.json"}}, {"family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}}, {"family": "S\u00f6derman", "given": "Jan", "initials": "J", "orcid": "0000-0001-7505-7210", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e27f9f58384d158dc7bb019e4a97db.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "J. Cell. Mol. Med.", "issn": "1582-4934", "volume": "29", "issue": "18", "pages": "e70854", "issn-l": "1582-1838"}, "abstract": "Celiac disease (CD) diagnosis in children with sub-threshold tissue transglutaminase autoantibody (anti-TG2) levels requires a small intestinal biopsy. Through RNA sequencing and real-time PCR of small intestinal biopsies, gene expression in such children was compared with the expression in children with active CD and anti-TG2 levels above the threshold, and with non-CD children. The study also included CD children with a non-diagnostic first biopsy to explore early gene expression changes in CD. The aim of the study was to explore gene expression in relation to anti-TG2 levels, investigate gene expression in Potential CD, and provide a gene expression profile to aid in CD diagnostics. The results showed that in active CD, expression changes involved genes associated with e.g., immune response, transport, angiogenesis, and epithelial barrier function, with even more pronounced changes of genes associated with cell cycle progression, absorption, lipid and lipoprotein processes, and retinoid metabolism in the active CD group with higher anti-TG2 levels. Gene expression changes in CD children with a non-diagnostic first biopsy showed large inter-individual variations, but in general, gene expressions were associated with many of the same biological contexts as in active CD, including epithelial barrier function. Overall, the results show that gene expression profiling has great potential as a complement to the histopathologic assessment in CD diagnostics, even early in the disease course, but probably cannot be used for prognostic purposes.", "doi": "10.1111/jcmm.70854", "pmid": "40977520", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12451401"}], "notes": [], "created": "2025-09-30T13:39:32.092Z", "modified": "2025-11-28T10:51:11.561Z"}, {"entity": "publication", "iuid": "0677b45be8814334a65d2195c9099d8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0677b45be8814334a65d2195c9099d8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0677b45be8814334a65d2195c9099d8c"}}, "title": "Among-individual asynchrony but not genetic diversity is associated with temporal stability of tree growth in natural Quercus robur oak stands.", "authors": [{"family": "Hall", "given": "Marcus", "initials": "M", "orcid": "0000-0002-9556-1235", "researcher": {"href": "https://publications.scilifelab.se/researcher/18148df55a9145a993d4cb287a529519.json"}}, {"family": "Sunde", "given": "Johanna", "initials": "J", "orcid": "0000-0002-3145-1475", "researcher": {"href": "https://publications.scilifelab.se/researcher/972ff747b7044a6096583673286e9443.json"}}, {"family": "Franz\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "9", "pages": "20250180", "issn-l": "1744-9561"}, "abstract": "Theory, manipulation experiments and observational studies on biodiversity and ecosystem functioning largely concur that higher intraspecific diversity may increase the overall productivity of populations, buffer against environmental change and stabilize long-term productivity. However, evidence comes primarily from small and short-lived organisms. We tested for effects of genetic diversity on variation in forest growth by combining long-term data on annual individual growth rate (basal area increment (BAI)) with estimates of intrapopulation genetic variation (based on RAD-seq SNPs) for 18 natural Quercus robur pedunculate oak populations. Higher total or adaptive genetic variability of populations was neither associated with faster average growth nor with increased temporal or spatial stability of growth nor with among-individual asynchrony in growth. However, as expected, we found that greater asynchrony of growth responses within the populations increased their temporal stability. Together, these findings point towards a negligible role of genetic variation in structuring growth patterns in natural populations of tree species. Identifying which environmental factors and phenotypic traits (and its genetic basis) contribute to asynchronous growth responses is an important next step towards a better mechanistic understanding of the causes of temporal stability in tree growth and forest productivity.", "doi": "10.1098/rsbl.2025.0180", "pmid": "40925550", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12419903"}], "notes": [], "created": "2025-11-26T08:53:50.190Z", "modified": "2025-11-28T10:50:14.392Z"}, {"entity": "publication", "iuid": "9d97c09fe92948a999a721fbc9eca073", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d97c09fe92948a999a721fbc9eca073.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d97c09fe92948a999a721fbc9eca073"}}, "title": "SMAD3 and p300 complex scaffolding by long non-coding RNA LIMD1-AS1 promotes TGF-\u03b2-induced breast cancer cell plasticity.", "authors": [{"family": "Fan", "given": "Chuannan", "initials": "C", "orcid": "0000-0001-8754-4913", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a665d568ce94fcbaaee270c6c7701a5.json"}}, {"family": "Cats", "given": "Davy", "initials": "D", "orcid": "0000-0001-9684-220X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23de688650944eca98ed9f9c1e8f19bb.json"}}, {"family": "Selle", "given": "Miriam", "initials": "M"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B"}, {"family": "Mei", "given": "Hailiang", "initials": "H", "orcid": "0000-0003-1781-5508", "researcher": {"href": "https://publications.scilifelab.se/researcher/7899dde247724b2aacd8ccb6e27fbd49.json"}}, {"family": "Ten Dijke", "given": "Peter", "initials": "P", "orcid": "0000-0002-7234-342X", "researcher": {"href": "https://publications.scilifelab.se/researcher/299812073080446a91fc6228efbdc1c5.json"}}, {"family": "Wang", "given": "Qian", "initials": "Q"}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "16", "pages": null}, "abstract": "Transforming growth factor (TGF)-\u03b2 signaling enhances cancer cell plasticity by inducing epithelial-to-mesenchymal transition (EMT). Here, we identified a TGF-\u03b2-induced long non-coding RNA, LIMD1 Antisense RNA 1 (LIMD1-AS1) that strengthens the SMAD-mediated transcriptional response to TGF-\u03b2. LIMD1-AS1 expression is upregulated in breast cancer tissues compared to normal breast tissues, and high LIMD1-AS1 expression is associated with poor prognosis in breast cancer patients. Depletion of LIMD1-AS1 hinders TGF-\u03b2-induced EMT, migration, and extravasation of breast cancer cells. Mechanistically, LIMD1-AS1 promotes the interaction between SMAD3 and its transcriptional coactivator p300, thereby enhancing SMAD3 transcriptional activity and TGF-\u03b2/SMAD signaling. We demonstrated that LIMD1-AS1 binds to the MAD homology 2 (MH2) domain of SMAD3 and the interferon-binding domain (IBiD) of p300. Displacing LIMD1-AS1 from p300 by its competitor interferon regulatory factor 3 (IRF3) suppressed the effects of LIMD1-AS1 on potentiating TGF-\u03b2/SMAD signaling. Furthermore, blockage of p300 acetyltransferase activity with a pharmacological inhibitor A-485 reduced the ability of LIMD1-AS1 to enhance SMAD3 transcriptional activity, TGF-\u03b2-induced EMT, and migration. This study identifies LIMD1-AS1 as a novel stimulator of TGF-\u03b2 signaling by establishing a positive feedback loop and highlights its potential as a therapeutic target for breast cancer.", "doi": "10.1093/nar/gkaf841", "pmid": "40889156", "labels": {"CRISPR Functional Genomics": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12400928"}, {"db": "pii", "key": "8245226"}], "notes": [], "created": "2025-09-05T13:25:16.080Z", "modified": "2026-03-18T09:37:05.489Z"}, {"entity": "publication", "iuid": "f9fa93241c55420684d17c40a4900126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9fa93241c55420684d17c40a4900126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9fa93241c55420684d17c40a4900126"}}, "title": "Environmental DNA from peck marks shows potential for non\u2011invasive monitoring of woodpeckers.", "authors": [{"family": "Sharif", "given": "Muhammad Bilal", "initials": "MB", "orcid": "0000-0002-0581-0542", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7d50e00ad8a448abafe330b8f92bbfe.json"}}, {"family": "Ferry", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-6372-4298", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d8ad3e349a54ad48dcd2f76f53a107e.json"}}, {"family": "Fuchs", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Cronholm", "given": "Bodil", "initials": "B"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-08-20", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "8", "pages": "e0328831", "issn-l": "1932-6203"}, "abstract": "Monitoring species' occurrences is essential for understanding ecosystem dynamics, tracking biodiversity changes, and guiding conservation efforts. Traditional monitoring methods, such as visual surveys, are challenging, particularly for elusive and endangered species. This proof-of-concept study explores the potential of environmental DNA (eDNA) collected from peck marks as a non-invasive tool for detecting and identifying woodpecker species. We collected nine samples from fresh peck marks on birch and spruce trees in the forests of Swedish Lapland. In two samples, we successfully amplified an 81 base-pair fragment of the woodpecker mitochondrial 16S rRNA gene. Taxonomic assignment identified the Eurasian three-toed woodpecker (Picoides tridactylus), a species classified as \"Near Threatened\" in Sweden. We collected an additional 15 samples from 4-19 years old peck marks preserved inside the trunks of birch and pine trees in the same area. No woodpecker DNA was detected in these samples, likely due to DNA degradation. Our findings demonstrate the potential of using eDNA from peck marks as a non-invasive approach for monitoring elusive woodpecker species.", "doi": "10.1371/journal.pone.0328831", "pmid": "40833950", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12367160"}, {"db": "pii", "key": "PONE-D-25-05526"}], "notes": [], "created": "2025-12-05T13:13:48.040Z", "modified": "2025-12-05T13:13:48.321Z"}, {"entity": "publication", "iuid": "56648ea2596d4aa49555ce26d1055513", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56648ea2596d4aa49555ce26d1055513.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56648ea2596d4aa49555ce26d1055513"}}, "title": "Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae).", "authors": [{"family": "Gross", "given": "Karin", "initials": "K", "orcid": "0000-0002-2363-452X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f4362c55ecf40ada48792ac03f1425a.json"}}, {"family": "Yazdi", "given": "Homa Papoli", "initials": "HP", "orcid": "0000-0001-8667-6279", "researcher": {"href": "https://publications.scilifelab.se/researcher/608729115444421b8c6db7eb852a059a.json"}}, {"family": "Schlager", "given": "Elisabeth", "initials": "E"}, {"family": "Lilley", "given": "Jodie", "initials": "J"}, {"family": "Romero-Bravo", "given": "Andr\u00e9s", "initials": "A"}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}, {"family": "Thompson", "given": "John N", "initials": "JN", "orcid": "0000-0001-5941-6498", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5702a533123466c8ae723cc5732e72f.json"}}, {"family": "Friberg", "given": "Magne", "initials": "M", "orcid": "0000-0003-4779-7881", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d19106d6be748d99ee049ea616fc9c2.json"}}], "type": "journal article", "published": "2025-08-19", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "33", "pages": "e2505119122", "issn-l": "0027-8424"}, "abstract": "Polyploidization is an important driver of evolution and diversification in flowering plants. Here, we assess how repeated polyploidization may have shaped diversification of floral morphology in Lithophragma bolanderi (Saxifragaceae). This species comprises multiple cytotypes and varies geographically in its interactions with specialized pollinating moths in the genus Greya (Prodoxidae). Past studies have shown that coevolution with these moths has favored particular suites of floral characters but does not fully explain local and regional floral diversification. We combined phenotypic and genomic data from more than 1,800 individuals from 40 L. bolanderi populations spread across its entire range. Flow-cytometric analyses revealed a geographic mosaic of populations comprising one to four of three dominant (diploid, tetraploid, hexaploid) and three rare (triploid, pentaploid, octoploid) cytotypes. Whole-genome resequencing of a subset of populations suggested that polyploids arose from multiple autopolyploidization events, rather than a single event and/or through hybridization, albeit with some signals consistent with low levels of introgression from the congener Lithophragma glabrum. Quantification of flower traits from plants grown in a common garden showed that cytotype explained more than 15% of the variation in floral morphology, with polyploids showing more variability than diploids. Experimental induction of neopolyploids directly induced phenotypic changes but also indicated that local selection may have favored subsequent convergence in floral morphology among cytotypes in natural populations. Collectively, this comprehensive and integrative approach provides insights into how variability generating processes, such as polyploidization integrates with selection from species interactions to shape local floral diversification.", "doi": "10.1073/pnas.2505119122", "pmid": "40802687", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12377753"}], "notes": [], "created": "2025-11-21T15:15:36.277Z", "modified": "2025-11-28T10:48:23.989Z"}, {"entity": "publication", "iuid": "f6b93bc63d7447ab8768a84e8c6aa42a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6b93bc63d7447ab8768a84e8c6aa42a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6b93bc63d7447ab8768a84e8c6aa42a"}}, "title": "Systems analysis of clinical malaria reveals proteomic perturbation and innate-adaptive crosstalk linked to disease severity.", "authors": [{"family": "Lautenbach", "given": "Maximilian Julius", "initials": "MJ"}, {"family": "Wyss", "given": "Katja", "initials": "K"}, {"family": "Yman", "given": "Victor", "initials": "V"}, {"family": "Foroogh", "given": "Fariba", "initials": "F"}, {"family": "Satarvandi", "given": "Donya", "initials": "D"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Sond\u00e9n", "given": "Klara", "initials": "K"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "\u00c1lvez", "given": "Mar\u00eda Bueno", "initials": "MB"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Brodin", "given": "Petter", "initials": "P"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Sundling", "given": "Christopher", "initials": "C"}, {"family": "F\u00e4rnert", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-08-12", "journal": {"title": "Immunity", "issn": "1097-4180", "issn-l": "1074-7613", "volume": "58", "issue": "8", "pages": "2120-2136.e5"}, "abstract": "Malaria presents with varying degrees of severity. To improve clinical management and prevention, it is crucial to understand the pathogenesis and host response. We analyzed 1,463 plasma proteins during and after acute Plasmodium falciparum malaria in adult travelers and linked responses to peripheral immune cells by integrating with single-cell RNA sequencing (RNA-seq) data from a subset of donors. We identified extensive perturbations in over 250 proteins with diverse origins, including many not previously analyzed in malaria patients, such as hormones, circulating receptors, and intracellular or membrane-bound proteins from affected tissues. The protein profiles clustered participants according to disease severity, enabling the identification of a compressed 11-protein signature enriched in severe malaria. Conceptually, this study advances our understanding of malaria by linking systemic proteomic changes to immune cell communication and organ-specific responses. This resource, which includes an interactive platform to explore data, opens new avenues for hypothesis generation, biomarker discovery, and therapeutic target identification.", "doi": "10.1016/j.immuni.2025.06.014", "pmid": "40664217", "labels": {"Affinity Proteomics Stockholm": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Affinity Proteomics Uppsala": "Service", "NGI Proteomics": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(25)00283-3"}], "notes": [], "created": "2025-11-17T08:54:30.240Z", "modified": "2025-11-26T11:07:57.819Z"}, {"entity": "publication", "iuid": "a58a549ff82149ffa87c6ec256ec94ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a58a549ff82149ffa87c6ec256ec94ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a58a549ff82149ffa87c6ec256ec94ef"}}, "title": "Unraveling Nitrogen Uptake and Metabolism: Gene Families, Expression Dynamics, and Functional Insights in Aspen (Populus tremula).", "authors": [{"family": "Zhang", "given": "Yupeng", "initials": "Y", "orcid": "0000-0001-9461-8554", "researcher": {"href": "https://publications.scilifelab.se/researcher/307e4bb258054d37bda861e64d5f893f.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S"}, {"family": "Renstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Luomaranta", "given": "Mikko", "initials": "M"}, {"family": "Chantreau", "given": "Maxime", "initials": "M"}, {"family": "Fleig", "given": "Verena", "initials": "V"}, {"family": "Gaboreanu", "given": "Ioana", "initials": "I"}, {"family": "Grones", "given": "Carolin", "initials": "C"}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Tuominen", "given": "Hannele", "initials": "H", "orcid": "0000-0002-4949-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fe575e1cb054ab08b57e05d3a1ee28d.json"}}], "type": "journal article", "published": "2025-08-11", "journal": {"title": "Tree Physiol", "issn": "1758-4469", "issn-l": "0829-318X"}, "abstract": "The influence of nitrogen on wood formation is well established. To gain insight into the underlying molecular mechanism, we first identified genes in fourteen gene families that are involved in nitrogen uptake and metabolism in European aspen (Populus tremula L.) genome annotation. Gene expression data from a de novo RNA sequencing (RNA-seq) analysis and data available from the AspWood database (plantgenie.org) provided putative candidate genes for the uptake of nitrate, ammonium and amino acids from the xylem sap as well as their further assimilation in the secondary xylem tissues of the stem. For a population-wide analysis of the nitrogen-related genes, we utilized RNA-seq data from the cambial region of the stems of 5-year-old aspen trees, representing 99 natural aspen accessions, and compared the expression of the nitrogen-related genes to stem diameter. Novel regulatory interactions were identified in expression quantitative loci and co-expression network analyses in these data. The expression of certain nitrate and amino acid transporters correlated negatively with stem diameter, suggesting that excessive nitrogen retrieval from the xylem sap suppresses radial growth of the stem. The expression of a glutamine synthetase correlated with the expression of these transporters, a link further supported by increased plant growth in transgenic glutamine synthetase overexpressing trees. This study provides insight into the genetic basis of nitrogen uptake and assimilation and its connection to wood formation, providing interesting targets for improving nitrogen use efficiency and growth of aspen trees.", "doi": "10.1093/treephys/tpaf099", "pmid": "40795931", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "8230290"}], "notes": [], "created": "2025-08-29T10:02:04.420Z", "modified": "2025-11-14T11:08:03.834Z"}, {"entity": "publication", "iuid": "a97b36bc55b94119b54060180a6e6305", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a97b36bc55b94119b54060180a6e6305.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a97b36bc55b94119b54060180a6e6305"}}, "title": "Genome-wide identification of modulators of Chlamydia trachomatis parasitophorous vacuole stability highlights an important role for sphingolipid supply.", "authors": [{"family": "Babu Sait", "given": "Mohammed Rizwan", "initials": "MR"}, {"family": "Jachmann", "given": "Lana H", "initials": "LH"}, {"family": "T\u00fcrk\u00f6z", "given": "G\u00f6zde", "initials": "G"}, {"family": "Milivojevic", "given": "Milica", "initials": "M"}, {"family": "Llorente-S\u00e1ez", "given": "Celia", "initials": "C"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Schumacher", "given": "Fabian", "initials": "F"}, {"family": "Henriksson", "given": "Sara", "initials": "S", "orcid": "0000-0003-1615-0583", "researcher": {"href": "https://publications.scilifelab.se/researcher/934e6f18e3c94684be715e7bdc28d9b7.json"}}, {"family": "Gayathri Vegesna", "given": "Naga Venkata", "initials": "NV"}, {"family": "Seddik", "given": "Noha", "initials": "N"}, {"family": "Chaban", "given": "Anastasiia", "initials": "A"}, {"family": "Mohanty", "given": "Partha", "initials": "P"}, {"family": "\u00d6lander", "given": "Magnus", "initials": "M"}, {"family": "Muraleedharan", "given": "Samada", "initials": "S"}, {"family": "Farmand Azadeh", "given": "Sepideh", "initials": "S"}, {"family": "Kleuser", "given": "Burkhard", "initials": "B"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Sixt", "given": "Barbara S", "initials": "BS", "orcid": "0000-0002-5607-8902", "researcher": {"href": "https://publications.scilifelab.se/researcher/998ac876b31f45c5b10d36f0d10c7390.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "PLoS Biol.", "issn": "1545-7885", "issn-l": "1544-9173", "volume": "23", "issue": "8", "pages": "e3003297"}, "abstract": "A mechanistic understanding of how intracellular pathogens evade the intrinsic defenses of their host cells could open up intriguing therapeutic opportunities. Here, we applied a genome-wide genetic screening approach to investigate the nature of the defensive host cell death response suppressed by the membrane trafficking modulator CpoS, an effector protein secreted by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Initially, this work revealed a CpoS-deficient mutant to exhibit a markedly increased dependence on host cellular synthesis of ceramides, the precursors of complex sphingolipids. Using novel microscopic reporters, we then established CpoS' role in defense evasion to occur by preserving the integrity of Chlamydia's parasitophorous vacuole (the inclusion) via ensuring an adequate sphingolipid supply. More specifically, we observed CpoS deficiency to destabilize inclusions, initially characterized by a release of individual bacteria into the host cell cytosol, then followed by inclusion rupture concomitant with host cell death. Exogenous addition of sphingosine stabilized CpoS-deficient inclusions, whereas disruption of host cellular ceramide synthesis destabilized wild-type inclusions. In combination, CpoS deficiency and impaired ceramide synthesis - presumably disrupting both Chlamydia's vesicular and non-vesicular sphingolipid supply routes - destabilized inclusions even earlier, resulting in infection clearance and host cell survival rather than host cell death. Overall, this study highlights how the vacuolar pathogen C. trachomatis maintains vacuole integrity by ensuring a steady sphingolipid supply, potentially offering inspiration and directions for future therapeutic strategies targeting parasitophorous vacuoles.", "doi": "10.1371/journal.pbio.3003297", "pmid": "40794560", "labels": {"CRISPR Functional Genomics": "Collaborative", "Integrated Microscopy Technologies Ume\u00e5": "Technology development", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Chemical Biology Consortium Sweden": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12342332"}, {"db": "pii", "key": "PBIOLOGY-D-24-02720"}], "notes": [], "created": "2025-09-04T09:04:13.790Z", "modified": "2026-03-18T09:37:39.227Z"}, {"entity": "publication", "iuid": "db8859e1f60843cfb22193244670316d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db8859e1f60843cfb22193244670316d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db8859e1f60843cfb22193244670316d"}}, "title": "Deep sequencing combined with high-throughput screening enables efficient development of a pH-dependent high-affinity binding domain targeting HER3.", "authors": [{"family": "M\u00f6ller", "given": "Marit", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Malin", "initials": "M"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "L\u00f6fblom", "given": "John", "initials": "J"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S", "orcid": "0000-0003-0605-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8dd8ee4264d4e4b912dacad3106f40a.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "8", "pages": "e70247", "issn-l": "0961-8368"}, "abstract": "In vitro methods for developing binding domains have been well-established for many years, owing to the cost-efficient synthesis of DNA and high-throughput selection and screening technologies. However, generating high-affinity binding domains often requires the development of focused maturation libraries for a second selection, which typically demands a detailed understanding of the binding surfaces from the initial selection, a process that can be time-consuming. In this study, we accelerated this process by using deep sequencing data from the first selection to guide the design of the maturation library. Additionally, we employed a high-throughput screening system using flow cytometry based on Escherichia coli display to identify conditional binding domains from the selection output. This approach enabled the development of a high-affinity binder targeting the cancer biomarker HER3, with a binding affinity of 3.3 nM at extracellular pH 7.4, 100 times higher than the first-generation binding domain. Notably, the binding domain features a pH-dependent release mechanism, enabling rapid release in slightly acidic environments (pH \u22486), which resemble endosomal conditions. When conjugated to the cytotoxin mertansine (DM1), the binding domain demonstrated specific cytotoxic activity against HER3-expressing cell lines, with an IC50 of 2-5 nM. The presented approach enables the efficient development of conditional binding domains which hold promise for therapeutic applications.", "doi": "10.1002/pro.70247", "pmid": "40716110", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T18:09:51.575Z", "modified": "2025-11-21T18:09:51.723Z"}, {"entity": "publication", "iuid": "8e3c080a6b6f4c1494f64bbfe3ee1dc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e3c080a6b6f4c1494f64bbfe3ee1dc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e3c080a6b6f4c1494f64bbfe3ee1dc4"}}, "title": "Identification of a small molecule targeting EPLIN as a novel strategy for the treatment of pediatric neuroblastoma and medulloblastoma.", "authors": [{"family": "Lindell", "given": "Emma", "initials": "E", "orcid": "0009-0001-2785-946X", "researcher": {"href": "https://publications.scilifelab.se/researcher/667fca56e7c74aa7984daf5dac4bbc2e.json"}}, {"family": "Guo", "given": "Jing", "initials": "J", "orcid": "0000-0002-6399-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e778f67395b491daec1b80d805ab6bd.json"}}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Rameika", "given": "Natallia", "initials": "N"}, {"family": "Lu", "given": "Xi", "initials": "X"}, {"family": "Wacker", "given": "Tabea", "initials": "T"}, {"family": "Zhong", "given": "Lei", "initials": "L"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Svanberg", "given": "Sara", "initials": "S"}, {"family": "Chowdhury", "given": "Azazul I", "initials": "AI"}, {"family": "Bergsten", "given": "Peter", "initials": "P"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Bexell", "given": "Daniel", "initials": "D"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Zhang", "given": "Xiaonan", "initials": "X", "orcid": "0000-0003-4359-9079", "researcher": {"href": "https://publications.scilifelab.se/researcher/306b1ef8c6904d6b936e11442b4515f4.json"}}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "issn-l": "2041-4889", "volume": "16", "issue": "1", "pages": "554"}, "abstract": "Amplification of the MYCN proto-oncogene serves as a key marker of aggressive disease and poor treatment outcomes in certain pediatric tumors originating from the nervous system, including neuroblastoma and medulloblastoma. However, the complex nature of the challenging MYCN protein underscores the urgent need for additional targets and therapies to tackle neuroblastoma and medulloblastoma. In this study, with a primary focus on neuroblastoma and the aim of also benefiting children with medulloblastoma, we identified FLIX5, a small compound that exhibits broad cytotoxicity against both neuroblastoma and medulloblastoma cells, primarily by triggering apoptosis. Furthermore, FLIX5 enhances the cholesterol dependency of neuroblastoma cells under conditions where mitochondrial function is impaired. FLIX5 as well shows a synergistic effect when combined with vincristine, a conventional anticancer drug, against neuroblastoma cells and organoids. Through proteome integral solubility alteration, computational molecular docking predictions, and cellular thermal shift assays for target identification and validation, FLIX5 reveals EPLIN (Epithelial Protein Lost In Neoplasm) as a previously unexplored drug target. EPLIN is involved in several cellular processes, including cholesterol uptake and mitochondrial function. The discovery of FLIX5 targeting EPLIN presents new opportunities for treating malignant pediatric tumors, with the potential to target chemoresistant dormant cancer cells and broaden its therapeutic applications to other tumor types.", "doi": "10.1038/s41419-025-07876-7", "pmid": "40701975", "labels": {"NGI Single cell": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Chemical Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287531"}, {"db": "pii", "key": "10.1038/s41419-025-07876-7"}], "notes": [], "created": "2025-09-30T09:25:55.225Z", "modified": "2025-11-25T17:06:41.935Z"}, {"entity": "publication", "iuid": "f0fcb0e459e6426fab71064e0db96eee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0fcb0e459e6426fab71064e0db96eee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0fcb0e459e6426fab71064e0db96eee"}}, "title": "Parathyroidectomy Restores Muscle Strength and Transcriptome in Individuals with Primary Hyperparathyroidism.", "authors": [{"family": "Bj\u00f6rnsdotter-\u00d6berg", "given": "Sofia", "initials": "S"}, {"family": "Koman", "given": "Anna", "initials": "A", "orcid": "0000-0003-3196-7057", "researcher": {"href": "https://publications.scilifelab.se/researcher/518d3806b27d4b19822b8572b90f36a5.json"}}, {"family": "Skorpil", "given": "Mikael", "initials": "M"}, {"family": "Ryd\u00e9n", "given": "Henric", "initials": "H"}, {"family": "Lanner", "given": "Johanna T", "initials": "JT"}, {"family": "Krook", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Inga-Lena", "initials": "IL"}, {"family": "Pillon", "given": "Nicolas J", "initials": "NJ"}, {"family": "Nyl\u00e9n", "given": "Carolina", "initials": "C", "orcid": "0000-0002-8445-7221", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb57024f0b2492988a3dbad9fafe198.json"}}], "type": "journal article", "published": "2025-07-21", "journal": {"title": "J. Clin. Endocrinol. Metab.", "issn": "1945-7197", "issn-l": "0021-972X"}, "abstract": "Primary hyperparathyroidism leads to hypercalcemia and muscle dysfunction. Muscle weakness is associated with increased morbidity and mortality but is overlooked in surgical treatment guidelines. While parathyroidectomy is the only curative treatment, its effects on skeletal muscle strength and molecular remodelling remain underexplored.\n\nDetermining functional and molecular changes in skeletal muscle before and after parathyroidectomy.\n\nA prospective observational study was conducted in the spring and fall of 2023.\n\nPatients underwent surgery at the Endocrine and Sarcoma section at the Karolinska University Hospital in Stockholm, Sweden.\n\n21 postmenopausal women with primary hyperparathyroidism planned for surgery were included, whereof 15 completed the study protocol. Participants had no disabling comorbidities.\n\nMuscle function tests, muscle biopsies, MRI, and biochemical panels were analyzed before and after parathyroidectomy.\n\nMuscle composition of m. vastus lateralis was tested with MRI and transcriptomic analysis of muscle biopsies. Leg strength was evaluated with timed stands test and peak torque tests. Activity level was estimated from questionnaires.\n\nParathyroidectomy normalized calcium levels (p<0.001) and improved muscle strength (p<0.005). Muscle volume increased (p=0.023) and fat fraction was reduced (p=0.013), without changes in physical activity levels. Transcriptomic analysis identified 981 differentially expressed genes post-surgery, enriched in pathways mirroring exercise-induced adaptations.\n\nThese findings highlight the impact of parathyroidectomy on skeletal muscle function and suggest that muscle assessments should be included in surgical referral criteria to address age-related muscle decline and improve long-term outcomes.", "doi": "10.1210/clinem/dgaf418", "pmid": "40690900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "8210038"}], "notes": [], "created": "2025-11-28T14:57:00.299Z", "modified": "2025-11-28T14:57:00.643Z"}, {"entity": "publication", "iuid": "f5c04bc9cc13408387b5cb7cbcd3cbc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5c04bc9cc13408387b5cb7cbcd3cbc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5c04bc9cc13408387b5cb7cbcd3cbc6"}}, "title": "The invasion phenotypes of glioblastoma depend on plastic and reprogrammable cell states.", "authors": [{"family": "Doroszko", "given": "Milena", "initials": "M"}, {"family": "Stockgard", "given": "Rebecka", "initials": "R"}, {"family": "Uppman", "given": "Irem", "initials": "I", "orcid": "0000-0003-3602-5544", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29421803962496880443d5772f4c97a.json"}}, {"family": "Heinold", "given": "Josephine", "initials": "J"}, {"family": "Voukelatou", "given": "Faidra", "initials": "F", "orcid": "0009-0007-4281-3041", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b89b587bcc740e691e8d0253a03e161.json"}}, {"family": "Mangukiya", "given": "Hitesh Bhagavanbhai", "initials": "HB", "orcid": "0000-0002-8460-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/d32958c394c749d19d7444dac9fe6c3b.json"}}, {"family": "Millner", "given": "Thomas O", "initials": "TO"}, {"family": "Skepp\u00e5s", "given": "Madeleine", "initials": "M", "orcid": "0009-0003-3741-4143", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0b0193e1c804b738dc4b2d5d735d53e.json"}}, {"family": "Ballester Bravo", "given": "Mar", "initials": "M"}, {"family": "Elgendy", "given": "Ramy", "initials": "R", "orcid": "0000-0002-2592-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a5ce4db4317446bb1ef113f7c6e8eb5.json"}}, {"family": "Berglund", "given": "Maria", "initials": "M"}, {"family": "Elfineh", "given": "Ludmila", "initials": "L"}, {"family": "Krona", "given": "Cecilia", "initials": "C"}, {"family": "Kundu", "given": "Soumi", "initials": "S", "orcid": "0000-0002-0759-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/e48ddbc3493247e4930203374878f4b7.json"}}, {"family": "Koltowska", "given": "Katarzyna", "initials": "K", "orcid": "0000-0002-6841-8900", "researcher": {"href": "https://publications.scilifelab.se/researcher/06a8aeda504340c1af3ab893fd413a65.json"}}, {"family": "Marino", "given": "Silvia", "initials": "S", "orcid": "0000-0002-9612-2883", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d040a587c9417b925d42b8e39a43e6.json"}}, {"family": "Larsson", "given": "Ida", "initials": "I", "orcid": "0000-0001-5422-4243", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ac604ca793048e9b6ddaa3459b4e97a.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S", "orcid": "0000-0003-1758-1262", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d684fc3b26d4741b850790ba0571c96.json"}}], "type": "journal article", "published": "2025-07-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "6662", "issn-l": "2041-1723"}, "abstract": "Glioblastoma (GBM) is the most common primary brain cancer. It causes death mainly by local invasion via several routes, including infiltration of white matter tracts and penetration of perivascular spaces. However, the pathways that mediate these invasion routes are only partly known. Here, we conduct an integrative study to identify cell states and central drivers of route-specific invasion in GBM. Combining single-cell profiling and spatial protein detection in patient-derived xenograft models and clinical tumor samples, we demonstrate a close association between the differentiation state of GBM cells and their choice of invasion route. Computational modeling identifies ANXA1 as a driver of perivascular involvement in GBM cells with mesenchymal differentiation and the transcription factors RFX4 and HOPX as orchestrators of growth and differentiation in diffusely invading GBM cells. Ablation of these targets in tumor cells alters their invasion route, redistributes the cell states, and extends survival in xenografted mice. Our results define a close association between GBM cell differentiation states and invasion routes, identify functional biomarkers of route-specific invasion, and point toward targeted modulation of specific invasive cell states as a therapeutic strategy in GBM.", "doi": "10.1038/s41467-025-61999-1", "pmid": "40683881", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12276355"}, {"db": "pii", "key": "10.1038/s41467-025-61999-1"}], "notes": [], "created": "2025-09-30T08:40:58.966Z", "modified": "2025-11-21T11:52:14.274Z"}, {"entity": "publication", "iuid": "19a4115c6ad14acaaf738a62c51e4f69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19a4115c6ad14acaaf738a62c51e4f69"}}, "title": "Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Feinauer", "given": "Isabelle S", "initials": "IS", "orcid": "0009-0004-4615-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d95245a50e408a9643a18b7c0fc3d2.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Kuzmina", "given": "Elena A", "initials": "EA"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Stewart", "given": "John R", "initials": "JR", "orcid": "0000-0002-3506-5264", "researcher": {"href": "https://publications.scilifelab.se/researcher/62e8f2e54f1a4f1d96d8f4ae1de97a93.json"}}, {"family": "Knul", "given": "Monika V", "initials": "MV", "orcid": "0000-0002-0650-0992", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff550d1088bb4857a28277ae1db41452.json"}}, {"family": "Noiret", "given": "Pierre", "initials": "P"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Ehrich", "given": "Dorothee", "initials": "D"}, {"family": "Pokrovsky", "given": "Ivan", "initials": "I"}, {"family": "Fedorov", "given": "Vadim B", "initials": "VB", "orcid": "0000-0003-3938-4200", "researcher": {"href": "https://publications.scilifelab.se/researcher/017b3cc7d41e46feb13e4e919b0c2dd5.json"}}, {"family": "Goropashnaya", "given": "Anna V", "initials": "AV", "orcid": "0009-0005-4712-6297", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e89f839e5c24f0dbef8deadb3a17f8d.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "122", "issue": "28", "pages": "e2424333122"}, "abstract": "The Norwegian lemming (Lemmus lemmus) is a small rodent distributed across the Fennoscandian mountain tundra and the Kola Peninsula. The Norwegian lemming likely evolved during the Late Pleistocene and inhabited Fennoscandia shortly prior to the Last Glacial Maximum. However, the exact timing and origins of the species, and its phylogenetic position relative to the closely related Siberian lemming (Lemmus sibiricus) remain disputed. Moreover, the presence of ancient or contemporary gene flow between both species is largely untested. The Norwegian lemming displays characteristic phenotypic and behavioral adaptations (e.g., coat color, aggression) that are not present in other Lemmus species. We generated a de novo genome assembly for the Norwegian lemming and resequenced nine modern and two ancient Lemmus spp. genomes. We show that all Lemmus species form distinct monophyletic clades, with concordant topology between the mitochondrial and nuclear genome phylogenies. The Siberian lemming is divided into two distinct but paraphyletic clades, one in the east and one in the west, where the western clade represents a sister taxon to the Norwegian lemming. We estimate that the Norwegian and western Siberian lemming diverged shortly before the Last Glacial Maximum, making the Norwegian lemming one of the youngest known mammalian species. We did not find any indication of gene flow between L. lemmus and L. sibiricus, suggesting postglacial isolation of L. lemmus. Furthermore, we identify species-specific genomic differences in genes related to coat color and fat transport, which are likely associated with the distinctive coloration and overwintering behavior observed in the Norwegian lemming.", "doi": "10.1073/pnas.2424333122", "pmid": "40587810", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12280882"}], "notes": [], "created": "2025-07-01T06:45:31.166Z", "modified": "2025-11-14T11:07:37.863Z"}, {"entity": "publication", "iuid": "3d5e24e8dc3542eab9713c6df3a7e8e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d5e24e8dc3542eab9713c6df3a7e8e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d5e24e8dc3542eab9713c6df3a7e8e5"}}, "title": "Reverse microdialysis of sucrose stimulates soil fungal and bacterial growth at the microscale.", "authors": [{"family": "Schneider", "given": "Andreas N", "initials": "AN"}, {"family": "Buckley", "given": "Scott", "initials": "S"}, {"family": "Lorenzo", "given": "Zulema Carracedo", "initials": "ZC"}, {"family": "Gratz", "given": "Regina", "initials": "R"}, {"family": "Nilsson", "given": "Lina", "initials": "L"}, {"family": "Swaine", "given": "Mark", "initials": "M"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Taylor", "given": "Andy F S", "initials": "AFS"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S"}], "type": "journal article", "published": "2025-07-14", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "436", "issn-l": "1471-2180"}, "abstract": "The rhizosphere is a critical microenvironment that plays key roles in plant nutrient availability, largely due to root interactions with rhizospheric microbes. However, we lack suitable methods that can elucidate mechanisms determining rhizospheric community structure and function within the context of a dynamic, undisturbed soil. Microdialysis has been used for low intrusive soil nutrient sampling at the scale of a fine root, with small probes that also enable release of defined compounds. We evaluated whether microdialysis could simulate exudation, by the release of sucrose, and stimulate changes in a soil microbial community, allowing us to determine the microbes that responded most to carbon release.\n\nMicrodialysis successfully stimulated growth on probe surfaces of fungi and bacteria, which were extracted and sequenced for identification. Microbial growth was also visualized with scanning electron microscopy. The majority of the species stimulated were classified as fast growing or opportunistic, e.g. yeasts, moulds, proteobacteria and actinobacteriota, which are known to respond quickly (within days) to the release of simple sugars as exudates in the rhizosphere.\n\nThe study demonstrates the potential of using microdialysis as a tool to investigate interactions between root exudation and soil microbial community composition, initially for individual compounds and in the future for more complex compositions.", "doi": "10.1186/s12866-025-04082-5", "pmid": "40660105", "labels": {"Integrated Microscopy Technologies Ume\u00e5": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12257659"}, {"db": "pii", "key": "10.1186/s12866-025-04082-5"}], "notes": [], "created": "2025-10-30T11:57:11.876Z", "modified": "2025-11-28T10:52:39.912Z"}, {"entity": "publication", "iuid": "7d1ba25b67c9423e84e530a52b63a532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d1ba25b67c9423e84e530a52b63a532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d1ba25b67c9423e84e530a52b63a532"}}, "title": "Cell atlas of the developing human meninges reveals a dura origin of meningioma.", "authors": [{"family": "Vinsland", "given": "Elin", "initials": "E", "orcid": "0000-0001-9695-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c7bf61b0d3348d9b966a7a018c8859d.json"}}, {"family": "Salas", "given": "Sergio Marco", "initials": "SM"}, {"family": "Kapustov\u00e1", "given": "Ivana", "initials": "I"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Webb", "given": "Simone", "initials": "S"}, {"family": "Li", "given": "Xiaofei", "initials": "X"}, {"family": "He", "given": "Xiaoling", "initials": "X"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M"}, {"family": "Barker", "given": "Roger", "initials": "R"}, {"family": "Persson", "given": "Oscar", "initials": "O"}, {"family": "Raleigh", "given": "David R", "initials": "DR"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}], "type": "journal article", "published": "2025-07-13", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The vertebrate central nervous system is enveloped by the meninges, consisting of the pia, arachnoid, and dura layers. The arachnoid is hypothesised to give rise to the most common primary intracranial tumours, meningiomas. However, molecular evidence supporting this hypothesis is lacking. There are no effective medical therapies to treat meningiomas that are resistant to local interventions, encumbered by our limited understanding of their cellular origin. To address this limitation in our understanding of meningioma biology, we generated a comprehensive reference single cell and spatial transcriptomic atlas of human fetal meninges at post-conceptional weeks 5-13. We found that the meningeal layers develop concurrently, and identified an inner CDH1-positive dura cell layer expressing tight junction genes consistent with barrier function. We show that transcriptionally, meningioma cells resemble dura-lineage cells, and that common meningioma driver genes were expressed preferentially in the dura lineage. Our findings suggest that meningiomas originate from dura lineage cells.", "doi": "10.1101/2025.07.08.663122", "pmid": "40672210", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12265625"}, {"db": "pii", "key": "2025.07.08.663122"}], "notes": [], "created": "2025-11-24T09:18:03.258Z", "modified": "2025-11-28T06:53:07.022Z"}, {"entity": "publication", "iuid": "3f94f51a9c5f47249cc487ebd66bad09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f94f51a9c5f47249cc487ebd66bad09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f94f51a9c5f47249cc487ebd66bad09"}}, "title": "Silk-Ovarioids: establishment and characterization of a human ovarian primary cell 3D-model system.", "authors": [{"family": "Di Nisio", "given": "Valentina", "initials": "V", "orcid": "0000-0002-8435-7925", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee1509ba58840f597b7fccc778a0a20.json"}}, {"family": "Li", "given": "Tianyi", "initials": "T", "orcid": "0000-0003-2246-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9d609023a624d80ac76d112661918f8.json"}}, {"family": "Xiao", "given": "Zhijie", "initials": "Z"}, {"family": "Papaikonomou", "given": "Kiriaki", "initials": "K"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1"}, {"family": "Lebre", "given": "Filipa", "initials": "F"}, {"family": "Alfaro-Moreno", "given": "Ernesto", "initials": "E"}, {"family": "Pedersen", "given": "Mikael", "initials": "M", "orcid": "0000-0001-6540-4805", "researcher": {"href": "https://publications.scilifelab.se/researcher/99fbf942a9324124813072f70ef9e1ee.json"}}, {"family": "Svingen", "given": "Terje", "initials": "T", "orcid": "0000-0003-4650-7651", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1900781448d4715a287420203765a44.json"}}, {"family": "Zubarev", "given": "Roman", "initials": "R"}, {"family": "Acharya", "given": "Ganesh", "initials": "G"}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P", "orcid": "0000-0001-8458-0855", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d258c0f0d9b417ea4608769fc3ebaaf.json"}}, {"family": "Salumets", "given": "Andres", "initials": "A", "orcid": "0000-0002-1251-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dcf4bacf5c4792bbfd111495d43595.json"}}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Hum Reprod Open", "issn": "2399-3529", "volume": "2025", "issue": "3", "pages": "hoaf042", "issn-l": null}, "abstract": "What is the best protocol to establish a long-term stable three-dimensional (3D) model for human primary ovarian cells?\n\nWe developed and characterized long-term cultured 3D models of primary ovarian somatic cells isolated from adult tissues, using Biosilk as a scaffold.\n\nIn vitro models that mimic ovaries are crucial for elucidating the biological mechanisms underlying follicle activation and growth, hormonal activity, ovarian angiogenesis, damage in response to toxic exposures, and other biological mechanisms that enable the functionality of this complex organ. Three-dimensional systems are particularly relevant because they replicate heterogeneity and cell-cell communication among different ovarian cell types. However, complex models using human ovarian primary cells are yet to be developed.\n\nOvarian tissue samples were collected from five patients (age 26 \u00b1 5 years) who underwent gender-affirming surgery. The cortex and medulla were separated and dissociated into single-cell suspensions using mechanical and enzymatic methods. Three approaches were tested to establish a 3D model culture system: matrix-free ovarian spheroids (MFOS), a Matrigel-based three-layer gradient system (3LGS), and Biosilk scaffolds (Silk-Ovarioid). In parallel, paired controls from each patient and ovarian area were cultured in a standard 2D system for the same duration.\n\nThe 3D culture systems were monitored every second day to detect signs of aggregation and growth. Freshly fixed tissue, as well as 2D- and 3D-cultured samples were further processed for transcriptomic profiling after 42 days of culture using RNA sequencing. The culture of the 3D system was further characterized, regarding its protein profile and steroid and cytokine production, through proteomics and liquid chromatography-tandem mass spectrometry and the Luminex platform, respectively. The key findings from the high-throughput assays were finally validated through RNA fluorescent in situ hybridization (RNA-FISH) and immunofluorescence staining.\n\nThe 3D model systems MFOS (n = 120) and 3LGS (n = 18) failed to form aggregates capable of long-term maintenance in culture (MFOS: maximum of 15 days for both cortex and medulla; 3LGS: maximum of 11 days for medulla only). In contrast, we successfully established ovarian cortex- and medulla-derived 3D systems using Biosilk, termed Silk-Ovarioids (n = 120). Silk-Ovarioids were maintained for up to 42 days as free-floating culture without any signs of cell death, as confirmed by the absence of TUNEL, \u03b3-H2A.X, and cleaved caspase 3 fluorescent signals. The presence of key ovarian somatic cell types, including granulosa, stromal, endothelial, and perivascular cells, was confirmed by transcriptomics and proteomics in the majority of Silk-Ovarioids. Validation through RNA-FISH and immunostaining was performed using the following markers: AMHR2 for granulosa cells, PDGFR\u03b1 for stromal cells, CLDN5 and GPIHBP1 for endothelial cells, GJA4/Cx37 and MCAM for perivascular cells. Notably, Silk-Ovarioids exhibited the formation of a pro-angiogenic hypoxic core, as evidenced by the transcriptomic and proteomic data and visualized by the expression of hypoxia markers MMP2 and PDGFR\u03b2. This hypoxic environment led to development of vessel-like structures after 4-6 weeks of culture, which were positive for the angiogenic markers TGFBR2, BMP2, and PDGF\u03b1. The functionality of Silk-Ovarioids was further confirmed by the identification of de novo extracellular matrix secretion (Col1\u03b11 and Lam\u03b11), and by the detection of pro-angiogenic cytokines (e.g. IL-6, IL-8, and GM-CSF) and steroids (e.g. pregnenolone and epitestosterone) in the culture media.\n\nThe RNA-sequencing count matrix is deposited in Gene Expression Omnibus with accession number GSE253571. Raw data are deposited in Swedish National Data Service with the DOI https://doi.org/10.48723/h8cm-bs19. Single-cell RNA-seq data have been downloaded from the ArrayExpress database at EMBL-EBI with the accession codes 'E-MTAb - 8381'. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD048710. The code used for the analysis can be found in https://github.com/tialiv/Silk-Ovarioid_project.\n\nThe ovarian samples were collected from patients undergoing androgen treatment, raising the concern that androgen exposure may alter the behavior of cells in Silk-Ovarioids compared to those derived from androgen-unstimulated patients. Furthermore, the cell culture media used in this study were supplemented with fetal bovine serum and did not contain any supplements or growth factors that could be essential for the resemblance of Silk-Ovarioids to the tissue of origin.\n\nThe Silk-Ovarioids exhibited low intra-batch variability and long-term culture stability, underscoring their potential as a robust step toward developing a bioengineered, patient-specific artificial ovary. In addition, Silk-Ovarioids could be utilized as the first ovarian angiogenesis in vitro model, function as biological scaffold for in vitro folliculogenesis, and be used for toxicological and pharmacological studies targeting the ovaries.\n\nThis study was funded by: a research grant from the Center for Innovative Medicine (CIMED) at Karolinska Insitutet; European Union's Horizon 2020 Research and Innovation Programme (project ERIN no. 952516); a Horizon Europe grant (NESTOR, grant no. 101120075) of the European Commission; the Swedish Research Council for Sustainable Development FORMAS (2018-02280, 2020-01621); StratRegen Funding from Karolinska Institute, Swedish Research Council VR (grant no. 2020-02132); Swedish Childhood Cancer Fund (Reference PR2017-0044, PR2020-0096); Estonian Research Council (grant no. PRG1076); Swedish Research Council (grant no. 2024-02530); Novo Nordisk Foundation (grant no. NNF24OC0092384); European Union's H2020 project Sinfonia (no. 857253) (INL research); and SbDToolBox, with reference NORTE-01-0145-FEDER-000047, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (INL research). The authors have no conflicts of interest to declare.", "doi": "10.1093/hropen/hoaf042", "pmid": "40799620", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12343022"}, {"db": "pii", "key": "hoaf042"}], "notes": [], "created": "2025-11-28T14:58:05.868Z", "modified": "2025-11-28T14:58:06.995Z"}, {"entity": "publication", "iuid": "e59a3f9900274a389b62b4915dc79be9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e59a3f9900274a389b62b4915dc79be9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e59a3f9900274a389b62b4915dc79be9"}}, "title": "Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment.", "authors": [{"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Holm", "given": "Matilda", "initials": "M"}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ"}, {"family": "Chen", "given": "Baizhen", "initials": "B"}, {"family": "Stepanauskait\u0117", "given": "Lina", "initials": "L"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Kutter", "given": "Claudia", "initials": "C"}, {"family": "Archer", "given": "Amena", "initials": "A"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Cancer Lett.", "issn": "1872-7980", "pages": "217661", "volume": "622", "issn-l": "0304-3835"}, "abstract": "Chronic inflammation contributes to the development of colorectal cancer, partly through its regulation of the microenvironment and antitumor immunity. Interestingly, women have a lower incidence of colorectal cancer, and estrogen treatment has been shown to reduce the occurrence of colorectal tumors. While intestinal estrogen receptor beta (ER\u03b2, Esr2) can protect against colitis and colitis-induced cancer in mice, its role in shaping the tumor microenvironment remains unknown. In this study, we performed RNA sequencing to analyze the transcriptome of colonic epithelia and tumors from azoxymethane/dextran sulfate sodium-treated wild-type and intestinal ER\u03b2 knockout (ER\u03b2KOVil) mice and vehicle-treated controls. This revealed significant differences in gene expression and enriched biological processes influenced by sex and genotype, with immune-related responses being overrepresented. Deconvolution supported differential immune cell abundance and immunostaining showed that tumors from ER\u03b2KOVil mice displayed significantly increased macrophage infiltration, decreased T cell infiltration, and impaired natural killer cell infiltration. Further, ER\u03b2 mRNA levels in clinical colorectal tumors correlated with immune signaling profiles and better survival. Our findings indicate that intestinal ER\u03b2 promotes an antitumor microenvironment and could potentially affect the effectiveness of immunotherapy. These insights highlight the importance of ER\u03b2 in modulating antitumor immunity and underscore its therapeutic potential in colorectal cancer.", "doi": "10.1016/j.canlet.2025.217661", "pmid": "40120798", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0304-3835(25)00227-7"}], "notes": [], "created": "2025-04-07T09:56:23.805Z", "modified": "2025-11-14T11:05:53.324Z"}, {"entity": "publication", "iuid": "36236e6be0ce4b17b39f3a3841e121fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36236e6be0ce4b17b39f3a3841e121fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36236e6be0ce4b17b39f3a3841e121fb"}}, "title": "Dissecting FAP+ Cell Diversity in Pancreatic Cancer Uncovers an Interferon-Response Subtype of Cancer-Associated Fibroblasts with Tumor-Restraining Properties.", "authors": [{"family": "Cumming", "given": "Joshua", "initials": "J", "orcid": "0000-0003-3661-7443", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd0f3e688ff047ef8e814134c0446774.json"}}, {"family": "Maneshi", "given": "Parniyan", "initials": "P", "orcid": "0000-0002-2180-4097", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c23ae21a4df4f319d2395580aa4fb2e.json"}}, {"family": "Dongre", "given": "Mitesh", "initials": "M", "orcid": "0000-0002-7151-1137", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acd00be909d41399277be66d9600d41.json"}}, {"family": "Alsaed", "given": "Tala", "initials": "T", "orcid": "0009-0009-5690-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/58e2e9329f714da7ad4892b11a3c726d.json"}}, {"family": "Dehghan-Nayeri", "given": "Mohammad Javad", "initials": "MJ", "orcid": "0009-0002-1538-4871", "researcher": {"href": "https://publications.scilifelab.se/researcher/8399aab605474070a84399a52d4befe2.json"}}, {"family": "Ling", "given": "Agnes", "initials": "A", "orcid": "0000-0002-9503-0784", "researcher": {"href": "https://publications.scilifelab.se/researcher/acb1fab24b604772bf2bb07fc10c056d.json"}}, {"family": "Pietras", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6738-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be0a3ec07654822a91df964eab1d6e4.json"}}, {"family": "Patthey", "given": "Cedric", "initials": "C", "orcid": "0000-0002-2627-9578", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7707e8bd3d4e029fb1e1f43df86ad4.json"}}, {"family": "\u00d6hlund", "given": "Daniel", "initials": "D", "orcid": "0000-0002-5847-2778", "researcher": {"href": "https://publications.scilifelab.se/researcher/42e9e473f68c460098a37e22d0a41369.json"}}], "type": "journal article", "published": "2025-07-02", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "85", "issue": "13", "pages": "2388-2411", "issn-l": "0008-5472"}, "abstract": "Within the stroma of pancreatic ductal adenocarcinoma (PDAC), mesenchymal cells differentiate into cancer-associated fibroblast (CAF) subtypes that differentially mediate disease progression. Defining the regulatory mechanism and diversity of CAF subtypes could identify potential therapeutic strategies to harness the tumor-suppressive activities of CAFs. To address this, we utilized single-cell RNA sequencing to profile fibroblast activation protein-\u03b1 (FAP)-expressing mesenchymal cells in human PDAC. The mesenchymal subpopulations in PDAC reflected mesenchymal cell heterogeneity found in the normal developing pancreas. In addition to characterizing inflammatory CAF and myofibroblastic CAF subpopulations in detail, the analysis uncovered a previously undescribed interferon-response CAF (ifCAF) subtype. Tumor-derived signals induced specific CAF subtypes from pancreatic stellate cells in an organoid-based coculture model, and time-course experiments revealed regulatory mechanisms that govern subtype formation. STING agonists promoted an ifCAF phenotype in vivo and in vitro. Importantly, induction of an ifCAF phenotype suppressed tumor cell invasiveness and induced an antitumor phenotype in tumor-associated neutrophils. Together, this study resolves FAP+ stromal cell heterogeneity in PDAC and identifies an ifCAF subtype that can be induced to suppress protumorigenic features of PDAC.\n\nCharacterization of FAP+ mesenchymal cell heterogeneity in pancreatic cancer identifies a tumor-suppressive interferon-response cancer-associated fibroblast subtype that can be induced by stimulating type I interferon signaling using STING agonists.", "doi": "10.1158/0008-5472.CAN-23-3252", "pmid": "40215177", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Clinical Genomics": "Service", "Clinical Genomics Ume\u00e5": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12214878"}, {"db": "pii", "key": "757349"}], "notes": [], "created": "2025-11-21T18:45:35.492Z", "modified": "2025-11-28T10:52:09.338Z"}, {"entity": "publication", "iuid": "3e287d397db04ea4a121c1a2cbd8a106", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e287d397db04ea4a121c1a2cbd8a106.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e287d397db04ea4a121c1a2cbd8a106"}}, "title": "Museomics unravels cryptic diversity in an endemic group of New Guinean songbirds.", "authors": [{"family": "Blom", "given": "Mozes Pil Kyu", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Bloom-Quinn", "given": "Saphira", "initials": "S", "orcid": "0009-0000-6457-8264", "researcher": {"href": "https://publications.scilifelab.se/researcher/766f9c58f99a4263a464c1138001ab83.json"}}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ", "orcid": "0000-0001-6990-9915", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ac768b5d0d540988dfeca8f83cf41cf.json"}}, {"family": "Koane", "given": "Bonny", "initials": "B", "orcid": "0000-0001-6770-5126", "researcher": {"href": "https://publications.scilifelab.se/researcher/966dc22dd4ca456294f7f2ed0a853c87.json"}}, {"family": "Joseph", "given": "Leo", "initials": "L", "orcid": "0000-0001-7564-1978", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a0b6c400914ba9aaca4a51587d1893.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "21", "issue": "7", "pages": "20240611", "issn-l": "1744-9561"}, "abstract": "Deciphering cryptic diversity can have substantial implications for our understanding of evolutionary processes and species conservation. Birds are arguably among the best studied organismal groups, but even in avian clades there are some genera that have not been thoroughly surveyed. This is particularly true for taxa that occur in hyperdiverse biogeographic regions. In this study, we focus on an endemic group of New Guinean birds, the jewel-babblers (genus: Ptilorrhoa), and study the diversification history of all known taxa. We assemble a de novo genome using linked-read sequencing and genomic data for 40 historical specimens. Both phylogenomic and population-genomic analyses strongly support the recovery of a cryptic species and shed new light on the diversification history of this group. The blue jewel-babbler (Ptilorrhoa caerulescens) is a paraphyletic species complex and P. c. nigricrissus is more closely related to the phenotypically distinct and sexually dimorphic P. geislerorum, than to other P. caerulescens subspecies. These findings demonstrate that even in well-studied groups such as birds, cryptic diversity can still be a prevalent reality. Moreover, by deciphering cryptic diversity, we shed new light on the processes driving speciation within Ptilorrhoa and the need to potentially revise the taxonomic status of all subspecies.", "doi": "10.1098/rsbl.2024.0611", "pmid": "40664242", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-07-18T10:24:09.986Z", "modified": "2025-07-18T10:24:10.511Z"}, {"entity": "publication", "iuid": "816528b47a0d4fec91f70570d313e5bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/816528b47a0d4fec91f70570d313e5bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/816528b47a0d4fec91f70570d313e5bc"}}, "title": "Gut microbiota mediates SREBP-1c-driven hepatic lipogenesis and steatosis in response to zero-fat high-sucrose diet.", "authors": [{"family": "Bergentall", "given": "Mattias", "initials": "M"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Sun", "given": "Chuqing", "initials": "C"}, {"family": "Henricsson", "given": "Marcus", "initials": "M"}, {"family": "Khan", "given": "Muhammad Tanweer", "initials": "MT"}, {"family": "Manner\u00e5s Holm", "given": "Louise", "initials": "L"}, {"family": "Olsson", "given": "Lisa", "initials": "L"}, {"family": "Bergh", "given": "Per-Olof", "initials": "PO"}, {"family": "Molinaro", "given": "Antonio", "initials": "A"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Caesar", "given": "Robert", "initials": "R"}, {"family": "Nieuwdorp", "given": "Max", "initials": "M"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "volume": "97", "pages": "102162", "issn-l": "2212-8778"}, "abstract": "Sucrose-rich diets promote hepatic de novo lipogenesis (DNL) and steatosis through interactions with the gut microbiota. However, the role of sugar-microbiota dynamics in the absence of dietary fat remains unclear. This study aimed to investigate the effects of a high-sucrose, zero-fat diet (ZFD) on hepatic steatosis and host metabolism in conventionally raised (CONVR) and germ-free (GF) mice.\n\nCONVR and GF mice were fed a ZFD, and hepatic lipid accumulation, gene expression, and metabolite levels were analyzed. DNL activity was assessed by measuring malonyl-CoA levels, expression of key DNL enzymes, and activation of the transcription factor SREBP-1c. Metabolomic analyses of portal vein plasma identified microbiota-derived metabolites linked to hepatic steatosis. To further examine the role of SREBP-1c, its hepatic expression was knocked down using antisense oligonucleotides in CONVR ZFD-fed mice.\n\nThe gut microbiota was essential for sucrose-induced DNL and hepatic steatosis. In CONVR ZFD-fed mice, hepatic fat accumulation increased alongside elevated expression of genes encoding DNL enzymes, higher malonyl-CoA levels, and upregulation of SREBP-1c. Regardless of microbiota status, ZFD induced fatty acid elongase and desaturase gene expression and increased hepatic monounsaturated fatty acids. Metabolomic analyses identified microbiota-derived metabolites associated with hepatic steatosis. SREBP-1c knockdown in CONVR ZFD-fed mice reduced hepatic steatosis and suppressed fatty acid synthase expression.\n\nSucrose-microbiota interactions and SREBP-1c are required for DNL and hepatic steatosis in the absence of dietary fat. These findings provide new insights into the complex interplay between diet, gut microbiota, and metabolic regulation.", "doi": "10.1016/j.molmet.2025.102162", "pmid": "40345386", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12145984"}, {"db": "pii", "key": "S2212-8778(25)00069-9"}], "notes": [], "created": "2025-05-26T07:51:16.266Z", "modified": "2025-11-14T11:06:18.789Z"}, {"entity": "publication", "iuid": "eee4ee4c42964130a2cc8776b8228c33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eee4ee4c42964130a2cc8776b8228c33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eee4ee4c42964130a2cc8776b8228c33"}}, "title": "Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean.", "authors": [{"family": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "Aydo\u011fan", "given": "Ay\u00e7a", "initials": "A", "orcid": "0000-0003-0171-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/191b5ce05f6343e4825ef86d5703f8df.json"}}, {"family": "Karamurat", "given": "Cansu", "initials": "C", "orcid": "0000-0002-3596-9036", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c6c312d10a4d5a8c806b8550709016.json"}}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0ad7b1c36784c0092fd82f6d792c4bb.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Kazanc\u0131", "given": "D Deniz", "initials": "DD", "orcid": "0000-0002-8333-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f28aea0bd7e4bb7b6ac3d8843cae17f.json"}}, {"family": "Do\u011fu", "given": "Ay\u00e7a K\u00fc\u00e7\u00fckakda\u011f", "initials": "AK", "orcid": "0000-0001-6208-4092", "researcher": {"href": "https://publications.scilifelab.se/researcher/5599e1dd0d34404cb490ae2da3213b17.json"}}, {"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC", "orcid": "0000-0003-4424-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57ecd0264874105bb04cf9eb0cfce25.json"}}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E", "orcid": "0000-0002-8194-0277", "researcher": {"href": "https://publications.scilifelab.se/researcher/c319bee9c36a4e6a88dee29c8edc9d0d.json"}}, {"family": "Moots", "given": "Hannah M", "initials": "HM", "orcid": "0000-0002-6637-6321", "researcher": {"href": "https://publications.scilifelab.se/researcher/5105354f578c480ba144061ffbb49bf5.json"}}, {"family": "Umurtak", "given": "G\u00fcls\u00fcn", "initials": "G", "orcid": "0000-0003-0493-1868", "researcher": {"href": "https://publications.scilifelab.se/researcher/797ff752aeb54d4f9ea67dc624e25380.json"}}, {"family": "Duru", "given": "Refik", "initials": "R"}, {"family": "Fidan", "given": "Erkan", "initials": "E", "orcid": "0000-0002-6777-927X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9cfca389b2f9421391c08cac15b6577b.json"}}, {"family": "\u00c7evik", "given": "\u00d6zlem", "initials": "\u00d6", "orcid": "0000-0001-5442-3744", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbb50dfe46c4ed4b3a2894df441dee4.json"}}, {"family": "Erdo\u011fu", "given": "Bur\u00e7in", "initials": "B"}, {"family": "Korkut", "given": "Taner", "initials": "T", "orcid": "0000-0001-9810-231X", "researcher": {"href": "https://publications.scilifelab.se/researcher/50588d8226e34cb6a6572eecdb51690d.json"}}, {"family": "Kn\u00fcsel", "given": "Christopher J", "initials": "CJ", "orcid": "0000-0002-2506-3652", "researcher": {"href": "https://publications.scilifelab.se/researcher/02d89a57c7ef4d7a8681d49fb13b9b97.json"}}, {"family": "Haddow", "given": "Scott", "initials": "S", "orcid": "0000-0002-3970-7447", "researcher": {"href": "https://publications.scilifelab.se/researcher/433ccd36adc742fc984c9db5f0bc5c25.json"}}, {"family": "Larsen", "given": "Clark Spencer", "initials": "CS", "orcid": "0000-0002-6905-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/9319177bbfe04b6d8c491ee0083c807f.json"}}, {"family": "\u00d6zbal", "given": "Rana", "initials": "R", "orcid": "0000-0001-6765-2765", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad960fa098e477eac6f367ce0e659c9.json"}}, {"family": "Gerritsen", "given": "Fokke", "initials": "F", "orcid": "0000-0002-6665-1928", "researcher": {"href": "https://publications.scilifelab.se/researcher/d447abfa3d8b42bd85d56693a1c9cbb0.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Eylem", "initials": "E", "orcid": "0000-0003-1314-3695", "researcher": {"href": "https://publications.scilifelab.se/researcher/501515d068784d6b8d38c053e6860ae5.json"}}, {"family": "Akbaba", "given": "Ali", "initials": "A", "orcid": "0000-0001-6755-6546", "researcher": {"href": "https://publications.scilifelab.se/researcher/757adfca411c4168a0a51c5765852aa9.json"}}, {"family": "Usanmaz", "given": "Uygar Ozan", "initials": "UO", "orcid": "0000-0002-7013-3023", "researcher": {"href": "https://publications.scilifelab.se/researcher/b125bb77ca0e4b4d8a91c7a0a0c1706b.json"}}, {"family": "Derici", "given": "Yasin Cemre", "initials": "YC", "orcid": "0000-0001-5631-9588", "researcher": {"href": "https://publications.scilifelab.se/researcher/548691e4be8e416ba6b7ba0ef06f6910.json"}}, {"family": "U\u00e7mazo\u011flu", "given": "Mine", "initials": "M", "orcid": "0009-0000-9101-6929", "researcher": {"href": "https://publications.scilifelab.se/researcher/79197c3193164647b40444bf386d0c6d.json"}}, {"family": "Jay", "given": "Flora", "initials": "F", "orcid": "0000-0001-5884-4730", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8c74aed5a8a4976be210b133fb905f5.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Mehmet", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS", "orcid": "0000-0001-8143-8159", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f77cf0f580409f98004f71cf99c001.json"}}, {"family": "Malaspinas", "given": "Anna-Sapfo", "initials": "AS", "orcid": "0000-0003-1001-7511", "researcher": {"href": "https://publications.scilifelab.se/researcher/883d44be08be42188c3423a3498ef898.json"}}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7", "orcid": "0000-0001-8675-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/acefd01d35f04a0b99350ec4828adfcb.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}], "type": "journal article", "published": "2025-06-26", "journal": {"title": "Science", "issn": "1095-9203", "volume": "388", "issue": "6754", "pages": "eadr3326", "issn-l": "0036-8075"}, "abstract": "West Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Holocene West Anatolia using 30 new paleogenomes. We show that Neolithization in West Anatolia was a multifaceted process, characterized by the assimilation of Neolithic practices by local foragers, the influx of eastern populations, and their admixture, with their descendants subsequently establishing Neolithic Southeast Europe. We then coanalyzed genetic and cultural similarities across early Holocene Anatolian and Aegean Neolithic villages using 58 material culture elements. Cultural distances among villages correlate with their spatial distances but not with their genetic distances after controlling for geography. This suggests that cultural change was often decoupled from genetically visible mobility.", "doi": "10.1126/science.adr3326", "pmid": "40570102", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-24T10:40:50.203Z", "modified": "2025-11-24T10:40:52.334Z"}, {"entity": "publication", "iuid": "00ab4a882a5c45daaf75dcb38a32836b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00ab4a882a5c45daaf75dcb38a32836b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00ab4a882a5c45daaf75dcb38a32836b"}}, "title": "Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation.", "authors": [{"family": "Marsh", "given": "Audrey J", "initials": "AJ"}, {"family": "Pirogov", "given": "Sergei", "initials": "S"}, {"family": "Kaur", "given": "Yadwinder", "initials": "Y"}, {"family": "Ruffridge", "given": "Abby J", "initials": "AJ"}, {"family": "Sajwan", "given": "Suresh", "initials": "S"}, {"family": "Gibson", "given": "Tyler J", "initials": "TJ"}, {"family": "Hunt", "given": "George", "initials": "G"}, {"family": "Harrison", "given": "Melissa M", "initials": "MM"}, {"family": "Mannervik", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2025-06-19", "journal": {"title": "Mol. Cell", "issn": "1097-4164", "volume": "85", "issue": "12", "pages": "2409-2424.e8", "issn-l": "1097-2765"}, "abstract": "Immediately after fertilization, the genome is transcriptionally quiescent. Maternally encoded pioneer factors reprogram the chromatin state and facilitate transcription of the zygotic genome. In Drosophila, transcription is initiated by the pioneer factor Zelda. While Zelda-occupied sites are enriched with histone acetylation, a post-translational mark associated with active cis-regulatory regions, the functional relationship between Zelda and histone acetylation remained unclear. We show that Zelda-mediated recruitment of the histone acetyltransferase CREB-binding protein (CBP) is essential for zygotic transcription. CBP catalytic activity is necessary for the release of RNA polymerase II (RNA Pol II) into elongation and for embryonic development. However, CBP also activates transcription independent of acetylation through RNA Pol II recruitment. Neither CBP-mediated acetylation nor CBP itself is required for the pioneering function of Zelda. Our data suggest that pioneer-factor-mediated recruitment of CBP is a conserved mechanism required to activate zygotic transcription but is separable from the function of pioneer factors in restructuring chromatin accessibility.", "doi": "10.1016/j.molcel.2025.05.009", "pmid": "40441155", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2081331"}, {"db": "pmc", "key": "PMC12181052"}, {"db": "pii", "key": "S1097-2765(25)00414-9"}], "notes": [], "created": "2025-07-18T10:23:07.052Z", "modified": "2025-07-18T10:23:07.057Z"}, {"entity": "publication", "iuid": "af31c78497dd425b9e018282d774153b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af31c78497dd425b9e018282d774153b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af31c78497dd425b9e018282d774153b"}}, "title": "Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.", "authors": [{"family": "An", "given": "Yueqing", "initials": "Y", "orcid": "0000-0003-0267-7106", "researcher": {"href": "https://publications.scilifelab.se/researcher/f83fa56252e649ffa3a39db8f3377932.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}], "type": "journal article", "published": "2025-06-17", "journal": {"title": "mSystems", "issn": "2379-5077", "pages": "e0172324", "volume": "10", "issue": "6", "issn-l": "2379-5077"}, "abstract": "Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the \u03b1-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.\n\nWe explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.", "doi": "10.1128/msystems.01723-24", "pmid": "40358205", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12172492"}], "notes": [], "created": "2025-05-26T07:50:58.503Z", "modified": "2025-11-14T11:08:35.746Z"}, {"entity": "publication", "iuid": "7f700b3e5e634b2295705bc2ae62f3eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f700b3e5e634b2295705bc2ae62f3eb"}}, "title": "Spatial organization, chromatin accessibility and gene-regulatory programs defining mouse sensory neurons.", "authors": [{"family": "Krauter", "given": "Doris", "initials": "D", "orcid": "0000-0002-1779-093X", "researcher": {"href": "https://publications.scilifelab.se/researcher/631f89b570c44663b8c6a29f0759aca2.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J", "orcid": "0000-0003-1540-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/96dfeacf7fe04bf099fbddf0c45ef693.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-06-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "908", "issn-l": "2399-3642"}, "abstract": "Heterogeneity among somatosensory neurons is necessary for internal and external sensation. Precise patterns of gene transcription orchestrated through enhancer activation maintain heterogeneity. Thus, high-resolution cell type classification, chromatin accessibility and its relation to enhancer activation can explain the governing principles for sensory neuron heterogeneity. Here, we present an integrated atlas from published high-quality scRNA-seq datasets and resequencing the dorsal root ganglion, including over 44,000 neurons. MERSCOPE spatial transcriptomics confirms cell types in situ, including previously unrecognized neuronal types, and a spatial zonation of both neurons and non-neuronal cells. We present a cell type specific open chromatin atlas revealing enhancer driven regulons and gene-regulatory networks organized into co-regulated gene-programs that together define sensory neuron diversity. Cell type complexity is shown to be generated by layered co-regulated transcriptional modules representing shared functions across different scales of the neuronal type hierarchy with cell type specific contribution as the exception.", "doi": "10.1038/s42003-025-08315-1", "pmid": "40500276", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12159162"}, {"db": "pii", "key": "10.1038/s42003-025-08315-1"}], "notes": [], "created": "2025-07-18T10:23:45.299Z", "modified": "2025-11-14T11:07:16.782Z"}, {"entity": "publication", "iuid": "674ed939c1a74109b72a53ce6576ea0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/674ed939c1a74109b72a53ce6576ea0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/674ed939c1a74109b72a53ce6576ea0d"}}, "title": "Unlocking novel T cell-based immunotherapy for hepatocellular carcinoma through neoantigen-driven T cell receptor isolation.", "authors": [{"family": "Maravelia", "given": "Panagiota", "initials": "P"}, {"family": "Yao", "given": "Haidong", "initials": "H", "orcid": "0009-0007-4791-5063", "researcher": {"href": "https://publications.scilifelab.se/researcher/03a40cff36064374912d40cc5a9c65db.json"}}, {"family": "Cai", "given": "Curtis", "initials": "C", "orcid": "0000-0002-3490-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ea25e71e96246d89437270a12cc9e47.json"}}, {"family": "Nascimento Silva", "given": "Daniela", "initials": "D", "orcid": "0000-0003-2165-4989", "researcher": {"href": "https://publications.scilifelab.se/researcher/061bbf2c5a864c5c9e852fcab907d29e.json"}}, {"family": "Fransson", "given": "Jennifer", "initials": "J", "orcid": "0000-0003-4762-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/30428cafc89647768f6c69eecf98efcf.json"}}, {"family": "Nilsson", "given": "Ola B", "initials": "OB", "orcid": "0000-0002-7516-1760", "researcher": {"href": "https://publications.scilifelab.se/researcher/096ce3bf888b4ad395d53bb3c11f6946.json"}}, {"family": "Lu", "given": "Yong-Chen William", "initials": "YW", "orcid": "0000-0002-0275-9825", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8d7936625c42078b815953810ee136.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Gatto", "given": "Francesca", "initials": "F"}, {"family": "Rovesti", "given": "Giulia", "initials": "G", "orcid": "0000-0002-2761-9482", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd6c4824c71c44378a7f45649766f4cd.json"}}, {"family": "Carlsten", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9815-0012", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dadae83c2494c7abc65118f04e1b6b6.json"}}, {"family": "Sallberg", "given": "Matti", "initials": "M", "orcid": "0000-0002-8858-5132", "researcher": {"href": "https://publications.scilifelab.se/researcher/89d4712be75441d6b49aca02c600bc70.json"}}, {"family": "St\u00e5l", "given": "Per", "initials": "P"}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Pasetto", "given": "Anna", "initials": "A", "orcid": "0000-0002-5254-2173", "researcher": {"href": "https://publications.scilifelab.se/researcher/781c8b467fa144e494d13c7a3e80b4fc.json"}}], "type": "journal article", "published": "2025-06-06", "journal": {"title": "Gut", "issn": "1468-3288", "volume": "74", "issue": "7", "pages": "1125-1136", "issn-l": "0017-5749"}, "abstract": "Tumour-infiltrating T cells can mediate both antitumour immunity and promote tumour progression by creating an immunosuppressive environment. This dual role is especially relevant in hepatocellular carcinoma (HCC), characterised by a unique microenvironment and limited success with current immunotherapy.\n\nWe evaluated T cell responses in patients with advanced HCC by analysing tumours, liver flushes and liver-draining lymph nodes, to understand whether reactive T cell populations could be identified despite the immunosuppressive environment.\n\nT cells isolated from clinical samples were tested for reactivity against predicted neoantigens. Single-cell RNA sequencing was employed to evaluate the transcriptomic and proteomic profiles of antigen-experienced T cells. Neoantigen-reactive T cells expressing 4-1BB were isolated and characterised through T-cell receptor (TCR)-sequencing.\n\nBioinformatic analysis identified 542 candidate neoantigens from seven patients. Of these, 78 neoantigens, along with 11 hotspot targets from HCC driver oncogenes, were selected for ex vivo T cell stimulation. Reactivity was confirmed in co-culture assays for 14 targets, with most reactive T cells derived from liver flushes and lymph nodes. Liver flush-derived T cells exhibited central memory and effector memory CD4+ with cytotoxic effector profiles. In contrast, tissue-resident memory CD4+ and CD8+ T cells with an exhausted profile were primarily identified in the draining lymph nodes.\n\nThese findings offer valuable insights into the functional profiles of neoantigen-reactive T cells within and surrounding the HCC microenvironment. T cells isolated from liver flushes and tumour-draining lymph nodes may serve as a promising source of reactive T cells and TCRs for further use in immunotherapy for HCC.", "doi": "10.1136/gutjnl-2024-334148", "pmid": "39832892", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12611799"}, {"db": "pii", "key": "gutjnl-2024-334148"}], "notes": [], "created": "2025-11-19T08:23:34.477Z", "modified": "2025-11-21T15:22:04.326Z"}, {"entity": "publication", "iuid": "f64e4dcded1240568e175d59318ecd68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f64e4dcded1240568e175d59318ecd68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f64e4dcded1240568e175d59318ecd68"}}, "title": "The genome sequence of the Eurasian Curlew, Numenius arquata (Linnaeus, 1758).", "authors": [{"family": "Walsh", "given": "Grace", "initials": "G"}, {"family": "Donoghue", "given": "Barry O'", "initials": "BO"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "McMahon", "given": "Barry John", "initials": "BJ", "orcid": "0000-0003-3143-8075", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ba44012f4b040ae918c7cabfdbb49ec.json"}}, {"family": "Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team", "given": "", "initials": ""}, {"family": "WellcomeSanger Institute Scientific Operations: Sequencing Operations", "given": "", "initials": ""}, {"family": "Wellcome Sanger Institute Tree of Life Core Informatics team", "given": "", "initials": ""}, {"family": "Tree of Life Core Informatics collective", "given": "", "initials": ""}, {"family": "Darwin Tree of Life Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "Wellcome Open Res", "issn": "2398-502X", "volume": "10", "pages": "298", "issn-l": "2398-502X"}, "abstract": "We present a genome assembly from a female specimen of Numenius arquata (Eurasian Curlew; Chordata; Aves; Charadriiformes; Scolopacidae). The assembly contains two haplotypes with total lengths of 1,348.86 megabases and 1,198.36 megabases. Most of haplotype 1 (89.99%) is scaffolded into 41 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 17.13 kilobases. Gene annotation of this assembly on Ensembl identified 15,412 protein-coding genes.", "doi": "10.12688/wellcomeopenres.24272.1", "pmid": "40880729", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12381557"}], "notes": [], "created": "2025-11-21T09:17:11.591Z", "modified": "2025-11-21T09:17:11.682Z"}, {"entity": "publication", "iuid": "2c7db473960c4c7fa52c676e6bfc84e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7db473960c4c7fa52c676e6bfc84e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7db473960c4c7fa52c676e6bfc84e0"}}, "title": "Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer.", "authors": [{"family": "Sur", "given": "Inderpreet", "initials": "I"}, {"family": "Zhao", "given": "Wenshuo", "initials": "W"}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Kling Pilstr\u00f6m", "given": "Margareta", "initials": "M"}, {"family": "Webb", "given": "Anna T", "initials": "AT", "orcid": "0000-0001-6045-415X", "researcher": {"href": "https://publications.scilifelab.se/researcher/909754226aa04eb0824fc87c9efc628a.json"}}, {"family": "Cheng", "given": "Huaitao", "initials": "H"}, {"family": "Ristim\u00e4ki", "given": "Ari", "initials": "A"}, {"family": "Katajisto", "given": "Pekka", "initials": "P", "orcid": "0000-0002-3033-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/68045c70bad544b68bbe913e7bf0ded8.json"}}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Rannikmae", "given": "Helena", "initials": "H"}, {"family": "de la Roche", "given": "Marc", "initials": "M"}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "8", "issue": "6", "issn-l": "2575-1077"}, "abstract": "Cancer has been characterized as a wound that does not heal. Malignant cells are morphologically distinct from normal proliferating cells but have extensive similarities to tissues undergoing wound healing and/or regeneration. The mechanistic basis of this similarity has, however, remained enigmatic. Here, we show that the genomic region upstream of Myc, which carries more cancer susceptibility in humans than any other genomic region, is required for intestinal regeneration after radiation damage. Failure to regenerate is associated with inefficient Ly6a/Sca1+ stem/progenitor cell mobilization, and almost complete failure to re-establish Lgr5+ cell compartment in the intestinal crypts. The Myc upstream region is also critical for growth of adult intestinal cells in 3D organoid culture. We show that culture conditions recapitulating most aspects of adult normal tissue architecture still reprogram normal cells to proliferate using a mechanism similar to that employed by cancer cells. Our results establish a function for the Myc super-enhancer region as the genetic link between tissue regeneration and tumorigenesis, and demonstrates that normal tissue renewal and regeneration of tissues after severe damage are mechanistically distinct.2-540", "doi": "10.26508/lsa.202403090", "pmid": "40180576", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969384"}, {"db": "pii", "key": "8/6/e202403090"}], "notes": [], "created": "2025-04-07T08:30:27.159Z", "modified": "2025-04-07T08:30:27.535Z"}, {"entity": "publication", "iuid": "f0769cf27b0a4d2db77bc3cfe4f6f8d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0769cf27b0a4d2db77bc3cfe4f6f8d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0769cf27b0a4d2db77bc3cfe4f6f8d1"}}, "title": "Phylogenetic relationships and the identification of allopolyploidy in circumpolar Silene sect. Physolychnis.", "authors": [{"family": "Quatela", "given": "Anne-Sophie", "initials": "AS", "orcid": "0009-0009-1449-2281", "researcher": {"href": "https://publications.scilifelab.se/researcher/abdbdd63913b492c808ef0f1d9b2a639.json"}}, {"family": "Cangren", "given": "Patrik", "initials": "P"}, {"family": "de Lima Ferreira", "given": "Paola", "initials": "P", "orcid": "0000-0002-6957-4243", "researcher": {"href": "https://publications.scilifelab.se/researcher/71143c335a5c4c21954e2730e8e7c528.json"}}, {"family": "Woudstra", "given": "Yannick", "initials": "Y", "orcid": "0000-0001-8861-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/424f227ccfbd44ed9c52387faa30269a.json"}}, {"family": "Zsoldos-Skahjem", "given": "Andreas", "initials": "A"}, {"family": "Bacon", "given": "Christine D", "initials": "CD", "orcid": "0000-0003-2341-2705", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4e957ca1d6049418d276fcc44e077fc.json"}}, {"family": "de Boer", "given": "Hugo J", "initials": "HJ", "orcid": "0000-0003-1985-7859", "researcher": {"href": "https://publications.scilifelab.se/researcher/a232c69265cb41c9980512b4a30c19f6.json"}}, {"family": "Oxelman", "given": "Bengt", "initials": "B", "orcid": "0000-0002-6104-4264", "researcher": {"href": "https://publications.scilifelab.se/researcher/516997145fcf40eb8a777d82d5f1dca1.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Am. J. Bot.", "issn": "1537-2197", "volume": "112", "issue": "6", "pages": "e70051", "issn-l": "0002-9122"}, "abstract": "Species complexes are groups of closely related species with ambiguous delimitation, often composed of recently diverged lineages. Polyploidization and uniparental reproduction (i.e., selfing and apomixis) can play important roles in the origin of species complexes. These complexes pose challenges for species-based scientific questions, such as the estimation of species richness or conservation prioritization.\n\nWe determined the potential of resolving taxonomically complex groups using target enrichment in the circumpolar Silene uralensis complex (Caryophyllaceae). We proposed a metric using genetic distances between phased alleles to distinguish diploids from allopolyploids.\n\nOur results identified geographic structure of populations, with the northern American and Greenlandic samples having a common ancestor. We found little phylogenetic support for the most recent taxonomic treatment of the Silene uralensis complex.\n\nThe study highlights the use of target enrichment in testing taxonomic hypotheses in diploids and the challenges of studying recently diverged lineages.", "doi": "10.1002/ajb2.70051", "pmid": "40405418", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12189834"}], "notes": [], "created": "2025-11-24T11:06:01.819Z", "modified": "2025-11-24T11:06:02.169Z"}, {"entity": "publication", "iuid": "0cf514f45b5e4d7fac663132f0139fab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cf514f45b5e4d7fac663132f0139fab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cf514f45b5e4d7fac663132f0139fab"}}, "title": "Green Listed v2.0: A Web Application for Streamlined Design of Custom CRISPR Screens.", "authors": [{"family": "Henkel", "given": "Esbj\u00f6rn", "initials": "E"}, {"family": "Li", "given": "Zhaojun", "initials": "Z"}, {"family": "Uvehag", "given": "Daniel", "initials": "D"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B"}, {"family": "Henkel", "given": "Martin", "initials": "M"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "CRISPR J", "issn": "2573-1602", "issn-l": null, "volume": "8", "issue": "3", "pages": "216-223"}, "abstract": "Custom CRISPR screens are powerful tools for rapid, hypothesis-driven discovery, but their design is often complex and time-consuming. Green Listed v2.0 simplifies this process with an intuitive workflow for designing custom CRISPR spacer libraries and supports downstream analysis for all users, irrespective of their computational experience. The web application features a user-friendly graphical interface freely accessible at https://greenlisted.cmm.se. Version 2.0 includes significant upgrades to the original 2016 version that were implemented based on user feedback. This includes a new gene synonym tool, expanded library options, optimized output lists, performance improvements, and linked scripts for the rational design of custom CRISPR screen gene sets.", "doi": "10.1089/crispr.2025.0023", "pmid": "40329823", "labels": {"CRISPR Functional Genomics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-05-09T09:28:25.653Z", "modified": "2025-09-05T13:57:58.831Z"}, {"entity": "publication", "iuid": "dbbacfc5e2734fc19c98ec14dd081705", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbbacfc5e2734fc19c98ec14dd081705"}}, "title": "Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "Nagombi", "given": "Elizah", "initials": "E"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "34", "issue": "11", "pages": "e17780", "issn-l": "0962-1083"}, "abstract": "Hybridisation is known to occur between a wide range of taxa, including species for which strong sexual selection has led to markedly different sexual phenotypes and lek-mating behaviours. To what extent occasional hybridisation can overcome the reproductive barriers in such systems and, for example, lead to the establishment of hybrid zones is poorly known. In this study, we address this question by focusing on one of the most well-known avian radiations in which sexual selection has resulted in an extraordinary assemblage of phenotypic diversity and lek-mating behaviours: the birds-of-paradise (Paradisaeidae). We quantify the genome-wide distribution of introgression and find multiple signals of recent and historical gene flow between and within two genera of birds-of-paradise, Astrapia and Paradigalla. In addition, we present the first empirical genomic indication of a putative hybrid zone between two lekking bird-of-paradise species that differ substantially in their sexually selected traits and behaviours. Our findings are consistent with the idea that behavioural and phenotypic traits may constitute weaker pre- and post-zygotic barriers to gene flow than generally thought in lek-mating species.", "doi": "10.1111/mec.17780", "pmid": "40298045", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12100584"}], "notes": [], "created": "2025-05-26T07:50:33.961Z", "modified": "2025-11-28T10:51:32.111Z"}, {"entity": "publication", "iuid": "20eb2f2bbb1c422eaa580402cd480382", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20eb2f2bbb1c422eaa580402cd480382.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20eb2f2bbb1c422eaa580402cd480382"}}, "title": "Fermentative Yeast Diversity at the Northern Range Limit of Their Oak Tree Hosts.", "authors": [{"family": "Pinto", "given": "Javier", "initials": "J"}, {"family": "Haberkorn", "given": "Chlo\u00e9", "initials": "C", "orcid": "0000-0002-7371-9177", "researcher": {"href": "https://publications.scilifelab.se/researcher/099838e4d3b94ee1af5cdfbf8ffea5d2.json"}}, {"family": "Franz\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "3", "pages": "e70110", "issn-l": "1758-2229"}, "abstract": "Fermentative yeasts play important roles in both ecological and industrial processes, but their distribution and abundance in natural environments are not well understood. We investigated the diversity of yeasts at the northern range limit of their oak tree hosts (Quercus spp.) in Sweden, and identified climatic and ecological conditions governing their distribution. Yeasts were isolated from bark samples from 28 forests and identified to the species level using DNA metabarcoding. Most communities were dominated by species in the Saccharomycetaceae family, especially by species of Saccharomyces, Kluyveromyces and Pichia. Each genus showed a distinct latitudinal and longitudinal distribution, and both temperature and precipitation metrics predicted significant variation in their abundance. Consistent with this, laboratory assays revealed significant effects of temperature on the growth of strains collected from different longitudes and latitudes. We found that older trees harbour more diverse and more balanced fermentative yeast communities with more evenly distributed species abundances. Communities across trees were more similar when sharing a common dominant species. This work provides a baseline for future studies on the impact of climate change on the fermentative yeast biodiversity of temperate forests in northern latitudes and contributes to a growing collection of wild isolates for potential biotechnological applications.", "doi": "10.1111/1758-2229.70110", "pmid": "40410946", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102073"}], "notes": [], "created": "2025-11-28T10:50:51.200Z", "modified": "2025-12-05T11:26:12.741Z"}, {"entity": "publication", "iuid": "2a2ca50ec2b44ca99ee63649522c4aaf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a2ca50ec2b44ca99ee63649522c4aaf"}}, "title": "Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes.", "authors": [{"family": "Papadopoulou", "given": "Sofia", "initials": "S", "orcid": "0000-0001-7315-3671", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f6cb7f8c28f4e0fbc030ee7311c6078.json"}}, {"family": "Linkhorst", "given": "Annika", "initials": "A", "orcid": "0000-0002-3609-5107", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba8c037d8ba4defbfa03364e2e264e7.json"}}, {"family": "Balmonte", "given": "John Paul", "initials": "JP", "orcid": "0000-0001-5571-4893", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3949f1396414e15a27c85460886d7ac.json"}}, {"family": "Csit\u00e1ri", "given": "Bianka", "initials": "B", "orcid": "0000-0002-5219-5829", "researcher": {"href": "https://publications.scilifelab.se/researcher/72ae1be693ac4900987f70a21a271494.json"}}, {"family": "Felf\u00f6ldi", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0003-2009-2478", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a452e1d353649bc860f59485fc8bf03.json"}}, {"family": "M\u00e1rton", "given": "Zsuzsanna", "initials": "Z", "orcid": "0000-0002-7420-5039", "researcher": {"href": "https://publications.scilifelab.se/researcher/631b674f8b91403e95b1bbc8383fd8a8.json"}}, {"family": "Mershad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A", "orcid": "0000-0002-7777-8166", "researcher": {"href": "https://publications.scilifelab.se/researcher/78425c54e73b4bc1bf8c8b900224d41d.json"}}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "issn-l": "1758-2229", "volume": "17", "issue": "3", "pages": "e70099"}, "abstract": "In the Boreal region, extreme seasonal variations in day-night length expose communities to dynamic light and temperature fluctuations. Freshwater bacterioplankton, representing key ecosystem components, faces climate-driven shifts; yet the fixed day-length patterns determined by latitude underscore the importance of studying light's role in predicting ecosystem responses. We investigated bacterial community composition in a brown peat bog and a clear oligotrophic lake across seasons with contrasting light regimes: the summer solstice (> 20 h of daylight) and the autumn equinox (equal day-night length). Using amplicon sequencing of 16S rRNA transcripts, alongside measurements of physicochemical parameters, organic matter characterisation and dissolved carbon dioxide and methane gas measurements, we found no diel cycling in the lake during either period or in the peat bog near the summer solstice. However, the structure of bacterial peat bog communities exhibited cyclic changes over diel cycles at the autumn equinox. Twelve amplicon sequence variants, including both phototrophic and heterotrophic taxa, increased in abundance at all measured morning sampling times. These findings provide valuable insights into the diel patterns of boreal lentic habitats and their bacterioplankton communities, highlighting the absence of diel fluctuations in some systems and seasons, while revealing cyclic dynamics in others, driven by conditionally rare taxa.", "doi": "10.1111/1758-2229.70099", "pmid": "40344486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12061850"}], "notes": [], "created": "2025-05-12T05:46:12.949Z", "modified": "2025-11-28T10:50:46.010Z"}, {"entity": "publication", "iuid": "3cba993176914d9489704b83ceb80532", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3cba993176914d9489704b83ceb80532"}}, "title": "Defining short linear motif binding determinants by phage display-based deep mutational scanning.", "authors": [{"family": "Benz", "given": "Caroline", "initials": "C"}, {"family": "Maassen", "given": "Lars", "initials": "L"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Tsitsa", "given": "Ifigenia", "initials": "I", "orcid": "0000-0001-8154-5528", "researcher": {"href": "https://publications.scilifelab.se/researcher/9afb0faf7a4c435cbba2b4aa63b99b51.json"}}, {"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Protein Sci.", "issn": "1469-896X", "volume": "34", "issue": "6", "pages": "e70174", "issn-l": "0961-8368"}, "abstract": "Deep mutational scanning (DMS) has emerged as a powerful approach for evaluating the effects of mutations on binding or function. Here, we developed a DMS by phage display protocol to define the specificity determinants of short linear motifs (SLiMs) binding to peptide-binding domains. We first designed a benchmarking DMS library to evaluate the performance of the approach on well-known ligands for 11 different peptide-binding domains, including the talin-1 PTB domain, the G3BP1 NTF2 domain, and the MDM2 SWIB domain. Comparison with a set of reference motifs from the eukaryotic linear motif (ELM) database confirmed that the DMS by phage display analysis correctly identifies known motif binding determinants and provides novel insights into specificity determinants, including defining a non-canonical talin-1 PTB binding motif with a putative extended conformation. A second DMS library was designed, aiming to provide information on the binding determinants for 19 SLiM-based interactions between human and SARS-CoV-2 proteins. The analysis confirmed the affinity determining residues of viral peptides binding to host proteins and refined the consensus motifs in human peptides binding to five domains from SARS-CoV-2 proteins, including the non-structural protein (NSP) 9. The DMS analysis further pinpointed mutations that increased the affinity of ligands for NSP3 and NSP9. An affinity-improved cell-permeable NSP9-binding peptide was found to exert stronger antiviral effects than the wild-type peptide. Our study demonstrates that DMS by phage display can efficiently be multiplexed and applied to refine binding determinants and shows how the results can guide peptide-engineering efforts.", "doi": "10.1002/pro.70174", "pmid": "40411416", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12102759"}], "notes": [], "created": "2025-09-08T11:37:16.206Z", "modified": "2025-11-21T18:30:05.510Z"}, {"entity": "publication", "iuid": "a853b1443cee4b79835aa5a9bc6e26fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a853b1443cee4b79835aa5a9bc6e26fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a853b1443cee4b79835aa5a9bc6e26fb"}}, "title": "A marine and salt marsh sediment organic carbon database for European regional seas (EURO-CARBON).", "authors": [{"family": "Graversen", "given": "Anna Elizabeth L\u00f8vgren", "initials": "AEL"}, {"family": "L\u00f8nborg", "given": "Christian", "initials": "C"}, {"family": "Addamo", "given": "Anna Maria", "initials": "AM"}, {"family": "Pedersen", "given": "Sidsel Gurholt", "initials": "SG"}, {"family": "Chemello", "given": "Silvia", "initials": "S"}, {"family": "Alejo", "given": "Irene", "initials": "I"}, {"family": "Apostolaki", "given": "Eugenia T", "initials": "ET"}, {"family": "Asplund", "given": "Maria E", "initials": "ME"}, {"family": "Austin", "given": "William E N", "initials": "WEN"}, {"family": "Berov", "given": "Dimitar", "initials": "D"}, {"family": "Berto", "given": "Daniela", "initials": "D"}, {"family": "Bj\u00f6rk", "given": "Mats", "initials": "M"}, {"family": "Black", "given": "Kirsty", "initials": "K"}, {"family": "Bobchev", "given": "Nikola", "initials": "N"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}, {"family": "Borgersen", "given": "Gunhild", "initials": "G"}, {"family": "Bouma", "given": "Tjeerd", "initials": "T"}, {"family": "Costello", "given": "Mark J", "initials": "MJ"}, {"family": "Dahl", "given": "Martin", "initials": "M"}, {"family": "Diaz-Almela", "given": "Elena", "initials": "E"}, {"family": "Dimitriou", "given": "Panagiotis D", "initials": "PD"}, {"family": "Duarte", "given": "Carlos M", "initials": "CM"}, {"family": "Due\u00f1as", "given": "Carmen Leiva", "initials": "CL"}, {"family": "Efthymiadis", "given": "Pavlos T", "initials": "PT"}, {"family": "Elosegui", "given": "Ines Mazarrasa", "initials": "IM"}, {"family": "Espinosa", "given": "Maria Recio", "initials": "MR"}, {"family": "Filipsson", "given": "Helena L", "initials": "HL"}, {"family": "Fontela", "given": "Marcos", "initials": "M"}, {"family": "Fredriksen", "given": "Stein", "initials": "S"}, {"family": "Frigstad", "given": "Helene", "initials": "H"}, {"family": "Gagnon", "given": "Karine", "initials": "K"}, {"family": "Garcia-Escudero", "given": "Catalina A", "initials": "CA"}, {"family": "Giani", "given": "Michele", "initials": "M"}, {"family": "Grouhel-Pellouin", "given": "Anne", "initials": "A"}, {"family": "Guerra", "given": "Roberta", "initials": "R"}, {"family": "Gullstr\u00f6m", "given": "Martin", "initials": "M"}, {"family": "Gundersen", "given": "Hege", "initials": "H"}, {"family": "Hancke", "given": "Kasper", "initials": "K"}, {"family": "Majt\u00e9nyi-Hill", "given": "Claudia", "initials": "C"}, {"family": "Hunt", "given": "Corallie", "initials": "C"}, {"family": "Inostroza", "given": "Karina", "initials": "K"}, {"family": "Karakassis", "given": "Ioannis", "initials": "I"}, {"family": "Karamfilov", "given": "Ventzislav", "initials": "V"}, {"family": "Klayn", "given": "Stefania", "initials": "S"}, {"family": "Koziorowska", "given": "Katarzyna", "initials": "K"}, {"family": "Kuli\u0144ski", "given": "Karol", "initials": "K"}, {"family": "Lavery", "given": "Paul", "initials": "P"}, {"family": "Lenstra", "given": "Wytze K", "initials": "WK"}, {"family": "Lilleb\u00f8", "given": "Ana I", "initials": "AI"}, {"family": "Logemann", "given": "Ella", "initials": "E"}, {"family": "Magni", "given": "Paolo", "initials": "P"}, {"family": "Marb\u00e0", "given": "N\u00faria", "initials": "N"}, {"family": "Marco-Mendez", "given": "Candela", "initials": "C"}, {"family": "Martins", "given": "Marcio", "initials": "M"}, {"family": "Mateo", "given": "Miguel Angel", "initials": "MA"}, {"family": "Monnier", "given": "Briac", "initials": "B"}, {"family": "Mueller", "given": "Peter", "initials": "P"}, {"family": "Neto", "given": "Joao M", "initials": "JM"}, {"family": "Papageorgiou", "given": "Nafsika", "initials": "N"}, {"family": "de Rezende", "given": "Carlos Eduardo", "initials": "CE"}, {"family": "Pardo", "given": "Juan Carlos Farias", "initials": "JCF"}, {"family": "Pe\u00f1a", "given": "Jose Antonio Juanes De La", "initials": "JAJ"}, {"family": "Pergent", "given": "G\u00e9rard", "initials": "G"}, {"family": "Pi\u00f1eiro-Juncal", "given": "Nerea", "initials": "N"}, {"family": "Preston", "given": "Joanne", "initials": "J"}, {"family": "Rampazzo", "given": "Federico", "initials": "F"}, {"family": "Reithmaier", "given": "Gloria", "initials": "G"}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH"}, {"family": "Reynolds", "given": "Sarah", "initials": "S"}, {"family": "Ricart", "given": "Aurora M", "initials": "AM"}, {"family": "Santos", "given": "Rui", "initials": "R"}, {"family": "de Los Santos", "given": "Carmen B", "initials": "CB"}, {"family": "Santos", "given": "Isaac R", "initials": "IR"}, {"family": "Serrano", "given": "Eduard", "initials": "E"}, {"family": "Serrano", "given": "Oscar", "initials": "O"}, {"family": "Slomp", "given": "Caroline P", "initials": "CP"}, {"family": "Smeaton", "given": "Craig", "initials": "C"}, {"family": "Soler", "given": "Montserrar", "initials": "M"}, {"family": "Sousa", "given": "Ana I", "initials": "AI"}, {"family": "Spiegel", "given": "Timo", "initials": "T"}, {"family": "Stevenson", "given": "Angela", "initials": "A"}, {"family": "Thormar", "given": "Jonas", "initials": "J"}, {"family": "Trannum", "given": "Hilde Cecilie", "initials": "HC"}, {"family": "van Helmond", "given": "Niels A G M", "initials": "NAGM"}, {"family": "Paradis", "given": "Sarah", "initials": "S"}, {"family": "Vizzini", "given": "Salvatrice", "initials": "S"}, {"family": "Ward", "given": "Emma A", "initials": "EA"}, {"family": "Yau", "given": "Yvonne Y Y", "initials": "YYY"}, {"family": "Zakhama-Sraieb", "given": "Rym", "initials": "R"}, {"family": "Zribi", "given": "Imen", "initials": "I"}, {"family": "Zygadlowska", "given": "Olga M", "initials": "OM"}, {"family": "Jensen", "given": "Dorte Krause", "initials": "DK"}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Data Brief", "issn": "2352-3409", "volume": "60", "pages": "111595", "issn-l": "2352-3409"}, "abstract": "Marine and salt marsh sediments contain large amounts of organic carbon (OC) and are therefore important in the global carbon cycle. Here, we collated previously published and unpublished measurements of sediment OC in marine and salt marsh sediments in European regional seas (EURO-CARBON; available at https://doi.org/10.5281/zenodo.14905489). To the extent possible the OC data were complemented by variables such as sediment porosity and dry bulk density. The EURO-CARBON dataset holds 61306 individual data entries of sediment OC content from different regions of European regional seas. Around three quarters (76%) were collected in coastal and deep sea bare sediments, 18% from salt marshes, 7% from seagrass habitats, and 0.03% from macroalgal habitats. For all habitats and sediment depth layers the OC content varied between <0.1 and 41.56 % (avg.: 2.47 \u00b1 3.37 %; median: 1.39 %), with the content generally decreasing in the following sequence: salt marsh (5.01 \u00b1 5.96 %; 3.03 %) > seagrass (2.37 \u00b1 5.96 %; 3.03 %) > bare sediment (1.88 \u00b1 2.03 %; 1.20 %). The EURO-CARBON dataset will serve as a basis for future work, and it will be an important resource for researchers, managers, and policymakers working towards protecting sediment OC pools.", "doi": "10.1016/j.dib.2025.111595", "pmid": "40496737", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12149566"}, {"db": "pii", "key": "S2352-3409(25)00327-0"}], "notes": [], "created": "2025-11-21T16:03:18.981Z", "modified": "2025-11-21T17:39:04.259Z"}, {"entity": "publication", "iuid": "db4d0488321c44809973ce6d788f31cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db4d0488321c44809973ce6d788f31cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db4d0488321c44809973ce6d788f31cf"}}, "title": "Seasonal dynamics and nutrient controls of biogenic silica in Baltic Sea surface microplankton and picoplankton communities.", "authors": [{"family": "Churakova", "given": "Yelena", "initials": "Y", "orcid": "0000-0002-8017-2122", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e4b7f5ea6e243b6b08008cdfa88c07f.json"}}, {"family": "Aguilera", "given": "Anabella", "initials": "A", "orcid": "0000-0001-6743-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6e88f127e7d49d09f593a57aa4a794e.json"}}, {"family": "Charalampous", "given": "Evangelia", "initials": "E", "orcid": "0000-0002-7724-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5c7828275bf44408584d66ceeefa6b6.json"}}, {"family": "Conley", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0001-9668-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d95efcbb3ce8420494cbc2260d2b1aa1.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "volume": "91", "issue": "5", "pages": "e0067625", "issn-l": "0099-2240"}, "abstract": "In recent years, new contributors to the marine silica cycle have emerged, including pico-sized phytoplankton (<2-3 \u00b5m in size) such as Synechococcus and picoeukaryotes. Their contribution and relevance to silica cycling are still under investigation. Field studies reporting the biogenic silica (bSi) standing stock in the pico-sized fraction are limited to silica-poor oligotrophic environments, and the mechanism of bSi accumulation in picoplankton remains unknown. We investigated the variability of bSi standing stocks in two size fractions (picoplankton, 0.22-3 \u00b5m and microplankton, >3 \u00b5m) in the dissolved silica-replete Baltic Sea via biweekly time series samplings spanning 2 years. Time series data showed that the large changes in bSi standing stock in the Baltic Proper were primarily related to microplankton biomass and community composition. Meanwhile, picoplankton were, at times, surprisingly high contributors to total bSi year-round (up to 21.6%). Simultaneously, we performed microcosm incubation experiments with natural phytoplankton communities in each season to examine how nutrient additions affected bSi concentrations. In these experiments, increases in microplankton bSi were directly correlated to increases in diatom biomass, highlighting their influential role in the Baltic Sea silica cycle. Meanwhile, phosphorus additions triggered an increase in picoplankton bSi accumulation in all experiments. This uncovers a potential control of bSi accumulation in picoplankton, which can help identify the cellular mechanisms behind this process and uncover their role in silica cycling. The results link phytoplankton community composition and silica cycling, which is important for understanding the consequences of organism shifts due to climate change.IMPORTANCEThe marine carbon and silica cycles are tightly intertwined and largely controlled by diatoms. Nevertheless, recent studies, mostly in oligotrophic waters, have proposed new contributors to the marine silica cycle: picoplankton. Here, we report the first study of seasonal dynamics of biogenic silica (bSi) standing stock in microplankton and picoplankton in the silica-replete Baltic Sea. Microplankton bSi dynamics were correlated with changes in composition and biomass. Picoplankton were consistent contributors to bSi, and for the first time in diverse natural communities, we found a direct correlation between phosphorus and bSi accumulation. The results are important for understanding how climate change-predicted phytoplankton composition shifts will affect carbon and silica cycling and provide a direction for future research on nutrient controls of silica accumulation in picoplankton.", "doi": "10.1128/aem.00676-25", "pmid": "40293244", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12094022"}], "notes": [], "created": "2025-11-26T08:38:35.731Z", "modified": "2025-11-26T08:38:36.366Z"}, {"entity": "publication", "iuid": "14a490b69be949de8cbbefbdfbe5d0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14a490b69be949de8cbbefbdfbe5d0e5"}}, "title": "Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar.", "authors": [{"family": "Miraldo", "given": "A", "initials": "A", "orcid": "0000-0001-6107-006X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1de25c21dc4c5fb541f4e8766de4b7.json"}}, {"family": "Sundh", "given": "J", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Iwaszkiewicz-Eggebrecht", "given": "E", "initials": "E"}, {"family": "Buczek", "given": "M", "initials": "M"}, {"family": "Goodsell", "given": "R", "initials": "R"}, {"family": "Johansson", "given": "H", "initials": "H"}, {"family": "Fisher", "given": "B L", "initials": "BL", "orcid": "0000-0002-4653-3270", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4747cc54254e8181f595e6fe21b953.json"}}, {"family": "Raharinjanahary", "given": "D", "initials": "D"}, {"family": "Rajoelison", "given": "E T", "initials": "ET"}, {"family": "Ranaivo", "given": "C", "initials": "C"}, {"family": "Randrianandrasana", "given": "C", "initials": "C"}, {"family": "Rafanomezantsoa", "given": "J-J", "initials": "J"}, {"family": "Manoharan", "given": "L", "initials": "L"}, {"family": "Granqvist", "given": "E", "initials": "E", "orcid": "0000-0002-1513-1674", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b07f15f8724fdbbcdf34e6d6837147.json"}}, {"family": "van Dijk", "given": "L J A", "initials": "LJA"}, {"family": "Alberg", "given": "L", "initials": "L"}, {"family": "\u00c5hl\u00e9n", "given": "D", "initials": "D"}, {"family": "Aspebo", "given": "M", "initials": "M"}, {"family": "\u00c5str\u00f6m", "given": "S", "initials": "S"}, {"family": "Bellviken", "given": "A", "initials": "A"}, {"family": "Bergman", "given": "P-E", "initials": "P"}, {"family": "Bj\u00f6rklund", "given": "S", "initials": "S"}, {"family": "Bj\u00f6rkman", "given": "M P", "initials": "MP", "orcid": "0000-0001-5768-1976", "researcher": {"href": "https://publications.scilifelab.se/researcher/9821ee4a87c74dde82d9a6a4ebc2b1fc.json"}}, {"family": "Deng", "given": "J", "initials": "J"}, {"family": "Desborough", "given": "L", "initials": "L"}, {"family": "Dolff", "given": "E", "initials": "E"}, {"family": "Eliasson", "given": "A", "initials": "A"}, {"family": "Elmquist", "given": "H", "initials": "H"}, {"family": "Emanuelsson", "given": "H", "initials": "H"}, {"family": "Erixon", "given": "R", "initials": "R"}, {"family": "Fahlen", "given": "L", "initials": "L"}, {"family": "Frogner", "given": "C", "initials": "C"}, {"family": "F\u00fcrst", "given": "P", "initials": "P"}, {"family": "Grabs", "given": "A", "initials": "A"}, {"family": "Grudd", "given": "H", "initials": "H", "orcid": "0000-0002-9033-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/97348870e86e4c75ae6ce0be4cc99699.json"}}, {"family": "Guasconi", "given": "D", "initials": "D"}, {"family": "Gunnarsson", "given": "M", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "S", "initials": "S"}, {"family": "Hed", "given": "A", "initials": "A"}, {"family": "H\u00f6rnstr\u00f6m", "given": "E", "initials": "E"}, {"family": "J\u00f6nsson", "given": "A", "initials": "A"}, {"family": "Kanerot", "given": "S", "initials": "S"}, {"family": "Karlsson", "given": "A", "initials": "A"}, {"family": "Karlsson", "given": "D", "initials": "D", "orcid": "0000-0003-4639-823X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ecfa3c78df4076bce64c7eeb36ee4f.json"}}, {"family": "Klinth", "given": "M", "initials": "M"}, {"family": "Kraft", "given": "T", "initials": "T", "orcid": "0000-0002-1143-5494", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd6da126be9d48658afb96aac9532ead.json"}}, {"family": "Lahti", "given": "R", "initials": "R"}, {"family": "Larsson", "given": "M", "initials": "M"}, {"family": "Lernefalk", "given": "H", "initials": "H"}, {"family": "Lestander", "given": "Y", "initials": "Y"}, {"family": "Lindholm", "given": "L-T", "initials": "L"}, {"family": "Lindholm", "given": "M", "initials": "M"}, {"family": "Ljung", "given": "U", "initials": "U"}, {"family": "Ljung", "given": "K", "initials": "K"}, {"family": "Lundberg", "given": "J", "initials": "J", "orcid": "0000-0003-4316-9183", "researcher": {"href": "https://publications.scilifelab.se/researcher/86b74c200f2b402cad6b82cdf63259c9.json"}}, {"family": "Lundin", "given": "E", "initials": "E", "orcid": "0000-0002-3785-8305", "researcher": {"href": "https://publications.scilifelab.se/researcher/842e65aa96ef4dcaa8af13bf9e3f73f8.json"}}, {"family": "Malmenius", "given": "M", "initials": "M"}, {"family": "Marquina", "given": "D", "initials": "D"}, {"family": "Martinelli", "given": "J", "initials": "J"}, {"family": "Mertz", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "J", "initials": "J"}, {"family": "Patchett", "given": "A", "initials": "A"}, {"family": "Persson", "given": "N", "initials": "N"}, {"family": "Persson", "given": "J", "initials": "J"}, {"family": "Prus-Frankowska", "given": "M", "initials": "M"}, {"family": "Regazzoni", "given": "E", "initials": "E"}, {"family": "Rosander", "given": "K-G", "initials": "K"}, {"family": "Rydg\u00e5rd", "given": "M", "initials": "M"}, {"family": "Sandblom", "given": "C", "initials": "C"}, {"family": "Skord", "given": "J", "initials": "J"}, {"family": "St\u00e5lhandske", "given": "T", "initials": "T"}, {"family": "Svensson", "given": "F", "initials": "F"}, {"family": "Szpryngiel", "given": "S", "initials": "S", "orcid": "0000-0003-2965-2873", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec77cb9136184887b68a4ae8c4360927.json"}}, {"family": "Tajani", "given": "K", "initials": "K"}, {"family": "Tyboni", "given": "M", "initials": "M"}, {"family": "Ugarph", "given": "C", "initials": "C"}, {"family": "Vestermark", "given": "L", "initials": "L"}, {"family": "Vilhelmsson", "given": "J", "initials": "J"}, {"family": "Wahlgren", "given": "N", "initials": "N"}, {"family": "Wass", "given": "A", "initials": "A"}, {"family": "Wetterstrand", "given": "P", "initials": "P"}, {"family": "\u0141ukasik", "given": "P", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Tack", "given": "A J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}, {"family": "Andersson", "given": "A F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Roslin", "given": "T", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Ronquist", "given": "F", "initials": "F"}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "12", "issue": "1", "pages": "835"}, "abstract": "We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.", "doi": "10.1038/s41597-025-05151-0", "pmid": "40399316", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12095508"}, {"db": "pii", "key": "10.1038/s41597-025-05151-0"}], "notes": [], "created": "2025-11-19T08:51:31.233Z", "modified": "2025-11-21T12:26:09.639Z"}, {"entity": "publication", "iuid": "4dba785f8bab418ca9f0391499da9572", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dba785f8bab418ca9f0391499da9572.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dba785f8bab418ca9f0391499da9572"}}, "title": "Single-cell RNA-sequencing reveals early mitochondrial dysfunction unique to motor neurons shared across FUS- and TARDBP-ALS.", "authors": [{"family": "Schweingruber", "given": "Christoph", "initials": "C", "orcid": "0000-0003-4505-9068", "researcher": {"href": "https://publications.scilifelab.se/researcher/df74f600399f4fabaa9d186d23172fef.json"}}, {"family": "Nijssen", "given": "Jik", "initials": "J", "orcid": "0000-0003-0013-9750", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e17dd67c1aa45b1b12e8d8a457236b8.json"}}, {"family": "Mechtersheimer", "given": "Jonas", "initials": "J", "orcid": "0000-0001-8818-7671", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d8e9b06cdda42979c1447bd305f5902.json"}}, {"family": "Reber", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4885-3550", "researcher": {"href": "https://publications.scilifelab.se/researcher/c18e3ec9b7b64d3f8a734a76b71e3bbe.json"}}, {"family": "Leb\u0153uf", "given": "M\u00e9lanie", "initials": "M", "orcid": "0000-0003-0033-7159", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a0014951aaa4e0582a0fef1ee11b5b1.json"}}, {"family": "O'Brien", "given": "Niamh L", "initials": "NL", "orcid": "0000-0001-5951-1305", "researcher": {"href": "https://publications.scilifelab.se/researcher/73741194e1794a5ca40148001344ee22.json"}}, {"family": "Mei", "given": "Irene", "initials": "I", "orcid": "0009-0007-8238-6224", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5b33928c6334f4b8c436ace690786c9.json"}}, {"family": "Hedges", "given": "Erin", "initials": "E", "orcid": "0000-0002-2519-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c84bf7c4b754f2094a163b0fede16f4.json"}}, {"family": "Keuper", "given": "Michaela", "initials": "M", "orcid": "0000-0003-0319-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/c290cd22791a4e91aee49265e6739b25.json"}}, {"family": "Benitez", "given": "Julio Aguila", "initials": "JA"}, {"family": "Radoi", "given": "Vlad", "initials": "V", "orcid": "0000-0002-9657-8303", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f50b39d18924acfb4061f5df3acd774.json"}}, {"family": "Jastroch", "given": "Martin", "initials": "M", "orcid": "0000-0003-0358-3865", "researcher": {"href": "https://publications.scilifelab.se/researcher/67ebcd9680e2445497d3a7ac50e7724d.json"}}, {"family": "Ruepp", "given": "Marc-David", "initials": "MD", "orcid": "0000-0003-3264-9800", "researcher": {"href": "https://publications.scilifelab.se/researcher/a720da7447c74bbe8fabedd01b8bea07.json"}}, {"family": "Hedlund", "given": "Eva", "initials": "E", "orcid": "0000-0001-6347-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/d517e76df2e944e09ddbe87b7e0329af.json"}}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "4633", "issn-l": "2041-1723"}, "abstract": "Mutations in FUS and TARDBP cause amyotrophic lateral sclerosis (ALS), but the precise mechanisms of selective motor neuron degeneration remain unresolved. To address if pathomechanisms are shared across mutations and related to either gain- or loss-of-function, we performed single-cell RNA sequencing across isogenic induced pluripotent stem cell-derived neuron types, harbouring FUS P525L, FUS R495X, TARDBP M337V mutations or FUS knockout. Transcriptional changes were far more pronounced in motor neurons than interneurons. About 20% of uniquely dysregulated motor neuron transcripts were shared across FUS mutations, half from gain-of-function. Most indicated mitochondrial impairments, with attenuated pathways shared with mutant TARDBP M337V as well as C9orf72-ALS patient motor neurons. Mitochondrial motility was impaired in ALS motor axons, even with nuclear localized FUS mutants, demonstrating shared toxic gain-of-function mechanisms across FUS- and TARDBP-ALS, uncoupled from protein mislocalization. These early mitochondrial dysfunctions unique to motor neurons may affect survival and represent therapeutic targets in ALS.", "doi": "10.1038/s41467-025-59679-1", "pmid": "40389397", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12089458"}, {"db": "pii", "key": "10.1038/s41467-025-59679-1"}], "notes": [], "created": "2025-10-03T08:47:44.009Z", "modified": "2025-10-03T08:47:45.216Z"}, {"entity": "publication", "iuid": "fec47bc65de942b98146974984fcd1f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fec47bc65de942b98146974984fcd1f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fec47bc65de942b98146974984fcd1f8"}}, "title": "QS molecules change the planktonic/mineral subpopulations distribution of moderately thermophilic leaching bacteria in pyrite and decrease leaching in chalcopyrite.", "authors": [{"family": "Salas", "given": "Beatriz", "initials": "B"}, {"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "L\u00f3pez-Tomasovic", "given": "Luna", "initials": "L"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Vera", "given": "Mario", "initials": "M"}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1592588", "issn-l": "1664-302X"}, "abstract": "Biomining is a sustainable alternative to conventional mineral processing that uses acidophilic microorganisms to catalyze the extraction of valuable metals from sulfide minerals. Mixed microbial consortia composed of moderate thermophiles such as Sulfobacillus and some Leptospirillum species improve metal extraction efficiency at higher temperatures compared to pure cultures of mesophiles. However, quorum sensing (QS), which regulates microbial interactions and likely influences bioleaching performance, has not been studied in these species. In this study, treatment of a moderately thermophilic biomining consortium with QS compounds, termed diffusible signal factors (DSF), reduced pyrite and chalcopyrite dissolution via an inhibitory effect on iron oxidation and mineral colonization by the mixed culture. Furthermore, QS molecules changed the distribution of planktonic/mineral subpopulations of the acidophilic species. In addition, DSF compounds induced Acidithiobacillus caldus motility and dispersion from pyrite with a concomitant expansion of Leptospirillum ferriphilum on the mineral surface while in contrast, the acyl-homoserine lactone mediated QS system repressed L. ferriphilum motility. Moreover, the addition of QS molecules induced a second response related to the detrimental effect of high concentrations of fatty acids on cells, with an activation of detoxification mechanisms. Overall, QS regulated key target microbial interactions that opens the possibility to improve chalcopyrite bioleaching in the studied consortia.", "doi": "10.3389/fmicb.2025.1592588", "pmid": "40454366", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12122527"}], "notes": [], "created": "2025-11-24T11:43:25.883Z", "modified": "2025-11-24T11:43:25.894Z"}, {"entity": "publication", "iuid": "dfca2e28bc7947fdad65ae9bd1ac974e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfca2e28bc7947fdad65ae9bd1ac974e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfca2e28bc7947fdad65ae9bd1ac974e"}}, "title": "Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease.", "authors": [{"family": "Barba-Reyes", "given": "Juan M", "initials": "JM"}, {"family": "Harder", "given": "Lisbeth", "initials": "L"}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "Jaisa-Aad", "given": "Methasit", "initials": "M"}, {"family": "Mu\u00f1oz-Castro", "given": "Clara", "initials": "C"}, {"family": "Garma", "given": "Leonardo D", "initials": "LD"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Hyman", "given": "Bradley T", "initials": "BT"}, {"family": "Serrano-Pozo", "given": "Alberto", "initials": "A"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}], "type": "journal article", "published": "2025-05-05", "journal": {"title": "Acta Neuropathol.", "issn": "1432-0533", "volume": "149", "issue": "1", "pages": "46", "issn-l": "0001-6322"}, "abstract": "Oligodendroglia are the responsible cells for myelination in the central nervous system and their involvement in Parkinson's disease (PD) is poorly understood. We performed sn-RNA-seq and image-based spatial transcriptomics of human caudate nucleus and putamen (dorsal striatum) from PD and control brain donors to elucidate the diversity of oligodendroglia and how they are affected by the disease. We profiled a total of ~ 200.000 oligodendroglial nuclei, defining 15 subclasses, from precursor to mature cells, 4 of which are disease-associated. These PD-specific populations are characterized by the overexpression of heat shock proteins, as well as distinct expression signatures related to immune responses, myelination alterations, and disrupted cell signaling pathways. We have also identified impairments in cell communication and oligodendrocyte development, evidenced by changes in neurotransmitter receptors expression and cell adhesion molecules. In addition, we observed significant disruptions in oligodendrocyte development, with aberrant differentiation trajectories and shifts in cell proportions, particularly in the transition from mature oligodendrocytes to disease-associated states. Quantitative immunohistochemical analysis revealed decreased myelin levels in the PD striatum, which correlated with transcriptomic alterations. Furthermore, spatial transcriptomics mapping revealed the distinct localization of disease-associated populations within the striatum, with evidence of impaired myelin integrity. Thus, we uncover oligodendroglia as a critical cell type in PD and a potential new therapeutic target for myelin-based interventions.", "doi": "10.1007/s00401-025-02884-5", "pmid": "40323467", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12053221"}, {"db": "pii", "key": "10.1007/s00401-025-02884-5"}], "notes": [], "created": "2025-11-19T08:34:23.054Z", "modified": "2025-11-28T06:50:44.043Z"}, {"entity": "publication", "iuid": "63a842231cd742ccb297c01941f01486", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a842231cd742ccb297c01941f01486.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a842231cd742ccb297c01941f01486"}}, "title": "Unexpectedly low recombination rates and presence of hotspots in termite genomes.", "authors": [{"family": "Everitt", "given": "Turid", "initials": "T", "orcid": "0000-0002-6273-4507", "researcher": {"href": "https://publications.scilifelab.se/researcher/403d4411d0a748eaad9d5810f68e1875.json"}}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T", "orcid": "0000-0003-2929-0585", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ecda02e06b04ead95eefe4e4ee9eed8.json"}}, {"family": "Elsner", "given": "Daniel", "initials": "D"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Liu", "given": "Yuanzhen", "initials": "Y"}, {"family": "Larva", "given": "Tuuli", "initials": "T"}, {"family": "Korb", "given": "Judith", "initials": "J", "orcid": "0000-0001-9577-9376", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95a4169232b4fba987bf584d68d41a6.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2025-05-02", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "35", "issue": "5", "pages": "1124-1137", "issn-l": "1088-9051"}, "abstract": "Meiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates among metazoans, whereas high recombination rates have not been found among nonsocial species from this insect order. It is unknown whether elevated recombination rates are a ubiquitous feature of all social insects. In many metazoan taxa, recombination is mainly restricted to hotspots a few kilobases in length. However, little is known about the prevalence of recombination hotspots in insect genomes. Here we infer recombination rate and its fine-scale variation across the genomes of two social species from the insect order Blattodea: the termites Macrotermes bellicosus and Cryptotermes secundus We used linkage disequilibrium-based methods to infer recombination rate. We infer that recombination rates are close to 1 cM/Mb in both species, similar to the average metazoan rate. We also observe a highly punctate distribution of recombination in both termite genomes, indicative of the presence of recombination hotspots. We infer the presence of full-length PRDM9 genes in the genomes of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low recombination rates in termites indicates that eusociality is not universally connected to elevated recombination rate. We speculate that the elevated recombination rates in social Hymenoptera are instead promoted by intense selection among haploid males.", "doi": "10.1101/gr.279180.124", "pmid": "40113265", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12047536"}, {"db": "pii", "key": "gr.279180.124"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2025-11-21T15:54:31.653Z", "modified": "2025-11-21T15:54:32.018Z"}, {"entity": "publication", "iuid": "063e2f807e9e47229d68693273e02694", "links": {"self": {"href": "https://publications.scilifelab.se/publication/063e2f807e9e47229d68693273e02694.json"}, "display": {"href": "https://publications.scilifelab.se/publication/063e2f807e9e47229d68693273e02694"}}, "title": "Museum Ecologies", "authors": [{"family": "Fredengren", "given": "Christina", "initials": "C"}, {"family": "Ewing", "given": "Annica", "initials": "A"}, {"family": "Owman", "given": "Caroline", "initials": "C"}, {"family": "Holmstedt", "given": "Janna", "initials": "J"}], "type": "journal-article", "published": "2025-05-01", "journal": {"title": "Mus. Soc.", "issn": "1479-8360", "issn-l": null, "volume": "23", "issue": "1", "pages": null}, "abstract": null, "doi": "10.29311/mas.v23i1.4698", "pmid": null, "labels": {"Ancient DNA": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-05-26T06:37:00.260Z", "modified": "2025-05-27T08:16:55.595Z"}, {"entity": "publication", "iuid": "ef4de967f197431087541882ba0bdb59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef4de967f197431087541882ba0bdb59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef4de967f197431087541882ba0bdb59"}}, "title": "Sex pheromone biosynthesis in the Oriental fruit moth Grapholita molesta involves \u03948 desaturation.", "authors": [{"family": "Dam", "given": "Marie Inger", "initials": "MI"}, {"family": "Ding", "given": "Bao-Jian", "initials": "BJ"}, {"family": "Brauburger", "given": "Kristina", "initials": "K"}, {"family": "Wang", "given": "Hong-Lei", "initials": "HL"}, {"family": "Powell", "given": "Daniel", "initials": "D"}, {"family": "Groot", "given": "Astrid T", "initials": "AT"}, {"family": "Heckel", "given": "David G", "initials": "DG"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Insect Biochem. Mol. Biol.", "issn": "1879-0240", "pages": "104307", "volume": "180", "issn-l": "0965-1748"}, "abstract": "The Oriental fruit moth Grapholita molesta is distributed throughout temperate regions and considered to be a pest in peach production and other high-value fruit crops in the rose family. Insecticide treatment has led to resistance development, but the use of sex pheromones in pest management has shown great promise. We investigated the pheromone biosynthesis pathway in G. molesta with the aim of elucidating pheromone evolution in the Olethreutinae subfamily of moths and harnessing pathway genes in biotechnological production of sex pheromone for use in pest management. In vivo labelling experiments suggested that an uncommon \u03948 fatty acyl desaturase is involved in sex pheromone biosynthesis. CRISPR/Cas9 knock-out of the highly expressed candidate desaturase gene Gmol_CPRQ almost completely blocked the production of \u03948 pheromone components in vivo. Heterologous expression of Gmol_CPRQ protein in yeast- or Sf9 insect cells, however, failed to demonstrate the expected \u03948 desaturase activity. Instead, \u03949 desaturase activity was observed. Co-expression in the yeast system of the electron donor, cytochrome b5, from G. molesta still produced only \u03949 desaturase activity. We suggest that Gmol_CPRQ is intimately involved in pheromone production in vivo, via an unknown reaction mechanism that may possibly involve another co-factor that is absent in the yeast and Sf9 expression systems, or depend on its subcellular site of activity. Solving this puzzle will shed further light on pheromone biosynthesis in the family Tortricidae and will be required for successful biotechnological production of fatty acids and pheromones requiring \u03948 desaturation.", "doi": "10.1016/j.ibmb.2025.104307", "pmid": "40169039", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0965-1748(25)00051-7"}], "notes": [], "created": "2025-04-07T09:58:55.450Z", "modified": "2025-11-28T10:43:19.399Z"}, {"entity": "publication", "iuid": "7a9207954e064e188159483708b530ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a9207954e064e188159483708b530ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a9207954e064e188159483708b530ef"}}, "title": "Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord.", "authors": [{"family": "Zhang", "given": "Ming-Dong", "initials": "MD", "orcid": "0000-0002-6348-1994", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1585272a1848508d8f2395ace61332.json"}}, {"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "Su", "given": "Jie", "initials": "J", "orcid": "0000-0001-9828-9794", "researcher": {"href": "https://publications.scilifelab.se/researcher/228f25d52aef47d9b5b0d1000fed5ea7.json"}}, {"family": "Magnusson", "given": "Kajsa A", "initials": "KA", "orcid": "0000-0001-9159-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf40497aadb44dabafaba5e8126d68a.json"}}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Calvo-Enrique", "given": "Laura", "initials": "L", "orcid": "0000-0002-9428-3974", "researcher": {"href": "https://publications.scilifelab.se/researcher/42206cbfcbb04c0188bea08535937cec.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9122-6387", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4848f28ec474a71b8240ff6ab553444.json"}}, {"family": "Albisetti", "given": "Gioele W", "initials": "GW"}, {"family": "Ceder", "given": "Mikaela M", "initials": "MM"}, {"family": "Henriksson", "given": "Katharina", "initials": "K"}, {"family": "Leavitt", "given": "Andrew D", "initials": "AD"}, {"family": "Zeilhofer", "given": "Hanns Ulrich", "initials": "HU", "orcid": "0000-0001-6954-4629", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8c122280e0449e6bcdc144cfdf2ebd8.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T", "orcid": "0000-0002-3587-0116", "researcher": {"href": "https://publications.scilifelab.se/researcher/e228cd63f3a84d999ca3781c53a18f27.json"}}, {"family": "Lagerstr\u00f6m", "given": "Malin C", "initials": "MC"}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "28", "issue": "5", "pages": "1012-1023", "issn-l": "1097-6256"}, "abstract": "Acute pain is an unpleasant experience caused by noxious stimuli. How the spinal neural circuits attribute differences in quality of noxious information remains unknown. By means of genetic capturing, activity manipulation and single-cell RNA sequencing, we identified distinct neural ensembles in the adult mouse spinal cord encoding mechanical and heat pain. Reactivation or silencing of these ensembles potentiated or stopped, respectively, paw shaking, lifting and licking within but not across the stimuli modalities. Within ensembles, polymodal Gal+ inhibitory neurons with monosynaptic contacts to A-fiber sensory neurons gated pain transmission independent of modality. Peripheral nerve injury led to inferred microglia-driven inflammation and an ensemble transition with decreased recruitment of Gal+ inhibitory neurons and increased excitatory drive. Forced activation of Gal+ neurons reversed hypersensitivity associated with neuropathy. Our results reveal the existence of a spinal representation that forms the neural basis of the discriminative and defensive qualities of acute pain, and these neurons are under the control of a shared feed-forward inhibition.", "doi": "10.1038/s41593-025-01921-6", "pmid": "40128392", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12081300"}, {"db": "pii", "key": "10.1038/s41593-025-01921-6"}], "notes": [], "created": "2025-04-07T09:57:28.435Z", "modified": "2025-11-28T10:46:43.366Z"}, {"entity": "publication", "iuid": "c7627b55efd14033b6996b8c5aab3b0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7627b55efd14033b6996b8c5aab3b0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7627b55efd14033b6996b8c5aab3b0d"}}, "title": "Large Inversions Shape Diversification and Genome Evolution in Common Quails.", "authors": [{"family": "Ravagni", "given": "Sara", "initials": "S", "orcid": "0000-0003-0320-3447", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb16a7faa1a4952b3247d440d2cdf5f.json"}}, {"family": "Montero-Mendieta", "given": "Santiago", "initials": "S", "orcid": "0000-0002-8350-4655", "researcher": {"href": "https://publications.scilifelab.se/researcher/c23cf6e0a3d84637b564cd4ece502dfa.json"}}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0003-0291-7819", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7aebc9371db4bbcb03eaef58473fc3e.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Rodr\u00edguez-Teijeiro", "given": "Jos\u00e9 Domingo", "initials": "JD"}, {"family": "Sanchez-Donoso", "given": "Ines", "initials": "I"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "9", "pages": "e17740"}, "abstract": "Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (Coturnix coturnix), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new de novo genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.", "doi": "10.1111/mec.17740", "pmid": "40183764", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "NGI Other": null}, "xrefs": [], "notes": [], "created": "2025-08-19T13:25:18.999Z", "modified": "2025-11-19T08:38:35.719Z"}, {"entity": "publication", "iuid": "62778e40786e4985a36189beca08011f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62778e40786e4985a36189beca08011f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62778e40786e4985a36189beca08011f"}}, "title": "High-throughput biodiversity surveying sheds new light on the brightest of insect taxa.", "authors": [{"family": "Iwaszkiewicz-Eggebrecht", "given": "Ela", "initials": "E", "orcid": "0000-0003-1412-1711", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c085bb455d44ceac2f050f5c38f683.json"}}, {"family": "Goodsell", "given": "Robert M", "initials": "RM"}, {"family": "Bengsson", "given": "Bengt-\u00c5ke", "initials": "B\u00c5"}, {"family": "Mutanen", "given": "Marko", "initials": "M"}, {"family": "Klinth", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0003-4755-6682", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c16d303d21743df8d9b9eebb4d2376b.json"}}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA", "orcid": "0000-0003-1015-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c9432c19234fd5bc5dfc0a037dae0f.json"}}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P", "orcid": "0000-0002-4164-6487", "researcher": {"href": "https://publications.scilifelab.se/researcher/71d69a579a304425b70249e7db42ad67.json"}}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}, {"family": "Andersson", "given": "Anders", "initials": "A"}, {"family": "Tack", "given": "Ayco Jerome Michel", "initials": "AJM"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "292", "issue": "2046", "pages": "20242974", "issn-l": "0962-8452"}, "abstract": "DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known taxa in underexplored regions. This study evaluates what an extensive sampling effort combined with metabarcoding can tell us about the lepidopteran fauna of Sweden-one of the best-understood insect taxa in one of the most-surveyed countries of the world. We deployed 197 Malaise traps across Sweden for a year, generating 4749 bulk samples for metabarcoding, and compared the results to existing data sources. We detected more than half (1535) of the 2990 known Swedish lepidopteran species and 323 species not reported during the sampling period by other data providers. Full-length barcoding confirmed three new species for the country, substantial range extensions for two species and eight genetically distinct barcode variants potentially representing new species, one of which has since been described. Most new records represented small, inconspicuous species from poorly surveyed regions, highlighting components of the fauna overlooked by traditional surveying. These findings demonstrate that DNA metabarcoding is a highly efficient and accurate biodiversity sampling method, capable of yielding significant new discoveries even for the most well known of insect faunas.", "doi": "10.1098/rspb.2024.2974", "pmid": "40359979", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12074807"}], "notes": [], "created": "2025-11-21T14:25:36.120Z", "modified": "2025-11-21T14:25:36.343Z"}, {"entity": "publication", "iuid": "ef42f05457244d9398ea8f053490771c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef42f05457244d9398ea8f053490771c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef42f05457244d9398ea8f053490771c"}}, "title": "Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.", "authors": [{"family": "Pinder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4407-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6d9f52178249f3995c3d276fbc2728.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Blossom", "given": "Hannah", "initials": "H"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Rengefors", "given": "Karin", "initials": "K", "orcid": "0000-0001-6297-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7353dd11fa445f9ff338db5ce8dadd.json"}}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "25", "issue": "4", "pages": "e14067", "issn-l": "1755-098X"}, "abstract": "Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample. We demonstrate its usefulness by identifying hypervariable barcoding loci (< 500 bp) from genomic data in two microalgal species, the diploid diatom Skeletonema marinoi and the haploid chlorophyte Chlamydomonas reinhardtii. Across the two genomes, four and twenty-two loci, respectively, were identified that could in silico resolve all analysed genotypes. All of the identified loci are within protein-coding genes with various metabolic functions. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and among 54 strains of S. marinoi, three 500 bp loci contained, on average, 46 SNPs, 103 strain-specific alleles, and displayed 100% heterozygosity. This high level of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track abundances of S. marinoi strains in an artificial selection experiment. As future genomic datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.", "doi": "10.1111/1755-0998.14067", "pmid": "39903046", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969633"}], "notes": [], "created": "2025-11-21T11:38:37.352Z", "modified": "2025-11-21T11:38:37.527Z"}, {"entity": "publication", "iuid": "c1c3b39dad864eed8d1aa7429c86a4dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1c3b39dad864eed8d1aa7429c86a4dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1c3b39dad864eed8d1aa7429c86a4dc"}}, "title": "A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.", "authors": [{"family": "Gilardet", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-4851-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f507b07ed934c73988dfd0537254485.json"}}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Garc\u00eda", "given": "Gonzalo Oteo", "initials": "GO"}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Douka", "given": "Katerina", "initials": "K"}, {"family": "Wooller", "given": "Matthew J", "initials": "MJ"}, {"family": "Rowe", "given": "Timothy", "initials": "T"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}, {"family": "Le Moullec", "given": "Mathilde", "initials": "M"}, {"family": "Anisimov", "given": "Michail", "initials": "M"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "25", "issue": "4", "pages": "e14077", "issn-l": "1755-098X"}, "abstract": "Large-scale DNA screening of palaeontological and archaeological collections remains a limiting and costly factor for ancient DNA studies. Several DNA extraction protocols are routinely used in ancient DNA laboratories and have even been automated on robotic platforms. Robots offer a solution for high-throughput screening but the costs, as well as necessity for trained technicians and engineers, can be prohibitive for some laboratories. Here, we present a high-throughput alternative to robot-based ancient DNA extraction using a 96-column plate. When compared to routine single MinElute columns, we retrieved highly similar endogenous DNA contents, an important metric in ancient DNA screening. Mitogenomes with a coverage depth greater than 0.1\u00d7 could be generated and allowed for taxonomic assignment. However, average fragment lengths, DNA damage and library complexities significantly differed between methods but these differences became nonsignificant after modification of our library purification protocol. Our high-throughput extraction method allows generation of 96 extracts within approximately 4 hours of laboratory work while bringing the cost down by ~39% compared to using single columns. Additionally, we formally demonstrate that the addition of Tween-20 during the elution step results in higher complexity libraries, thereby enabling higher genome coverage for the same sequencing effort.", "doi": "10.1111/1755-0998.14077", "pmid": "39912442", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11969639"}, {"db": "RefSeq", "key": "GCA_018282365.1"}, {"db": "RefSeq", "key": "KX269145.1"}, {"db": "RefSeq", "key": "GCA_951394145.1"}, {"db": "RefSeq", "key": "NC_007703.1"}, {"db": "RefSeq", "key": "GCA_024166365.1"}, {"db": "RefSeq", "key": "DQ188829.2"}, {"db": "RefSeq", "key": "NC_007596.2"}], "notes": [], "created": "2026-02-26T11:50:43.248Z", "modified": "2026-02-26T11:50:43.282Z"}, {"entity": "publication", "iuid": "408127f4edb9428db0ff41f5175bbd16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/408127f4edb9428db0ff41f5175bbd16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/408127f4edb9428db0ff41f5175bbd16"}}, "title": "A CRISPR homing screen finds a chloroquine resistance transporter-like protein of the Plasmodium oocyst essential for mosquito transmission of malaria.", "authors": [{"family": "Balakrishnan", "given": "Arjun", "initials": "A", "orcid": "0000-0002-8845-5741", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bd36ee6f81049b09972a9ad3f56dae4.json"}}, {"family": "Hunziker", "given": "Mirjam", "initials": "M"}, {"family": "Tiwary", "given": "Puja", "initials": "P"}, {"family": "Pandey", "given": "Vikash", "initials": "V"}, {"family": "Drew", "given": "David", "initials": "D", "orcid": "0000-0001-8866-6349", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc19844f8147480fb0af2e437744131b.json"}}, {"family": "Billker", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1716-168X", "researcher": {"href": "https://publications.scilifelab.se/researcher/baa3de453a8047688800db0d5a14e291.json"}}], "type": "journal article", "published": "2025-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3895", "issn-l": "2041-1723"}, "abstract": "Genetic screens with barcoded PlasmoGEM vectors have identified thousands of Plasmodium berghei gene functions in haploid blood stages, gametocytes and liver stages. However, the formation of diploid cells by fertilisation has hindered similar research on the parasites' mosquito stages. In this study, we develop a scalable genetic system that uses barcoded gene targeting vectors equipped with a CRISPR-mediated homing mechanism to generate homozygous loss-of-function mutants after one parent introduces a modified allele into the zygote. To achieve this, we use vectors additionally expressing a target gene specific gRNA. When integrated into one of the parental alleles it directs Cas9 to the intact allele after fertilisation, leading to its disruption. This homing strategy is 90% effective at generating homozygous gene editing of a fluorescence-tagged reporter locus in the oocyst. A pilot screen identifies PBANKA_0916000 as a chloroquine resistance transporter-like protein (CRTL) essential for oocyst growth and sporogony, pointing to an unexpected importance for malaria transmission of the poorly understood digestive vacuole of the oocyst that contains hemozoin granules. Homing screens provide a method for the systematic discovery of malaria transmission genes whose first essential functions are after fertilisation in the bloodmeal, enabling their potential as targets for transmission-blocking interventions to be assessed.", "doi": "10.1038/s41467-025-59099-1", "pmid": "40274854", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cryo-EM": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12022033"}, {"db": "pii", "key": "10.1038/s41467-025-59099-1"}], "notes": [], "created": "2025-09-29T11:07:05.501Z", "modified": "2025-11-18T13:13:42.205Z"}, {"entity": "publication", "iuid": "bf30bef38e144822aa0db8832eae0142", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf30bef38e144822aa0db8832eae0142.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf30bef38e144822aa0db8832eae0142"}}, "title": "The evaluation of biogenic silica in brackish and freshwater strains reveals links between phylogeny and silica accumulation in picocyanobacteria.", "authors": [{"family": "Aguilera", "given": "Anabella", "initials": "A", "orcid": "0000-0001-6743-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6e88f127e7d49d09f593a57aa4a794e.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Charalampous", "given": "Evangelia", "initials": "E"}, {"family": "Churakova", "given": "Yelena", "initials": "Y"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "\u015aliwi\u0144ska-Wilczewska", "given": "Sylwia", "initials": "S"}, {"family": "Conley", "given": "Daniel J", "initials": "DJ"}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2025-04-23", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "issn-l": "0099-2240", "volume": "91", "issue": "4", "pages": "e0252724"}, "abstract": "Through biosilicification, organisms incorporate dissolved silica (dSi) and deposit it as biogenic silica (bSi), driving the silicon (Si) cycle in aquatic systems. While Si accumulation in marine picocyanobacteria has been recently observed, its mechanisms and ecological implications remain unclear. This study investigates biosilicification in marine and brackish picocyanobacteria of the Synechococcus clade and two model freshwater coccoid cyanobacteria. Brackish strains showed significantly higher Si quotas when supplemented with external dSi (100 \u00b5M) compared to controls (up to 60.0 \u00b1 7.3 amol Si.cell-1 versus 9.2 to 16.3 \u00b1 2.9 amol Si.cell-1). Conversely, freshwater strains displayed no significant differences in Si quotas between dSi-enriched treatments and controls, emphasizing that not all phytoplanktons without an obligate Si requirement accumulate this element. The Si-accumulating marine and brackish picocyanobacteria clustered within the Synechococcus clade, whereas their freshwater counterparts formed a distinct sister group, suggesting a link between phylogeny and silicification. Rapid culture growth caused increased pH and led to dSi precipitation, influencing apparent dSi uptake; this was mitigated by pH control through bubbling. This phenomenon has significant implications for natural systems affected by phytoplankton blooms. In such environments, pH-induced silicon precipitation may reduce dSi availability impacting Si-dependent populations like diatoms. Our findings suggest brackish picocyanobacteria could significantly influence the Si cycle through at least two mechanisms: cellular Si accumulation and biologically induced changes in dSi concentrations.IMPORTANCEThis work provides the first evidence of biogenic silica accumulation in brackish picocyanobacteria and uncovers a link between phylogeny and biosilicification patterns. Our findings demonstrate that picocyanobacterial growth induces pH-dependent silica precipitation, which could lead to overestimations of cellular Si quotas by up to 85%. This process may drive substantial silica precipitation in highly productive freshwater and coastal marine systems, with potential effects on silica cycling and the population dynamics of Si-dependent phytoplankton. The extent of biosilicification in modern picocyanobacteria offers insights into the rock record, shedding light on the evolutionary and ecological dynamics that influence sedimentary processes and the preservation of biosilicification signatures in geological formations. Overall, this research adds to the significant impact that microorganisms lacking an obligate silica requirement may have on silica dynamics.", "doi": "10.1128/aem.02527-24", "pmid": "40145754", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12016540"}], "notes": [], "created": "2025-08-19T13:32:14.905Z", "modified": "2025-11-28T10:52:04.161Z"}, {"entity": "publication", "iuid": "fd8026fc626a4b06a20c3d7bb29a29e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd8026fc626a4b06a20c3d7bb29a29e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd8026fc626a4b06a20c3d7bb29a29e6"}}, "title": "Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Jansson", "given": "Ingela", "initials": "I", "orcid": "0000-0002-2255-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/44e799cd5f7f4343955b0a261ff6df96.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Packer", "given": "Craig", "initials": "C", "orcid": "0000-0002-3939-8162", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cacbf9051428186cf6fe23d4f8a02.json"}}, {"family": "Norman", "given": "Anita", "initials": "A"}, {"family": "Kissui", "given": "Bernard M", "initials": "BM"}, {"family": "E Mjingo", "given": "Ernest", "initials": "E"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-1246-5046", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccdce43407204828b73bce24fc4e6453.json"}}], "type": "journal article", "published": "2025-04-21", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "640", "issn-l": "2399-3642"}, "abstract": "Small, isolated populations are at greater risk of genome erosion than larger populations. Successful conservation efforts may lead to demographic recovery and mitigate the negative genetic effects of bottlenecks. However, constrained gene flow can hamper genomic recovery. Here, we use population genomic analyses and forward simulations to assess the genomic impacts of near extinction in the isolated Ngorongoro Crater lion (Panthera leo) sub-population. We show that 200 years of quasi-isolation and the recent epizootic in 1962 resulted in a two-fold increase in inbreeding and an excess in the frequency of highly deleterious mutations relative to other populations of the Greater Serengeti. There was little evidence for purging of genetic load. Furthermore, forward simulations indicate that higher gene flow from outside of the Crater is needed to prevent future genomic erosion in the population, with a minimum of one to five effective male migrants per decade required to reduce the risk of long-term inbreeding depression and reduction in genetic diversity. Our results suggest that in spite of a rapid post-epizootic demographic recovery since the 1970s, continued isolation of the population driven by habitat fragmentation and potentially male territoriality, exacerbate the effects of genome erosion.", "doi": "10.1038/s42003-025-07986-0", "pmid": "40258987", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12012037"}, {"db": "pii", "key": "10.1038/s42003-025-07986-0"}], "notes": [], "created": "2025-05-26T07:51:41.058Z", "modified": "2025-11-14T11:07:11.711Z"}, {"entity": "publication", "iuid": "c98d5ccd590e4c039a3d963c2cbb2bd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c98d5ccd590e4c039a3d963c2cbb2bd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c98d5ccd590e4c039a3d963c2cbb2bd1"}}, "title": "Disruption-induced changes in syntrophic propionate and acetate oxidation: flocculation, cell proximity, and microbial activity.", "authors": [{"family": "Weng", "given": "Nils", "initials": "N"}, {"family": "Najafabadi", "given": "Hossein Nadali", "initials": "HN"}, {"family": "Westerholm", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2025-04-19", "journal": {"title": "Biotechnol Biofuels Bioprod", "issn": "2731-3654", "issn-l": null, "volume": "18", "issue": "1", "pages": "45"}, "abstract": "Syntrophic propionate- and acetate-oxidising bacteria (SPOB and SAOB) play a crucial role in biogas production, particularly under high ammonia conditions that are common in anaerobic degradation of protein-rich waste streams. These bacteria rely on close interactions with hydrogenotrophic methanogens to facilitate interspecies electron transfer and maintain thermodynamic feasibility. However, the impact of mixing-induced disruption of these essential syntrophic interactions in biogas systems remains largely unexplored. This study investigates how magnetic stirring and orbital shaking influence degradation dynamics, microbial community composition, and gene expression in syntrophic enrichment communities under high-ammonia conditions.\r\n\r\nStirring significantly delayed the initiation of propionate degradation in one culture and completely inhibited it in the other two parallel cultures, whereas acetate degradation was less affected. Computational fluid dynamics modelling revealed that stirring generated higher shear rates (~ 20 s-1) and uniform cell distribution, while shaking led to lower shear rates and cell accumulation at the bottom of the culture bottle. Visual observations confirmed that stirring inhibited floc formation, while shaking promoted larger flocs compared to the static control condition, which formed smaller flocs and a sheet-like biofilm. Microbial community analysis identified substrate type and degradation progress as primary drivers of community structure, with motion displaying minimal influence. However, metatranscriptomic analysis revealed that motion-induced gene downregulation was associated with motility, surface sensing, and biofilm formation in SAOB and another bacterial species expressing genes for the glycine synthase reductase pathway. Stirring also suppressed oxalate-formate antiporter expression in SPOB, suggesting its dependence on spatial proximity for this energy-conserving mechanism. The strongest gene expression changes of stirring were observed in methanogens, indicating a coupling of the first and last steps of hydrogenotrophic methanogenesis, likely an adaptive strategy for efficient energy conservation. Other downregulated genes included ferrous iron transporters and electron transfer-associated enzymes.\r\n\r\nThis study highlights that stirring critically disrupts the initial syntrophic connection between SPOB and methanogens, whereas SAOB communities exhibit greater tolerance to shear stress and disruptive conditions that inhibits aggregate formation. These findings emphasize the importance of carefully managing mixing regimes, especially when attempting to reactivate ammonia-tolerant syntrophic propionate degraders in biogas systems experiencing rapid propionate accumulation under high-ammonia conditions.", "doi": "10.1186/s13068-025-02644-3", "pmid": "40253350", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC12008871"}, {"db": "pii", "key": "10.1186/s13068-025-02644-3"}], "notes": [], "created": "2025-09-08T11:37:37.001Z", "modified": "2025-10-08T15:40:18.553Z"}, {"entity": "publication", "iuid": "784df73e8dc84ac78534a0c33e5aec03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/784df73e8dc84ac78534a0c33e5aec03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/784df73e8dc84ac78534a0c33e5aec03"}}, "title": "Cytoskeletal alterations in neuronal cells implicate Toxoplasma gondii secretory machinery and host microRNA-containing extracellular vesicles.", "authors": [{"family": "Mazza", "given": "Thomas", "initials": "T"}, {"family": "Aslanzadeh", "given": "Morteza", "initials": "M"}, {"family": "Berentsen", "given": "L\u00efse", "initials": "L"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Barragan", "given": "Antonio", "initials": "A", "orcid": "0000-0001-7746-9964", "researcher": {"href": "https://publications.scilifelab.se/researcher/4eefb95f00db42e3891769f384269c6c.json"}}], "type": "journal article", "published": "2025-04-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "12606", "issn-l": "2045-2322"}, "abstract": "The widespread protozoan Toxoplasma gondii chronically infects neural tissue in vertebrates and is linked to various neurological and neuropsychiatric disorders in humans. However, its effects on sparsely infected neurons and on broader neural circuits remain elusive. Our study reveals that T. gondii infection disrupts cytoskeletal dynamics in SH-SY5Y neuronal cells and primary cortical neurons. Infected neuronal cells undergo significant cytomorphological changes, including retraction of dendritic extensions and alterations in microtubule and F-actin networks, across both parasite genotypes I and II. These cytoskeletal alterations were notably diminished in cells exposed to T. gondii mutants with impaired secretion via the MYR translocon, and were independent of intraneuronal parasite replication. Moreover, a bystander effect was observed, with supernatants from T. gondii-challenged cells inducing similar cytoskeletal changes in uninfected cells. Analyses of extracellular vesicles (EVs) in supernatants revealed differential expression of host microRNAs in response to infection, most notably the upregulation of miR-221-3p, a microRNA not previously associated with T. gondii. The data indicate that unidentified parasite-derived effector(s) secreted via the MYR translocon, in conjunction with MYR-independently induced EV-associated host microRNAs, mediate cytoskeletal alterations in both infected and bystander neuronal cells. The findings provide new insights into molecular mechanisms by which T. gondii infection may disrupt neural networks, shedding light on its potential role in neuronal dysregulation.", "doi": "10.1038/s41598-025-96298-8", "pmid": "40221584", "labels": {"NGI Short read": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Other": "Collaborative", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11993698"}, {"db": "pii", "key": "10.1038/s41598-025-96298-8"}], "notes": [], "created": "2025-06-03T09:17:07.614Z", "modified": "2025-06-03T09:17:07.717Z"}, {"entity": "publication", "iuid": "5693c08391ae49c7a5b87864c53e6f34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5693c08391ae49c7a5b87864c53e6f34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5693c08391ae49c7a5b87864c53e6f34"}}, "title": "Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation.", "authors": [{"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Fong", "given": "Michelle", "initials": "M"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Besavilla", "given": "Danica F", "initials": "DF"}, {"family": "Huynh", "given": "Hang T", "initials": "HT"}, {"family": "Sch\u00f6n", "given": "Karin", "initials": "K"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Fernandez", "given": "Carola", "initials": "C"}, {"family": "Patel", "given": "Angana A H", "initials": "AAH"}, {"family": "Wiel", "given": "Clotilde", "initials": "C"}, {"family": "Sayin", "given": "Volkan I", "initials": "VI"}, {"family": "Anastasakis", "given": "Dimitrios G", "initials": "DG"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "7", "pages": null}, "abstract": "The role of Argonaute (AGO) proteins and the RNA interference (RNAi) machinery in mammalian antiviral response has been debated. Therefore, we set out to investigate how mammalian RNAi impacts influenza A virus (IAV) infection. We reveal that IAV infection triggers nuclear accumulation of AGO2, which is directly facilitated by p53 activation. Mechanistically, we show that IAV induces nuclear AGO2 targeting of TRIM71and type-I interferon-pathway genes for silencing. Accordingly, Tp53-/- mice do not accumulate nuclear AGO2 and demonstrate decreased susceptibility to IAV infection. Hence, the RNAi machinery is highjacked by the virus to evade the immune system and support viral replication. Furthermore, the FDA-approved drug, arsenic trioxide, prevents p53 nuclear translocation, increases interferon response and decreases viral replication in vitro and in a mouse model in vivo. Our data indicate that targeting the AGO2:p53-mediated silencing of innate immunity may offer a promising strategy to mitigate viral infections.", "doi": "10.1093/nar/gkaf268", "pmid": "40219968", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "CRISPR Functional Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11992678"}, {"db": "pii", "key": "8112696"}], "notes": [], "created": "2025-04-16T07:03:31.301Z", "modified": "2026-07-23T19:08:11.961Z"}, {"entity": "publication", "iuid": "5a3168f3bf534a2380eced3612fd46f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a3168f3bf534a2380eced3612fd46f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a3168f3bf534a2380eced3612fd46f3"}}, "title": "Ectoderm barcoding reveals neural and cochlear compartmentalization.", "authors": [{"family": "de Haan", "given": "Sandra", "initials": "S", "orcid": "0000-0001-9335-1149", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec4f3aeba7b449a9b0973f235b26eb9d.json"}}, {"family": "He", "given": "Jingyan", "initials": "J", "orcid": "0000-0002-7405-5800", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a69849650d4fd0897fb4e983824d05.json"}}, {"family": "Corbat", "given": "Agustin A", "initials": "AA", "orcid": "0000-0001-8068-3486", "researcher": {"href": "https://publications.scilifelab.se/researcher/b05e4776694041d6bd47b35b69a23304.json"}}, {"family": "Belicova", "given": "Lenka", "initials": "L", "orcid": "0000-0002-6687-630X", "researcher": {"href": "https://publications.scilifelab.se/researcher/149297e7f15e4a3281be3895d45725e3.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M"}, {"family": "Vinsland", "given": "Elin", "initials": "E", "orcid": "0000-0001-9695-9192", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c7bf61b0d3348d9b966a7a018c8859d.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Kelley", "given": "Matthew W", "initials": "MW", "orcid": "0000-0001-7367-8697", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bcfe32fbc984d0a8aee2e897db13489.json"}}, {"family": "Andersson", "given": "Emma R", "initials": "ER", "orcid": "0000-0002-8608-625X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c7313cdcd5f41d4a567a6c315aac3a1.json"}}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "388", "issue": "6742", "pages": "60-68"}, "abstract": "Placodes and the neural crest are defining features of vertebrates. In this study, we investigate their lineages in mice using in utero approaches. We demonstrated that nanoinjection at embryonic day 7.5 targeted the ectoderm, including the future nervous system, placodes, and neural crest, allowing highly efficient manipulation of the future nervous system and inner ear. By using heritable DNA barcodes and high-throughput next-generation single-cell lineage tracing, we elucidated convergent differentiation pathways and identified distinct nervous system-, neural crest-, and otic placode-derived lineages. Clonal analyses identified early neural and cochlear compartmentalization, linking differentiated cell types to their progenitors or cellular siblings. This provides foundational insights for neuroscience and developmental biology.", "doi": "10.1126/science.adq9248", "pmid": "40179197", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-04-15T07:21:08.071Z", "modified": "2025-11-28T10:51:53.564Z"}, {"entity": "publication", "iuid": "872ce4cf695e4085883f7519f1ec7712", "links": {"self": {"href": "https://publications.scilifelab.se/publication/872ce4cf695e4085883f7519f1ec7712.json"}, "display": {"href": "https://publications.scilifelab.se/publication/872ce4cf695e4085883f7519f1ec7712"}}, "title": "The identity of Canthydrus testaceus (Boheman, 1858) and a new faunistic record of Sternocanthus indicus (Wehncke, 1876) (Coleoptera: Noteridae).", "authors": [{"family": "Toledo", "given": "Mario E", "initials": "ME"}, {"family": "Negri", "given": "Ilaria", "initials": "I"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "Zootaxa", "issn": "1175-5334", "volume": "5618", "issue": "2", "pages": "284-286", "issn-l": null}, "abstract": null, "doi": "10.11646/zootaxa.5618.2.7", "pmid": "40173460", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T13:15:43.074Z", "modified": "2025-11-21T13:15:43.092Z"}, {"entity": "publication", "iuid": "e75a307f49d94747b12d89e0fb944131", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e75a307f49d94747b12d89e0fb944131.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e75a307f49d94747b12d89e0fb944131"}}, "title": "On the origin of an insular hybrid butterfly lineage.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Nolen", "given": "Zachary J", "initials": "ZJ"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2025-04-02", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "79", "issue": "4", "pages": "510-524", "issn-l": "0014-3820"}, "abstract": "A new species can form through hybridization between species. Hybrid speciation in animals has been intensely debated, partly because hard evidence for the process has been difficult to obtain. Here, we report the discovery of a European hybrid butterfly lineage, a finding that can be considered surprising given the intense and long-term study of European butterflies. The lineage we describe is mainly inhabiting an island in the Baltic Sea and was previously designated as a subspecies (horkei) of one of the parental species (Aricia artaxerxes). By analyzing whole-genome resequencing data and developing a novel cluster analysis based on historical recombination events (Fisher junctions), we determine that horkei originated by hybridization between the nonsister species A. artaxerxes and A. agestis. This hybridization event occurred approximately 54,000 years ago, predating the last glaciation of the current distribution range. Horkei must therefore have persisted long enough to be able to colonize its current range, despite that this area lies between the current distributions of the parental species. The hybrid origin, the maintenance of genomic integrity across times of dramatic climate change, and the expression of a combination of parental traits suggest that horkei could be in the process of hybrid speciation.", "doi": "10.1093/evolut/qpaf017", "pmid": "39869437", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7984342"}], "notes": [], "created": "2025-11-21T13:35:47.293Z", "modified": "2025-11-28T10:48:44.944Z"}, {"entity": "publication", "iuid": "a609fcce04e94ce4a51830b45ac8941d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a609fcce04e94ce4a51830b45ac8941d"}}, "title": "A Million Years of Mammoth Mitogenome Evolution.", "authors": [{"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC", "orcid": "0000-0003-0715-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/7515c0a212ec4ba4997bc43bff1b662e.json"}}, {"family": "Thomas Thorpe", "given": "Jessica A", "initials": "JA", "orcid": "0000-0003-2302-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7ce837837546e48d5debf6d6aa9b41.json"}}, {"family": "Li", "given": "Wenxi", "initials": "W", "orcid": "0009-0001-5130-9521", "researcher": {"href": "https://publications.scilifelab.se/researcher/f001ea19092e433b9abc9431fe45b63e.json"}}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patricia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Barlow", "given": "Axel", "initials": "A", "orcid": "0000-0002-5532-9458", "researcher": {"href": "https://publications.scilifelab.se/researcher/293d4982ed124c75896e1838bab18b8f.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Henneberger", "given": "Kirstin", "initials": "K"}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Moreland", "given": "Kelsey N", "initials": "KN", "orcid": "0000-0002-3571-0876", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44fb07639f84500b325ea44d7faf08d.json"}}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA", "orcid": "0000-0002-1938-7052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bac46fda6c98402aa8743eeacef7a962.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/06418b4f9e90443d94452c87fb0b0588.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Hall", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-6998-0156", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcfa42cd57c645ba868b8ab621a1be14.json"}}, {"family": "Hewitson", "given": "Susan", "initials": "S", "orcid": "0000-0003-0091-012X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0a989b12c524e859eb20fdc38d2c111.json"}}, {"family": "Mol", "given": "Dick", "initials": "D", "orcid": "0009-0005-4772-4625", "researcher": {"href": "https://publications.scilifelab.se/researcher/9baa2917aafa4ab59b27c7be2a2f246a.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P", "orcid": "0000-0001-6547-9890", "researcher": {"href": "https://publications.scilifelab.se/researcher/14e81a9e6a164940a46a57249be26006.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Vartanyan", "given": "Sergey", "initials": "S", "orcid": "0000-0001-7806-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c472e06d8fa43a0b8a5575d5aec48e8.json"}}, {"family": "Zazula", "given": "Grant D", "initials": "GD", "orcid": "0000-0001-8436-1783", "researcher": {"href": "https://publications.scilifelab.se/researcher/077650a2501a49eaa9aba0a8b8fc4a56.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2025-04-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "42", "issue": "4", "pages": null}, "abstract": "The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.", "doi": "10.1093/molbev/msaf065", "pmid": "40202893", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11980863"}, {"db": "pii", "key": "8107989"}], "notes": [], "created": "2025-05-05T12:32:34.796Z", "modified": "2025-11-28T10:49:58.497Z"}, {"entity": "publication", "iuid": "2e02af05ec4f41039901b42de46ac5b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e02af05ec4f41039901b42de46ac5b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e02af05ec4f41039901b42de46ac5b8"}}, "title": "Host Plasma Microenvironment in Immunometabolically Impaired HIV Infection Leads to Dysregulated Monocyte Function and Synaptic Transmission Ex Vivo.", "authors": [{"family": "Mikaeloff", "given": "Flora", "initials": "F"}, {"family": "Gelpi", "given": "Marco", "initials": "M"}, {"family": "Esc\u00f3s", "given": "Alejandra", "initials": "A"}, {"family": "Wang", "given": "Tianqi", "initials": "T"}, {"family": "Gupta", "given": "Soham", "initials": "S"}, {"family": "Olofsson", "given": "Anna", "initials": "A"}, {"family": "Akusj\u00e4rvi", "given": "Sara Svensson", "initials": "SS"}, {"family": "Schuster", "given": "Sabrina", "initials": "S"}, {"family": "Naval", "given": "Prajakta", "initials": "P"}, {"family": "Sood", "given": "Vikas", "initials": "V"}, {"family": "Nikouyan", "given": "Negin", "initials": "N"}, {"family": "Knudsen", "given": "Andreas D", "initials": "AD"}, {"family": "Vestad", "given": "Beate", "initials": "B"}, {"family": "H\u00f8gh", "given": "Julie", "initials": "J"}, {"family": "Hov", "given": "Johannes R", "initials": "JR"}, {"family": "Benfield", "given": "Thomas", "initials": "T"}, {"family": "Tr\u00f8seid", "given": "Marius", "initials": "M"}, {"family": "Pawar", "given": "Vinay", "initials": "V"}, {"family": "Rucevic", "given": "Marijana", "initials": "M"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1"}, {"family": "O'Mahony", "given": "Liam", "initials": "L"}, {"family": "Savai", "given": "Rajkumar", "initials": "R"}, {"family": "Bj\u00f6rkstr\u00f6m", "given": "Niklas K", "initials": "NK"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "de Magalh\u00e3es", "given": "Jo\u00e3o Pedro", "initials": "JP"}, {"family": "Weiss", "given": "Siegfried", "initials": "S"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Varshney", "given": "Mukesh Kumar", "initials": "MK"}, {"family": "Karlsson", "given": "Annika C", "initials": "AC"}, {"family": "Syed", "given": "Yasir Ahmed", "initials": "YA"}, {"family": "Nielsen", "given": "Susanne D", "initials": "SD"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U", "orcid": "0000-0002-0844-3338", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f8094017c2a4d0a94d72813cab526f7.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "12", "issue": "16", "pages": "e2416453", "issn-l": null}, "abstract": "Risk stratification using multi-omics data deepens understanding of immunometabolism in successfully treated people with HIV (PWH) is inadequately explained. A personalized medicine approach integrating blood cell transcriptomics, plasma proteomics, and metabolomics is employed to identify the mechanisms of immunometabolic complications in prolonged treated PWH from the COCOMO cohort. Among the PWHs, 44% of PWH are at risk of experiencing immunometabolic complications identified using the network-based patient stratification method. Utilizing advanced machine learning techniques and a Bayesian classifier, five plasma protein biomarkers; Tubulin Folding Cofactor B (TBCB), Gamma-Glutamylcyclotransferase (GGCT), Taxilin Alpha (TXLNA), Pyridoxal Phosphate Binding Protein (PLPBP) and Large Tumor Suppressor Kinase 1 (LATS1) are identified as highly differentially abundant between healthy control (HC)-like and immunometabolically at-risk PWHs (all FDR<10-10). The personalized metabolic models predict metabolic perturbations, revealing disruptions in central carbon metabolic fluxes and host tryptophan metabolism in at-risk phenotype. Functional assays in primary cells and cortical forebrain organoids (FBOs) further validate this. Metabolic perturbations lead to persistent monocyte activation, thereby impairing their functions ex vivo. Furthermore, the chronic inflammatory plasma microenvironment contributes to synaptic dysregulation in FBOs. The endogenous plasma inflammatory microenvironment is responsible for chronic inflammation in treated immunometabolically complicated at-risk PWH who have a higher risk of cardiovascular and neuropsychiatric disorders.", "doi": "10.1002/advs.202416453", "pmid": "40013867", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12021100"}], "notes": [], "created": "2025-11-25T10:19:00.216Z", "modified": "2025-11-25T10:19:00.307Z"}, {"entity": "publication", "iuid": "2cac06ed9ba246d490141086a39f3ee0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cac06ed9ba246d490141086a39f3ee0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cac06ed9ba246d490141086a39f3ee0"}}, "title": "Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes - With particular focus on Hymenocoleus Robbr.", "authors": [{"family": "Thil\u00e9n", "given": "Lovisa", "initials": "L"}, {"family": "Lachenaud", "given": "Olivier", "initials": "O"}, {"family": "Thureborn", "given": "Olle", "initials": "O"}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "pages": "108338", "issn-l": "1055-7903"}, "abstract": "Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus Hymenocoleus. Using coalescent-based inference methods, we find that Puffia gerrardii (recently separated from Geophila) is sister to Hymenocoleus. The deepest split in Hymenocoleus is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in Hymenocoleus could be confidently resolved and while Robbrecht's traditional subgeneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.", "doi": "10.1016/j.ympev.2025.108338", "pmid": "40158785", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(25)00055-7"}], "notes": [], "created": "2025-04-07T10:00:09.487Z", "modified": "2025-04-07T10:00:09.492Z"}, {"entity": "publication", "iuid": "c1da9377c9ef4f588decef70299d0c40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1da9377c9ef4f588decef70299d0c40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1da9377c9ef4f588decef70299d0c40"}}, "title": "Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity.", "authors": [{"family": "Fan", "given": "Chuannan", "initials": "C", "orcid": "0000-0001-8754-4913", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a665d568ce94fcbaaee270c6c7701a5.json"}}, {"family": "Wang", "given": "Qian", "initials": "Q", "orcid": "0000-0002-5196-4972", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4009e7b4ef0473a91c6e39b315e0f16.json"}}, {"family": "Krijger", "given": "Peter H L", "initials": "PHL", "orcid": "0000-0003-1702-348X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0cacf162ca643a68ea2bd723fa3a2b6.json"}}, {"family": "Cats", "given": "Davy", "initials": "D", "orcid": "0000-0001-9684-220X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23de688650944eca98ed9f9c1e8f19bb.json"}}, {"family": "Selle", "given": "Miriam", "initials": "M"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O", "orcid": "0009-0001-0786-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ada08b5ada04dfb8e948e0873ccf07d.json"}}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Mei", "given": "Hailiang", "initials": "H"}, {"family": "de Laat", "given": "Wouter", "initials": "W", "orcid": "0000-0002-5603-0095", "researcher": {"href": "https://publications.scilifelab.se/researcher/4025d8f21a1f4f71a1a1e7d1f1afdc59.json"}}, {"family": "Ten Dijke", "given": "Peter", "initials": "P", "orcid": "0000-0002-7234-342X", "researcher": {"href": "https://publications.scilifelab.se/researcher/299812073080446a91fc6228efbdc1c5.json"}}], "type": "journal article", "published": "2025-03-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "2890"}, "abstract": "Enhancer RNAs (eRNAs) are a pivotal class of enhancer-derived non-coding RNAs that drive gene expression. Here we identify the SNAI1 enhancer RNA (SNAI1e; SCREEM2) as a key activator of SNAI1 expression and a potent enforcer of transforming growth factor-\u03b2 (TGF-\u03b2)/SMAD signaling in cancer cells. SNAI1e depletion impairs TGF-\u03b2-induced epithelial-mesenchymal transition (EMT), migration, in vivo extravasation, stemness, and chemotherapy resistance in breast cancer cells. SNAI1e functions as an eRNA to cis-regulate SNAI1 enhancer activity by binding to and strengthening the enrichment of the transcriptional co-activator bromodomain containing protein 4 (BRD4) at the local enhancer. SNAI1e selectively promotes the expression of SNAI1, which encodes the EMT transcription factor SNAI1. Furthermore, we reveal that SNAI1 interacts with and anchors the inhibitory SMAD7 in the nucleus, and thereby prevents TGF-\u03b2 type I receptor (T\u03b2RI) polyubiquitination and proteasomal degradation. Our findings establish SNAI1e as a critical driver of SNAI1 expression and TGF-\u03b2-induced cell plasticity.", "doi": "10.1038/s41467-025-58032-w", "pmid": "40133308", "labels": {"CRISPR Functional Genomics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11937597"}, {"db": "pii", "key": "10.1038/s41467-025-58032-w"}], "notes": [], "created": "2025-03-27T09:27:46.634Z", "modified": "2026-03-18T09:38:07.353Z"}, {"entity": "publication", "iuid": "14386c68de7943c09413a06f0c389687", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14386c68de7943c09413a06f0c389687.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14386c68de7943c09413a06f0c389687"}}, "title": "A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness.", "authors": [{"family": "Schlesinger", "given": "D\u00f6rte", "initials": "D"}, {"family": "Dirks", "given": "Christopher", "initials": "C"}, {"family": "Navarro", "given": "Carmen", "initials": "C"}, {"family": "Lafranchi", "given": "Lorenzo", "initials": "L"}, {"family": "Spinner", "given": "Anna", "initials": "A"}, {"family": "Raja", "given": "Glancis Luzeena", "initials": "GL"}, {"family": "Mun-Sum Tong", "given": "Gregory", "initials": "G"}, {"family": "Eirich", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Martinez", "given": "Thomas Farid", "initials": "TF"}, {"family": "Els\u00e4sser", "given": "Simon Johannes", "initials": "SJ"}], "type": "journal article", "published": "2025-03-21", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "28", "issue": "3", "pages": "111884"}, "abstract": "The human genome contains thousands of potentially coding short open reading frames (sORFs). While a growing set of microproteins translated from these sORFs have been demonstrated to mediate important cellular functions, the majority remains uncharacterized. In our study, we performed a high-throughput CRISPR-Cas9 knock-out screen targeting 11,776 sORFs to identify microproteins essential for cancer cell line growth. We show that the CENPBD2P gene encodes a translated sORF and promotes cell fitness. We selected five additional candidate sORFs encoding microproteins between 11 and 63 amino acids in length for further functional assessment. Green fluorescent protein fusion constructs of these microproteins localized to distinct subcellular compartments, and the majority showed reproducible biochemical interaction partners. Studying the fitness and transcriptome of sORF knock-outs and complementation with the corresponding microprotein, we identify rescuable phenotypes while also illustrating the limitations and caveats of our pipeline for sORF functional screening and characterization.", "doi": "10.1016/j.isci.2025.111884", "pmid": "40124493", "labels": {"CRISPR Functional Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11929002"}, {"db": "pii", "key": "S2589-0042(25)00144-0"}], "notes": [], "created": "2025-04-30T17:31:37.359Z", "modified": "2025-11-14T11:06:08.650Z"}, {"entity": "publication", "iuid": "f971c5ac1eee407e8f0a6ea9a6805b1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f971c5ac1eee407e8f0a6ea9a6805b1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f971c5ac1eee407e8f0a6ea9a6805b1b"}}, "title": "The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Chisausky", "given": "Jacob", "initials": "J"}, {"family": "Galindo-Pellicena", "given": "\u00c1ngeles M", "initials": "\u00c1M"}, {"family": "Iriarte", "given": "Eneko", "initials": "E"}, {"family": "Cortes Gardyn", "given": "Oscar", "initials": "O", "orcid": "0000-0001-7685-3980", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d3ec08f74ef47ebbab08a298b2da649.json"}}, {"family": "Eusebi", "given": "Paulina G", "initials": "PG"}, {"family": "Garc\u00eda-Gonz\u00e1lez", "given": "Rebeca", "initials": "R"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Moreno-Garc\u00eda", "given": "Marta", "initials": "M", "orcid": "0000-0002-6735-9355", "researcher": {"href": "https://publications.scilifelab.se/researcher/31bc572fc9d740699fab5fb59977d5b3.json"}}, {"family": "Alday", "given": "Alfonso", "initials": "A"}, {"family": "Rojo", "given": "Manuel", "initials": "M"}, {"family": "P\u00e9rez", "given": "Amalia", "initials": "A"}, {"family": "Tejedor Rodr\u00edguez", "given": "Cristina", "initials": "C"}, {"family": "Garc\u00eda Mart\u00ednez de Lagr\u00e1n", "given": "I\u00f1igo", "initials": "I"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Carretero", "given": "Jos\u00e9-Miguel", "initials": "JM"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}], "type": "journal article", "published": "2025-03-19", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.", "doi": "10.7554/eLife.93076", "pmid": "40106345", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11922504"}, {"db": "pii", "key": "93076"}, {"db": "SRA", "key": "PRJNA838078"}, {"db": "Dryad", "key": "10.5061/dryad.f2d1q"}], "notes": [], "created": "2025-11-21T14:24:17.213Z", "modified": "2025-11-21T14:24:17.614Z"}, {"entity": "publication", "iuid": "3f77b47c2c9d4cb4b7c69ccd9596688c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c"}}, "title": "A chromosome-level genome assembly of the European green toad (Bufotes viridis).", "authors": [{"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Choi", "given": "Eunkyoung", "initials": "E", "orcid": "0009-0007-7147-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4255b0cdeec4f43885e730affd1246b.json"}}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Diedericks", "given": "Genevieve", "initials": "G", "orcid": "0000-0001-7700-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/7506eb0e88da4e4da970947289df5c4c.json"}}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA", "orcid": "0000-0003-1427-8946", "researcher": {"href": "https://publications.scilifelab.se/researcher/93fd5ac3fe64467d9e617b2bf14fea71.json"}}, {"family": "Einarsd\u00f3ttir", "given": "El\u00edsabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "F\u00f6rs\u00e4ter", "given": "Kristofer", "initials": "K", "orcid": "0009-0009-7670-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2e8576dc5354bef84f13f2e6a3fc1b6.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Jons\u00e4ll", "given": "Linnea", "initials": "L", "orcid": "0009-0004-6729-0185", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c8f571a5be4dfeb7ebf5b35f4b4ae7.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Laurila", "given": "Anssi", "initials": "A", "orcid": "0000-0001-8090-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b55d6c459ef448c992a37db2a02c3ea.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG", "orcid": "0000-0002-9212-4590", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f0492e152466f8f02cb6b7365ca6b.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Natali", "given": "Chiara", "initials": "C", "orcid": "0000-0002-0293-171X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df472019f49541f3bd455f1d8b1aea91.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Svardal", "given": "Hannes", "initials": "H", "orcid": "0000-0001-7866-7313", "researcher": {"href": "https://publications.scilifelab.se/researcher/4aee397f0ff64641a9c2033d56c6effb.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "15", "issue": "3", "pages": null}, "abstract": "The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status is labeled as of least concern by the IUCN, it is declining in many parts of its range where populations are fragmented and isolated. A high-quality reference genome is an important resource for conservation genomic researchers who are trying to understand and interpret the genomic signals of population decline, inbreeding, and the accumulation of deleterious mutations. Here, we assembled and annotated a chromosome-level reference genome for B. viridis as part of the European Reference Genome Atlas pilot project. The genome assembly, with a size of \u223c3.89 Gb consists of 11 chromosomes and an additional 2,096 unplaced scaffolds. The final assembly had a scaffold N50 value of 478.39 Mb and covered 90.4% single copy tetrapod orthologs, and 46.7% repetitive elements. Finally, a total of 23,830 protein-coding genes matching a known gene, together with 56,974 mRNAs were predicted. This high-quality reference genome will benefit amphibian evolutionary genomics research and enable conservation genetic studies to inform practical conservation work on this species.", "doi": "10.1093/g3journal/jkaf002", "pmid": "39969399", "labels": {"NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11917475"}, {"db": "pii", "key": "8024180"}], "notes": [], "created": "2025-02-28T07:50:03.734Z", "modified": "2025-11-21T12:40:15.314Z"}, {"entity": "publication", "iuid": "db7bafd701444e32b52fe11feea86f7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db7bafd701444e32b52fe11feea86f7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db7bafd701444e32b52fe11feea86f7b"}}, "title": "Sox9 and nuclear factor I transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors.", "authors": [{"family": "Lahti", "given": "Laura", "initials": "L", "orcid": "0000-0003-2929-1975", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ee35dc36f440d197afe3cd433d64ca.json"}}, {"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Yaghmaeian Salmani", "given": "Behzad", "initials": "B", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Tiklov\u00e1", "given": "Katar\u00edna", "initials": "K", "orcid": "0000-0002-9529-4552", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bbad41b8ed42268b71014ce111d247.json"}}, {"family": "Kee", "given": "Nigel", "initials": "N", "orcid": "0000-0002-7095-0760", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa213cf47c30423e8be78d0e8968b0b3.json"}}, {"family": "Lund\u00e9n-Miguel", "given": "Hilda", "initials": "H"}, {"family": "Werkman", "given": "Maarten", "initials": "M", "orcid": "0009-0000-6880-0897", "researcher": {"href": "https://publications.scilifelab.se/researcher/0eecf2c25f464784bf84003d051279ba.json"}}, {"family": "Piper", "given": "Michael", "initials": "M", "orcid": "0000-0002-6759-2560", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f040420470a4f11852954781cd23c15.json"}}, {"family": "Gronostajski", "given": "Richard", "initials": "R", "orcid": "0000-0003-4264-208X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff92d5fdb7fe4967a3f1af62077ef82e.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4821-8036", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c8dc93c324455b93aa392fcbb67315.json"}}], "type": "journal article", "published": "2025-03-15", "journal": {"title": "Development", "issn": "1477-9129", "issn-l": "0950-1991", "volume": "152", "issue": "6", "pages": null}, "abstract": "Correct timing of neurogenesis is crucial for generating the correct number and subtypes of glia and neurons in the embryo, and for preventing tumours and stem cell depletion in the adults. Here, we analyse how the midbrain dopamine (mDA) neuron progenitors transition into cell cycle arrest (G0) and begin to mature into ependymal cells. Comparison of mDA progenitors from different embryonic stages revealed upregulation of the genes encoding Sox9 and nuclear factor I transcription factors during development. Their conditional inactivation in the early embryonic midbrain led to delayed G0 entry and ependymal maturation in the entire midbrain ventricular zone, reduced gliogenesis and increased generation of neurons, including mDA neurons. In contrast, their inactivation in late embryogenesis did not result in mitotic re-entry, suggesting that these factors are necessary for G0 induction, but not for its maintenance. Our characterisation of adult ependymal cells by single-cell RNA sequencing and histology show that mDA-progenitor-derived cells retain several progenitor features but also secrete neuropeptides and contact neighbouring cells and blood vessels, indicating that these cells may form part of the circumventricular organ system.", "doi": "10.1242/dev.204421", "pmid": "39995267", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "367503"}], "notes": [], "created": "2025-04-07T09:04:57.491Z", "modified": "2025-11-28T10:53:42.874Z"}, {"entity": "publication", "iuid": "3448380f4dca4f2c9218130e25c03172", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3448380f4dca4f2c9218130e25c03172.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3448380f4dca4f2c9218130e25c03172"}}, "title": "Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.", "authors": [{"family": "Kistler", "given": "Logan", "initials": "L", "orcid": "0000-0002-5730-5986", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7f9fed415ac4818b28b9854af1cd996.json"}}, {"family": "de Oliveira Freitas", "given": "Fabio", "initials": "F", "orcid": "0000-0002-1242-6119", "researcher": {"href": "https://publications.scilifelab.se/researcher/70f51b4d4c8a4f0b96e76565d21cf168.json"}}, {"family": "Gutaker", "given": "Rafal M", "initials": "RM", "orcid": "0000-0001-9226-879X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fd4f6274b604cd786fb41b41ab65d13.json"}}, {"family": "Maezumi", "given": "S Yoshi", "initials": "SY", "orcid": "0000-0002-4333-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/71b2aba560e24fbd8fb3c706304ea872.json"}}, {"family": "Ramos-Madrigal", "given": "Jazm\u00edn", "initials": "J", "orcid": "0000-0002-1661-7991", "researcher": {"href": "https://publications.scilifelab.se/researcher/31e1ca5ba0dc44fbbb8106beab9e4e44.json"}}, {"family": "Simon", "given": "Marcelo F", "initials": "MF", "orcid": "0000-0002-5732-1716", "researcher": {"href": "https://publications.scilifelab.se/researcher/e25bce0105914ce1a7346a2c0543420d.json"}}, {"family": "Mendoza F", "given": "J Moises", "initials": "JM", "orcid": "0000-0003-1835-7051", "researcher": {"href": "https://publications.scilifelab.se/researcher/09f3e77a361a41d1ae8e6c36248ca7cd.json"}}, {"family": "Drovetski", "given": "Sergei V", "initials": "SV", "orcid": "0000-0002-1832-5597", "researcher": {"href": "https://publications.scilifelab.se/researcher/133195ffac4f44a6a020cb2926316cb1.json"}}, {"family": "Loiselle", "given": "Hope", "initials": "H", "orcid": "0000-0002-6197-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bb9a722e5bd42429281694720bd9ae9.json"}}, {"family": "de Oliveira", "given": "Eder Jorge", "initials": "EJ", "orcid": "0000-0001-8992-7459", "researcher": {"href": "https://publications.scilifelab.se/researcher/6734816913324f93b622c552c8285a7d.json"}}, {"family": "Vieira", "given": "Eduardo Alano", "initials": "EA", "orcid": "0000-0003-4931-3895", "researcher": {"href": "https://publications.scilifelab.se/researcher/fddd391a36e44014bb46559b5e3b482e.json"}}, {"family": "Carvalho", "given": "Luiz Joaquim Castelo Branco", "initials": "LJCB"}, {"family": "Ellis Perez", "given": "Marina", "initials": "M", "orcid": "0009-0000-1271-536X", "researcher": {"href": "https://publications.scilifelab.se/researcher/020a3d5f06724a8ca3b30682d84c5615.json"}}, {"family": "Lin", "given": "Audrey T", "initials": "AT", "orcid": "0000-0003-2505-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1f6e691ce04fd396757c4918535cc2.json"}}, {"family": "Liu", "given": "Hsiao-Lei", "initials": "H"}, {"family": "Miller", "given": "Rachel", "initials": "R", "orcid": "0009-0006-9322-2930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0caea54e94e948de803f092ec62d480d.json"}}, {"family": "Przelomska", "given": "Natalia A S", "initials": "NAS", "orcid": "0000-0001-9207-4565", "researcher": {"href": "https://publications.scilifelab.se/researcher/8de86c85c2ac47e398e8cd0175fcda35.json"}}, {"family": "Ratan", "given": "Aakrosh", "initials": "A", "orcid": "0000-0002-0782-3056", "researcher": {"href": "https://publications.scilifelab.se/researcher/da8fc51b280d4283b7ce57ef8063600d.json"}}, {"family": "Wales", "given": "Nathan", "initials": "N", "orcid": "0000-0003-0359-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c5af47529d418eb93ba5e51eeee86e.json"}}, {"family": "Wann", "given": "Kevin", "initials": "K", "orcid": "0009-0005-1045-3833", "researcher": {"href": "https://publications.scilifelab.se/researcher/f355d3d4244346b98228fdb85ed8e030.json"}}, {"family": "Zhang", "given": "Shuya", "initials": "S", "orcid": "0009-0008-7061-7627", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62a05ea897644338e66ec5af2db1052.json"}}, {"family": "Garc\u00eda", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-1128-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/878832e786334905817869afbb67e8b5.json"}}, {"family": "Valenzuela", "given": "Daniela", "initials": "D", "orcid": "0000-0001-7318-1947", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e80dc46b654a9daeb81a8e212e8077.json"}}, {"family": "Rothhammer", "given": "Francisco", "initials": "F"}, {"family": "Santoro", "given": "Calogero M", "initials": "CM"}, {"family": "Domic", "given": "Alejandra I", "initials": "AI", "orcid": "0000-0003-0762-3967", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbc5a934524147c39c493caa59cd79fc.json"}}, {"family": "Capriles", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0001-6046-0939", "researcher": {"href": "https://publications.scilifelab.se/researcher/54d972de19d04c9c828afa2a43b4d24f.json"}}, {"family": "Allaby", "given": "Robin G", "initials": "RG", "orcid": "0000-0001-5046-002X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6cf7900088744c6b2270d8bbea4ff94.json"}}], "type": "journal article", "published": "2025-03-07", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "387", "issue": "6738", "pages": "eadq0018"}, "abstract": "Manioc-also called cassava and yuca-is among the world's most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity.", "doi": "10.1126/science.adq0018", "pmid": "40048537", "labels": {"Ancient DNA": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-03-10T08:05:58.525Z", "modified": "2025-11-21T18:14:52.315Z"}, {"entity": "publication", "iuid": "5d8481ffcfb0478cb49fb65a406e33f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d8481ffcfb0478cb49fb65a406e33f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d8481ffcfb0478cb49fb65a406e33f3"}}, "title": "Continuous map of early hematopoietic stem cell differentiation across human lifetime.", "authors": [{"family": "Komic", "given": "Hana", "initials": "H", "orcid": "0000-0001-5209-393X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e58a972d4a584a0886d0a64c7966cb2a.json"}}, {"family": "Schmachtel", "given": "Tessa", "initials": "T"}, {"family": "Simoes", "given": "Catia", "initials": "C"}, {"family": "K\u00fclp", "given": "Marius", "initials": "M", "orcid": "0000-0002-6594-8412", "researcher": {"href": "https://publications.scilifelab.se/researcher/673d10466a874f31a0be9fe2162d8311.json"}}, {"family": "Yu", "given": "Weijia", "initials": "W", "orcid": "0000-0001-8471-3048", "researcher": {"href": "https://publications.scilifelab.se/researcher/6663774d48534299b5bc56d45db1f817.json"}}, {"family": "Jolly", "given": "Adrien", "initials": "A", "orcid": "0000-0002-2609-5621", "researcher": {"href": "https://publications.scilifelab.se/researcher/bba8ced4f36d4dcd8035149d9c5fe32e.json"}}, {"family": "Nilsson", "given": "Malin S", "initials": "MS", "orcid": "0000-0002-0981-2617", "researcher": {"href": "https://publications.scilifelab.se/researcher/83fab5fb78c043e9affbbabd7a4d43e8.json"}}, {"family": "Gonzalez", "given": "Carmen", "initials": "C", "orcid": "0009-0001-3074-9229", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6ee53d6ea9447bbd8ec7e595e2fe89.json"}}, {"family": "Prosper", "given": "Felipe", "initials": "F", "orcid": "0000-0001-6115-8790", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa428789689a41f396098ee1edd3f8da.json"}}, {"family": "Bonig", "given": "Halvard", "initials": "H"}, {"family": "Paiva", "given": "Bruno", "initials": "B", "orcid": "0000-0003-1977-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cf6f4d344b54bcab428014c4191cf27.json"}}, {"family": "Thor\u00e9n", "given": "Fredrik B", "initials": "FB", "orcid": "0000-0003-2167-7451", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e8a4846c6f44c0793f4cb5d73b66de6.json"}}, {"family": "Rieger", "given": "Michael A", "initials": "MA", "orcid": "0000-0002-4158-5872", "researcher": {"href": "https://publications.scilifelab.se/researcher/753728d6825443299274a4c5dfdacd75.json"}}], "type": "journal article", "published": "2025-03-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "2287", "issn-l": "2041-1723"}, "abstract": "Uncovering early gene network changes of human hematopoietic stem cells (HSCs) leading to differentiation induction is of utmost importance for therapeutic manipulation. We employed single cell proteo-transcriptomic sequencing to FACS-enriched bone marrow hematopoietic stem and progenitor cells (HSPCs) from 15 healthy donors. Pseudotime analysis reveals four major differentiation trajectories, which remain consistent upon aging, with an early branching point into megakaryocyte-erythroid progenitors. However, young donors suggest a more productive differentiation from HSPCs to committed progenitors of all lineages. tradeSeq analysis depicts continuous changes in gene expression of HSPC-related genes (DLK1, ADGRG6), and provides a roadmap of gene expression at the earliest branching points. We identify CD273/PD-L2 to be highly expressed in a subfraction of immature multipotent HSPCs with enhanced quiescence. Functional experiments confirm the immune-modulatory function of CD273/PD-L2 on HSPCs in regulating T-cell activation and cytokine release. Here, we present a molecular map of early HSPC differentiation across human life.", "doi": "10.1038/s41467-025-57096-y", "pmid": "40055319", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11889232"}, {"db": "pii", "key": "10.1038/s41467-025-57096-y"}], "notes": [], "created": "2025-04-07T10:01:27.833Z", "modified": "2025-11-28T10:45:24.290Z"}, {"entity": "publication", "iuid": "53004388459e465ab3c59b47d352f040", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53004388459e465ab3c59b47d352f040"}}, "title": "Systems-level immunomonitoring in children with solid tumors to enable precision medicine.", "authors": [{"family": "Chen", "given": "Qi", "initials": "Q", "orcid": "0000-0002-5864-7574", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dde05e01624f07a374810c1086f20a.json"}}, {"family": "Zhao", "given": "Binbin", "initials": "B", "orcid": "0000-0002-5560-6750", "researcher": {"href": "https://publications.scilifelab.se/researcher/22329dc812fc4684acce02c18ae6fa18.json"}}, {"family": "Tan", "given": "Ziyang", "initials": "Z", "orcid": "0000-0001-5958-2584", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd87015d70fb4f71a9c5c40a22b84d4e.json"}}, {"family": "Hedberg", "given": "Gustav", "initials": "G"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Negrini", "given": "Erika", "initials": "E"}, {"family": "P\u00e1ez", "given": "Laura Pi\u00f1ero", "initials": "LP"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2cfec48e4c4d8e9bc528a02d489b.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Reitzner", "given": "Stefan Markus", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca59c30b2e45459eb3638c65b452b3.json"}}, {"family": "von Walden", "given": "Ferdinand", "initials": "F"}, {"family": "O'Neill", "given": "Olivia", "initials": "O"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f0d6085e774a0fbdc1ad8d6eea3c23.json"}}, {"family": "Wang", "given": "Chunlin", "initials": "C"}, {"family": "Davis", "given": "Mark M", "initials": "MM"}, {"family": "Carlson", "given": "Lena-Maria", "initials": "LM"}, {"family": "Pal", "given": "Niklas", "initials": "N"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}, {"family": "Repsilber", "given": "Dirk", "initials": "D", "orcid": "0000-0002-7173-5579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86ad21e955ed4524b24822ba4c0de43e.json"}}, {"family": "Herold", "given": "Nikolas", "initials": "N", "orcid": "0000-0001-9468-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2af6f17f76457680908c36693f2de5.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Ljungblad", "given": "Linda", "initials": "L"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2025-03-06", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "188", "issue": "5", "pages": "1425-1440.e11", "issn-l": "0092-8674"}, "abstract": "Cancer is the leading cause of death from disease in children. Survival depends not only on surgery, cytostatic drugs, and radiation but also on systemic immune responses. Factors influencing these immune responses in children of different ages and tumor types are unknown. Novel immunotherapies can enhance anti-tumor immune responses, but few children have benefited, and markers of effective responses are lacking. Here, we present a systems-level analysis of immune responses in 191 children within a population-based cohort with diverse tumors and reveal that age and tumor type shape immune responses differently. Systemic inflammation and cytotoxic T cell responses correlate with tumor mutation rates and immune cell infiltration. Clonally expanded T cell responses are rarely detected in blood or tumors at diagnosis but are sometimes elicited during treatment. Expanded T cells are similarly regulated in children and adults with more immunogenic cancers. This research aims to facilitate the development of precision immunotherapies for children with cancer.", "doi": "10.1016/j.cell.2024.12.014", "pmid": "39837329", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)01427-2"}], "notes": [], "created": "2025-01-30T10:50:10.864Z", "modified": "2025-11-28T10:42:05.786Z"}, {"entity": "publication", "iuid": "9cffa610a5254003956c5dedb591e1d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cffa610a5254003956c5dedb591e1d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cffa610a5254003956c5dedb591e1d0"}}, "title": "Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.", "authors": [{"family": "Rosenqvist", "given": "Tage", "initials": "T"}, {"family": "Hilding", "given": "Johanna", "initials": "J"}, {"family": "Suarez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5988-4048", "researcher": {"href": "https://publications.scilifelab.se/researcher/86cadb16f7cf45eca8030af1a8ae860e.json"}}, {"family": "Paul", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0003-0323-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c169e96b18c403b9c18228126e6fd8d.json"}}], "type": "journal article", "published": "2025-02-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "issn-l": "0043-1354", "volume": "270", "issue": null, "pages": "122843"}, "abstract": "Changing natural organic matter quality from anthropogenic activity and stricter requirements for micropollutant removal challenges existing systems for drinking water production. Ozonation of water followed by biofiltration, such as passage through a slow sand filter (SSF), is a partial solution. Biofiltration relies on biofilms (microbial communities within extracellular matrices). However, the effects of ozonation on SSF microbial communities are unknown. In this study, genome-resolved and read-based metagenomics were used to compare the microbial communities of two full-scale SSFs employing conventional pre-treatment to a 20 m2 SSF operated in parallel with ozonation as additional pre-treatment. The SSF microbial community receiving ozonated water was less diverse than those receiving non-ozonated water. Families Hyphomicrobiaceae, Acetobacteraceae, Sphingomonadaceae and Burkholderiaceae were more abundant when ozone was used, as were genes for metabolism of single-carbon organic compounds. Conversely, genes for metabolism of aromatic compounds and fatty acids were less abundant. Metagenome assembled genomes associated with the non-ozonated SSFs were enriched with several glycoside hydrolases, while those associated with the ozonated SSF were enriched with genes for 1-2 carbon compound metabolism. No indications of increased microbial risk (pathogens or antibiotic resistance genes) were detected as a consequence of ozonation. This study shows how microbial communities of SSFs adapt to changes in organic matter quality, highlighting the key role of biofilters for production of safe and sustainable drinking water in a changing climate.", "doi": "10.1016/j.watres.2024.122843", "pmid": "39612821", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(24)01742-1"}], "notes": [], "created": "2025-02-28T14:13:29.572Z", "modified": "2025-05-27T08:38:18.414Z"}, {"entity": "publication", "iuid": "dcfeee20dac44d149e7456edf098d297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcfeee20dac44d149e7456edf098d297"}}, "title": "Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.", "authors": [{"family": "Brown", "given": "Thomas", "initials": "T"}, {"family": "Mishra", "given": "Ketan", "initials": "K"}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Iarovenko", "given": "Svetlana", "initials": "S"}, {"family": "Subramanian", "given": "Elaiyaraja", "initials": "E"}, {"family": "Araus", "given": "Alberto Joven", "initials": "AJ"}, {"family": "Petzold", "given": "Andreas", "initials": "A"}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "Rikk", "given": "Lennart", "initials": "L"}, {"family": "Suzuki", "given": "Miyuki", "initials": "M"}, {"family": "Suzuki", "given": "Ken-Ichi T", "initials": "KT"}, {"family": "Hayashi", "given": "Toshinori", "initials": "T"}, {"family": "Toyoda", "given": "Atsushi", "initials": "A"}, {"family": "Oliveira", "given": "Catarina R", "initials": "CR"}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}, {"family": "Yun", "given": "Maximina H", "initials": "MH"}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}], "type": "journal article", "published": "2025-02-12", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "issn-l": null, "volume": "5", "issue": "2", "pages": "100761"}, "abstract": "Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.3 Gb genome of the Iberian ribbed newt, Pleurodeles waltl, with a hitherto unprecedented contiguity and completeness among giant genomes. Utilizing this assembly, we demonstrate conserved synteny as well as genetic rearrangements, such as in the major histocompatibility complex locus. We provide evidence suggesting that intronic repeat elements drive newt-specific circular RNA (circRNA) biogenesis and show their regeneration-specific expression. We also present a comprehensive in-depth annotation and chromosomal mapping of microRNAs, highlighting genomic expansion profiles as well as a distinct regulatory pattern in the regenerating limb. These data reveal links between repeat elements, non-coding RNAs, and adult regeneration and provide key resources for addressing developmental, regenerative, and evolutionary principles.", "doi": "10.1016/j.xgen.2025.100761", "pmid": "39874962", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11872487"}, {"db": "pii", "key": "S2666-979X(25)00017-5"}], "notes": [], "created": "2025-01-30T10:51:47.306Z", "modified": "2025-11-14T11:06:23.898Z"}, {"entity": "publication", "iuid": "1a5ce794e0674881af7391905b14b2f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a5ce794e0674881af7391905b14b2f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a5ce794e0674881af7391905b14b2f4"}}, "title": "Human MAIT cell response profiles biased toward IL-17 or IL-10 are distinct effector states directed by the cytokine milieu.", "authors": [{"family": "Boulouis", "given": "Caroline", "initials": "C", "orcid": "0000-0003-0562-5395", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e56706dacb2488384512533e63fec75.json"}}, {"family": "Mouchtaridi", "given": "Elli", "initials": "E", "orcid": "0009-0005-4154-9010", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b6cef1d4cec4c06b939ed1831f85e4a.json"}}, {"family": "M\u00fcller", "given": "Thomas R", "initials": "TR"}, {"family": "Mak", "given": "Jeffrey Y W", "initials": "JYW", "orcid": "0000-0002-8011-4539", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3b541f7d3b043989ab612d5f2678ee0.json"}}, {"family": "Fairlie", "given": "David P", "initials": "DP", "orcid": "0000-0002-7856-8566", "researcher": {"href": "https://publications.scilifelab.se/researcher/35fe17dcf6bb494f9c95e2dfab5ada19.json"}}, {"family": "Bergman", "given": "Peter", "initials": "P", "orcid": "0000-0003-3306-3713", "researcher": {"href": "https://publications.scilifelab.se/researcher/397d11713c80456bb600b1e4c88ff843.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0122-7234", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c18b8a6cc54dfa8ad14b0c97261bfa.json"}}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7468c415a46645a3a4c3d28badcff954.json"}}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "122", "issue": "6", "pages": "e2414230122", "issn-l": "0027-8424"}, "abstract": "Mucosal-associated invariant T (MAIT) cells are unconventional T cells that mediate rapid antimicrobial immune responses to antigens derived from microbial riboflavin pathway metabolites presented by the evolutionarily conserved MR1 molecules. MAIT cells represent a large pre-expanded T cell subset in humans and are involved in both protective immunity and inflammatory immunopathology. However, what controls the functional heterogeneity of human MAIT cell responses is still largely unclear. Here, combining functional and transcriptomic analyses, we investigate how MAIT cell response programs are influenced by the cytokine milieu at the time of antigen recognition. Activation by MR1-presented antigen together with IL-12 induces intermediate levels of IFN\u03b3 and TNF, as well as a regulatory profile with substantial IL-10 production and elevated expression of TIM-3, LAG-3, and PD-1. Activation by the combination of antigen and IL-12 induces a c-MAF-dependent program required for IL-10 production. The MAIT cell-derived IL-10 mediates both autocrine and paracrine immune regulation. In contrast, coactivation of MAIT cells with IL-18 induces IL-17, GM-CSF, IFN\u03b3, and TNF, without IL-10. Notably, IL-18 dominantly counteracts IL-10 expression. The activation states biased toward IL-10 or IL-17 production are reversible and do not represent stable subsets. Finally, MR1-restricted TCR-mediated activation without cytokine coactivation drives primarily granzyme B cytolytic arming. Altogether, these findings demonstrate that human MAIT cells adapt their functional effector response during antigen recognition to cytokine cues in the microenvironment, and identify programs biased toward either regulatory c-MAF-dependent IL-10 expression, or an inflammatory IL-17 and GM-CSF profile.", "doi": "10.1073/pnas.2414230122", "pmid": "39903121", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11831165"}], "notes": [], "created": "2025-11-21T14:09:08.705Z", "modified": "2025-11-21T14:09:09.031Z"}, {"entity": "publication", "iuid": "f92276fcc0404b76b42475aafb471f44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f92276fcc0404b76b42475aafb471f44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f92276fcc0404b76b42475aafb471f44"}}, "title": "A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data.", "authors": [{"family": "Abalde", "given": "Samuel", "initials": "S", "orcid": "0000-0001-7790-0603", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca4ab7834dc493daaa1eb96b5d980c2.json"}}, {"family": "Jondelius", "given": "Ulf", "initials": "U", "orcid": "0000-0003-2847-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/6582e2e560474080a7d89240a3d43edd.json"}}], "type": "journal article", "published": "2025-02-10", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "74", "issue": "1", "pages": "70-85", "issn-l": "1063-5157"}, "abstract": "Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs-which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella-have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.", "doi": "10.1093/sysbio/syae057", "pmid": "39451056", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11809588"}, {"db": "pii", "key": "7841810"}], "notes": [], "created": "2024-10-31T12:39:22.128Z", "modified": "2025-11-28T10:50:09.314Z"}, {"entity": "publication", "iuid": "5e435d0ba83e41edb4806fba16d0da8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e435d0ba83e41edb4806fba16d0da8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e435d0ba83e41edb4806fba16d0da8c"}}, "title": "Evolution of Hybrid Inviability Associated With Chromosome Fusions.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K"}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17672", "issn-l": "0962-1083"}, "abstract": "Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we use crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We map hybrid inviability candidate loci by contrasting allele frequencies between F2 hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability candidate regions have high genetic differentiation between parental populations, reduced recombination rates, and are enriched near chromosome fusions. By analysing sequencing coverage, we exclude aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reduced recombination in fused chromosomes. Thus, we map postzygotic isolation to chromosomal rearrangements, providing crucial empirical evidence for the idea that chromosome number differences between taxa can contribute to speciation.", "doi": "10.1111/mec.17672", "pmid": "39895489", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-21T13:45:03.334Z", "modified": "2025-11-21T13:45:03.397Z"}, {"entity": "publication", "iuid": "9ee81994e9304be4a943c473379bdab4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ee81994e9304be4a943c473379bdab4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ee81994e9304be4a943c473379bdab4"}}, "title": "Modelling age at death reveals Nordic Corded Ware paleodemography", "authors": [{"family": "Tornberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-3323-8512", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fdbf302337d475b88ffbdf48065a5b0.json"}}, {"family": "Vandkilde", "given": "Helle", "initials": "H", "orcid": "0000-0001-9326-7633", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffe755bd12534d9899484dd9756cf5d8.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Archaeol Anthropol Sci", "issn": "1866-9557", "issn-l": null, "volume": "17", "issue": "2", "pages": null}, "abstract": null, "doi": "10.1007/s12520-024-02159-2", "pmid": null, "labels": {"Ancient DNA": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2025-01-21T08:24:34.306Z", "modified": "2025-05-27T08:39:33.518Z"}, {"entity": "publication", "iuid": "96d10598a8c646709a856908160899d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96d10598a8c646709a856908160899d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96d10598a8c646709a856908160899d8"}}, "title": "Isotope geolocation and population genomics in Vanessa cardui: Short- and long-distance migrants are genetically undifferentiated.", "authors": [{"family": "Reich", "given": "Megan S", "initials": "MS", "orcid": "0000-0002-0597-4854", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe7c3c3a6e8346e4b235a5c6476bc9dc.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Bahleman", "given": "Farid", "initials": "F"}, {"family": "K\u00e9b\u00e9", "given": "Khadim", "initials": "K", "orcid": "0000-0003-0041-4919", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46e3cc21b2949eb9611d101fe31b7dc.json"}}, {"family": "Berger", "given": "Johanna L", "initials": "JL", "orcid": "0000-0003-4847-2413", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b1d5d0f9e5e4d39ab429f6dc6905550.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}, {"family": "Bataille", "given": "Cl\u00e9ment P", "initials": "CP", "orcid": "0000-0001-8625-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/70612fa6163b42c6b62ec5aca937421d.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "PNAS Nexus", "issn": "2752-6542", "volume": "4", "issue": "2", "pages": "pgae586", "issn-l": null}, "abstract": "The painted lady butterfly Vanessa cardui is renowned for its virtually cosmopolitan distribution and the remarkable long-distance migrations as part of its annual, multigenerational migratory cycle. In winter, V. cardui individuals inhabit breeding grounds north and south of the Sahara, suggesting distinct migratory behaviors within the species as individuals migrate southward from Europe in the autumn. However, the evolutionary and ecological factors shaping these differences in migratory behavior remain largely unexplored. Here, we performed whole-genome resequencing and analyzed the hydrogen and strontium isotopes of 40 V. cardui individuals simultaneously collected in the autumn from regions both north and south of the Sahara. Our investigation revealed two main migratory groups: (i) short-distance migrants, journeying from temperate Europe to the circum-Mediterranean region and (ii) long-distance migrants, originating from Europe, crossing the Mediterranean Sea and Sahara, and reaching West Africa, covering up to over 4,000 km. Despite these stark differences in migration distance, a genome-wide analysis revealed that short- and long-distance migrants belong to a single intercontinental panmictic population extending from northern Europe to sub-Saharan Africa. Contrary to common biogeographic patterns, the Sahara is not a catalyst for population structuring in this species. No significant genetic differentiation or signs of adaptation and selection were observed between the two migratory phenotypes. Nonetheless, two individuals, who were early arrivals to West Africa covering longer migration distances, exhibited some genetic differentiation. The lack of genetic structure between short- and long-distance migrants suggests that migration distance in V. cardui is a plastic response to environmental conditions.", "doi": "10.1093/pnasnexus/pgae586", "pmid": "39906311", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11792081"}, {"db": "pii", "key": "pgae586"}], "notes": [], "created": "2025-11-21T13:43:02.246Z", "modified": "2025-11-21T13:43:02.809Z"}, {"entity": "publication", "iuid": "d822f5357c6a448b82142e0a1e71bdac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d822f5357c6a448b82142e0a1e71bdac"}}, "title": "Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche.", "authors": [{"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Ortega Gim\u00e9nez", "given": "Jes\u00fas", "initials": "J", "orcid": "0000-0001-6599-1675", "researcher": {"href": "https://publications.scilifelab.se/researcher/e60538dadc0a4ee9ade7bc0015d67491.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S", "orcid": "0000-0002-6146-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ebad9d4ddf40949a19776df31a00c7.json"}}, {"family": "Moss", "given": "Oliver", "initials": "O"}, {"family": "Su", "given": "Yi", "initials": "Y", "orcid": "0009-0001-4802-5210", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7f56487ba584ac5b08cfa6c06c6f7a6.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "4", "pages": "e17653"}, "abstract": "How gene expression evolves to enable divergent ecological adaptation and how changes in gene expression relate to genomic architecture are pressing questions for understanding the mechanisms enabling adaptation and ecological speciation. Furthermore, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is crucial to understanding gene expression evolution, colonisation of novel niches and response to rapid environmental change. Here, we investigate the role of constitutive and plastic gene expression differences between host races, or host-specific ecotypes, of the peacock fly Tephritis conura, a thistle bud specialist. By cross-fostering larvae to new buds of their natal host plant or the alternative, novel host plant, we uncover extensive constitutive differences in gene expression between the host races, especially genes associated with processing of host plant chemicals. However, evidence for expression plasticity was minimal and limited to the ancestral host race. Genes with host race-specific expression are found more often than expected within a large inversion in the T. conura genome, adding to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that altered gene expression may be key to understanding the evolutionary consequences of inversions.", "doi": "10.1111/mec.17653", "pmid": "39783891", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11789552"}], "notes": [], "created": "2025-01-30T10:48:38.552Z", "modified": "2025-11-28T10:51:21.794Z"}, {"entity": "publication", "iuid": "58bd3a84e43d45578c5613d806758ac1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58bd3a84e43d45578c5613d806758ac1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58bd3a84e43d45578c5613d806758ac1"}}, "title": "Earliest modern human genomes constrain timing of Neanderthal admixture.", "authors": [{"family": "S\u00fcmer", "given": "Arev P", "initials": "AP", "orcid": "0009-0001-4834-4414", "researcher": {"href": "https://publications.scilifelab.se/researcher/862f71c337ad4775bb2cdb7cec947e39.json"}}, {"family": "Rougier", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0003-0358-0285", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f83f613a0f4d9fba2f1b9f9d6db45c.json"}}, {"family": "Villalba-Mouco", "given": "Vanessa", "initials": "V", "orcid": "0000-0002-9357-5238", "researcher": {"href": "https://publications.scilifelab.se/researcher/23941efc34474847bc42265d30fd9e58.json"}}, {"family": "Huang", "given": "Yilei", "initials": "Y"}, {"family": "Iasi", "given": "Leonardo N M", "initials": "LNM"}, {"family": "Essel", "given": "Elena", "initials": "E", "orcid": "0000-0002-2642-8043", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c289ad6c2c443dab3e8ac7f9e85979e.json"}}, {"family": "Bossoms Mesa", "given": "Alba", "initials": "A", "orcid": "0009-0008-7556-1722", "researcher": {"href": "https://publications.scilifelab.se/researcher/b11dd9c4aea34fb8bde542f5e983b723.json"}}, {"family": "Furtwaengler", "given": "Anja", "initials": "A"}, {"family": "Peyr\u00e9gne", "given": "St\u00e9phane", "initials": "S", "orcid": "0000-0002-9823-9102", "researcher": {"href": "https://publications.scilifelab.se/researcher/1659db1df364436d87f40641f0778251.json"}}, {"family": "de Filippo", "given": "Cesare", "initials": "C"}, {"family": "Rohrlach", "given": "Adam B", "initials": "AB", "orcid": "0000-0002-4204-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/7627382e0fd34de9ae719356e46d720d.json"}}, {"family": "Pierini", "given": "Federica", "initials": "F"}, {"family": "Mafessoni", "given": "Fabrizio", "initials": "F"}, {"family": "Fewlass", "given": "Helen", "initials": "H"}, {"family": "Zavala", "given": "Elena I", "initials": "EI"}, {"family": "Mylopotamitaki", "given": "Dorothea", "initials": "D"}, {"family": "Bianco", "given": "Raffaela A", "initials": "RA", "orcid": "0009-0004-6087-8031", "researcher": {"href": "https://publications.scilifelab.se/researcher/7270ec1ad3be465db60ff387055b4981.json"}}, {"family": "Schmidt", "given": "Anna", "initials": "A"}, {"family": "Zorn", "given": "Julia", "initials": "J"}, {"family": "Nickel", "given": "Birgit", "initials": "B"}, {"family": "Patova", "given": "Anna", "initials": "A"}, {"family": "Posth", "given": "Cosimo", "initials": "C", "orcid": "0000-0002-8206-3907", "researcher": {"href": "https://publications.scilifelab.se/researcher/828edab40ca74c89947aa70526e7e339.json"}}, {"family": "Smith", "given": "Geoff M", "initials": "GM", "orcid": "0000-0001-7155-5140", "researcher": {"href": "https://publications.scilifelab.se/researcher/15e8227c27944ddb88aebf8a5f7c9e74.json"}}, {"family": "Ruebens", "given": "Karen", "initials": "K"}, {"family": "Sinet-Mathiot", "given": "Virginie", "initials": "V", "orcid": "0000-0003-3228-5824", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ddbcd4720eb4256a8442803e40edcf5.json"}}, {"family": "Stoessel", "given": "Alexander", "initials": "A"}, {"family": "Dietl", "given": "Holger", "initials": "H"}, {"family": "Orschiedt", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0003-3629-8251", "researcher": {"href": "https://publications.scilifelab.se/researcher/877fc9ff7958467d95c83eb661be2631.json"}}, {"family": "Kelso", "given": "Janet", "initials": "J", "orcid": "0000-0002-3618-322X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57db79fef05b4743bff8345f8c3dfc04.json"}}, {"family": "Zeberg", "given": "Hugo", "initials": "H", "orcid": "0000-0001-7118-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/090e842ed8ff4cf2a3fe5f8e58118e58.json"}}, {"family": "Bos", "given": "Kirsten I", "initials": "KI", "orcid": "0000-0003-2937-3006", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d58da73fd8f409dac1e23a4b9f6b49f.json"}}, {"family": "Welker", "given": "Frido", "initials": "F", "orcid": "0000-0002-4846-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/7652762c05444a1d86c4b12c637b529b.json"}}, {"family": "Weiss", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0778-5520", "researcher": {"href": "https://publications.scilifelab.se/researcher/1688a83f780c44ba937de8577a9e3956.json"}}, {"family": "McPherron", "given": "Shannon P", "initials": "SP", "orcid": "0000-0002-2063-468X", "researcher": {"href": "https://publications.scilifelab.se/researcher/82ef55ca1bf84d1f9f14ddc414c2e1e4.json"}}, {"family": "Sch\u00fcler", "given": "Tim", "initials": "T", "orcid": "0000-0001-9190-8054", "researcher": {"href": "https://publications.scilifelab.se/researcher/433420b892e444b59e0701877ca6c4cb.json"}}, {"family": "Hublin", "given": "Jean-Jacques", "initials": "J"}, {"family": "Velem\u00ednsk\u00fd", "given": "Petr", "initials": "P", "orcid": "0000-0003-3691-7817", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdae571d1fbd442cad2a729beeb536d9.json"}}, {"family": "Br\u016f\u017eek", "given": "Jaroslav", "initials": "J", "orcid": "0000-0002-2478-9662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a50959d29e93439b8d74e45d321f0004.json"}}, {"family": "Peter", "given": "Benjamin M", "initials": "BM", "orcid": "0000-0003-2526-8081", "researcher": {"href": "https://publications.scilifelab.se/researcher/1860ed14a48048fdb14d9d183e1ee869.json"}}, {"family": "Meyer", "given": "Matthias", "initials": "M", "orcid": "0000-0002-4760-558X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4bd87e0225d422ea165ab0670f6cb20.json"}}, {"family": "Meller", "given": "Harald", "initials": "H", "orcid": "0000-0002-7590-0375", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fa5a199c61b47cb9b4fa3c7ea494ba7.json"}}, {"family": "Ringbauer", "given": "Harald", "initials": "H", "orcid": "0000-0002-4884-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8b1cf3531d40fd9d601705da089011.json"}}, {"family": "Hajdinjak", "given": "Mateja", "initials": "M", "orcid": "0000-0002-4064-0331", "researcher": {"href": "https://publications.scilifelab.se/researcher/cec10fd428c64857b2dc7017e390ab9b.json"}}, {"family": "Pr\u00fcfer", "given": "Kay", "initials": "K", "orcid": "0000-0001-6242-3058", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f96f223bf843a0949f1efa2a44513f.json"}}, {"family": "Krause", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9144-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2416e8bd2bfb4aa3988f4a37fca2de2e.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "638", "issue": "8051", "pages": "711-717"}, "abstract": "Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals1-4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlat\u00fd k\u016f\u0148, Czechia3 and Bacho Kiro, Bulgaria2. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenh\u00f6hle in Ranis, Germany4, and a further high-coverage genome from Zlat\u00fd k\u016f\u0148. We show that distant familial relationships link the Ranis and Zlat\u00fd k\u016f\u0148 individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.", "doi": "10.1038/s41586-024-08420-x", "pmid": "39667410", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11839475"}, {"db": "pii", "key": "10.1038/s41586-024-08420-x"}], "notes": [], "created": "2025-02-28T14:15:29.929Z", "modified": "2025-05-27T08:41:54.814Z"}, {"entity": "publication", "iuid": "f1a9c58aaeef4132b2cdec07c05109a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a9c58aaeef4132b2cdec07c05109a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a9c58aaeef4132b2cdec07c05109a4"}}, "title": "Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity.", "authors": [{"family": "Cougnoux", "given": "Antony", "initials": "A"}, {"family": "Mahmoud", "given": "Loay", "initials": "L"}, {"family": "Johnsson", "given": "Per A", "initials": "PA"}, {"family": "Eroglu", "given": "Alper", "initials": "A"}, {"family": "Gsell", "given": "Louise", "initials": "L"}, {"family": "Rosenbauer", "given": "Jakob", "initials": "J"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Hausser", "given": "Jean", "initials": "J"}], "type": "journal article", "published": "2025-01-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "3811", "issn-l": "2045-2322"}, "abstract": "Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. Yet, this potential is presently limited by technical and financial challenges of spatial omics methods and 3D cultures. To address this, we combine dye diffusion, the Smart-seq3xpress protocol for deep single-cell gene expression profiling, and dedicated probabilistic inference methods into diffusion Smart-seq3 (Smart-seq3D), to reveal the transcriptome of single cells along with their position along the core-periphery axis of spheroids. Applying Smart-seq3D to triple-negative breast tumor spheroids identifies thousands of spatial genes and reveals continuous, ungated spatial gene expression. Spatial gene and pathway expression patterns suggest biologies specific to spheroid regions, which we validate by immunostainings and pharmacological interventions. We use the Smart-seq3D data to test evolutionary principles of spatial tumor heterogeneity. Finally, we characterize aspects of tumor heterogeneity captured by 3D spheroids that are missing from 2D cultures but found in tumors in vivo. Smart-seq3D can offer a cost-efficient approach to explore how cells adapt their transcriptome to different micro-environments, reveal spatial determinants of drug resistance and could serve to characterize spatial interactions between cancer and stromal/immune cells in 3D co-cultures.", "doi": "10.1038/s41598-024-83989-x", "pmid": "39885179", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11782488"}, {"db": "pii", "key": "10.1038/s41598-024-83989-x"}], "notes": [], "created": "2025-04-07T08:46:18.744Z", "modified": "2025-04-07T08:46:18.749Z"}, {"entity": "publication", "iuid": "e91f3d289b5744af8e560cfea7c0910e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e91f3d289b5744af8e560cfea7c0910e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e91f3d289b5744af8e560cfea7c0910e"}}, "title": "A de novo, mosaic and complex chromosome 21 rearrangement causes APP triplication and familial autosomal dominant early onset Alzheimer disease.", "authors": [{"family": "Ehn", "given": "Emma", "initials": "E"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Laffita-Mesa", "given": "Jose M", "initials": "JM"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0003-4503-4717", "researcher": {"href": "https://publications.scilifelab.se/researcher/481958db26a2433ea8d5cc786c3b2bca.json"}}, {"family": "Schoumans", "given": "Jacqueline", "initials": "J"}, {"family": "Portaankorva", "given": "Anne M", "initials": "AM"}, {"family": "Viitanen", "given": "Matti", "initials": "M"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Graff", "given": "Caroline", "initials": "C", "orcid": "0000-0002-9949-2951", "researcher": {"href": "https://publications.scilifelab.se/researcher/3faadb7b187046b090d947f85d8c4dd1.json"}}], "type": "journal article", "published": "2025-01-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "2912", "issn-l": "2045-2322"}, "abstract": "Copy number variation (CNV) of the amyloid-\u03b2 precursor protein gene (APP) is a known cause of autosomal dominant Alzheimer disease (ADAD), but de novo genetic variants causing ADAD are rare. We report a mother and daughter with neuropathologically confirmed definite Alzheimer disease (AD) and extensive cerebral amyloid angiopathy (CAA). Copy number analysis identified an increased number of APP copies and genome sequencing (GS) revealed the underlying complex genomic rearrangement (CGR) including a triplication of APP with two unique breakpoint junctions (BPJs). The mosaic state in the mother had likely occurred de novo. Digital droplet PCR (ddPCR) on 42 different tissues, including 17 different brain regions, showed the derivative chromosome at varying mosaic levels (20-96%) in the mother who had symptom onset at age 58 years. In contrast, the derivative chromosome was present in all analyzed cells in the daughter whose symptom onset was at 34 years. This study reveals the architecture of a de novo CGR causing APP triplication and ADAD with a striking difference in age at onset between the fully heterozygous daughter compared to the mosaic mother. The GS analysis identified the complexity of the CGR illustrating its usefulness in identifying structural variants (SVs) in neurodegenerative disorders.", "doi": "10.1038/s41598-025-86645-0", "pmid": "39849058", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11759332"}, {"db": "pii", "key": "10.1038/s41598-025-86645-0"}], "notes": [], "created": "2025-01-30T10:52:39.932Z", "modified": "2025-11-18T20:45:12.186Z"}, {"entity": "publication", "iuid": "2d986718e5874eb7957b646b4e881227", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d986718e5874eb7957b646b4e881227.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d986718e5874eb7957b646b4e881227"}}, "title": "Low impact of Zostera marina meadows on sediment and water microbiota under brackish conditions.", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Delgado", "given": "Luis F", "initials": "LF"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pansch", "given": "Christian", "initials": "C"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G"}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G"}, {"family": "Piwosz", "given": "Kasia", "initials": "K"}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}], "type": "journal article", "published": "2025-01-11", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "20", "issue": "1", "pages": "2", "issn-l": null}, "abstract": "Zostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions. Changes in salinity generally have a strong impact on the biota, especially at the salty divide between salinity 6 and 9. To better understand the impact of the salty divide on the interaction between Z. marina and the surrounding sediment and water microbiota, we investigated the effects of Z. marina meadows on the surrounding microbiota across a salinity range of 6-15 in the Baltic Sea during the summer using 16S and 18S rRNA gene amplicon sequencing.\n\nSalinity was the most important factor for structuring the microbiota within both water and sediment. The presence of Z. marina affected the composition of the bacterial and eukaryotic community and bacterial alpha diversity in the sediment. However, this effect was confined to alpha-mesohaline conditions (salinity 9-15). The impact of Z. marina below salinity 9 on water and sediment microbiota was insignificant.\n\nIncreasing salinity was associated with a longer leaf length of Z. marina, causing an increased canopy height, which affects the sediment microbiota through reduced water velocity. Hence, we propose that the canopy effect may be the major predictor explaining Z. marina's interactions with the surrounding microbiota at salinity 9-15. These findings emphasize the importance of the physical effects of Z. marina meadow ecosystem services and have important implications for Z. marina management under brackish conditions in a changing climate.", "doi": "10.1186/s40793-024-00662-6", "pmid": "39799374", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11724437"}, {"db": "pii", "key": "10.1186/s40793-024-00662-6"}], "notes": [], "created": "2025-11-21T13:50:12.826Z", "modified": "2025-11-21T13:50:12.830Z"}, {"entity": "publication", "iuid": "ff3859bb07664273873b0c450fa280cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff3859bb07664273873b0c450fa280cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff3859bb07664273873b0c450fa280cc"}}, "title": "A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei.", "authors": [{"family": "Jonsdottir", "given": "Thorey K", "initials": "TK", "orcid": "0000-0002-0618-4731", "researcher": {"href": "https://publications.scilifelab.se/researcher/43607032b6e9486889f0c34a4e0437f6.json"}}, {"family": "Paoletta", "given": "Martina S", "initials": "MS", "orcid": "0000-0001-7318-489X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f221d2972a8945b4b0d49bfa602c64a0.json"}}, {"family": "Ishizaki", "given": "Takahiro", "initials": "T", "orcid": "0000-0002-4677-5608", "researcher": {"href": "https://publications.scilifelab.se/researcher/adcbcb52e9ba4744a10527038143d759.json"}}, {"family": "Hernandez", "given": "Sophia", "initials": "S", "orcid": "0000-0002-7851-5501", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae5365af3a2f43548e1a2c72bf341e79.json"}}, {"family": "Ivanova", "given": "Maria", "initials": "M", "orcid": "0000-0003-1063-3576", "researcher": {"href": "https://publications.scilifelab.se/researcher/f179f259deb24b3a9dc6d8329cc42ee5.json"}}, {"family": "Herrera Curbelo", "given": "Alicia", "initials": "A"}, {"family": "Saiki", "given": "Paulina A", "initials": "PA"}, {"family": "Selinger", "given": "Martin", "initials": "M", "orcid": "0000-0002-5420-9702", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc68cdd8b8d748499e552a6e700d7e55.json"}}, {"family": "Das", "given": "Debojyoti", "initials": "D", "orcid": "0000-0001-6811-3333", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c763bab024a492d8e534a1e541c21dc.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Bushell", "given": "Ellen S C", "initials": "ESC", "orcid": "0000-0003-2863-4112", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6d25e8481034aaaafb7453ab00af664.json"}}], "type": "journal article", "published": "2025-01-11", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "53", "issue": "2", "pages": null}, "abstract": "Many Plasmodium genes remain uncharacterized due to low genetic tractability. Previous large-scale knockout screens have only been able to target about half of the genome in the more genetically tractable rodent malaria parasite Plasmodium berghei. To overcome this limitation, we have developed a scalable CRISPR system called P. berghei high-throughput (PbHiT), which uses a single cloning step to generate targeting vectors with 100-bp homology arms physically linked to a guide RNA (gRNA) that effectively integrate into the target locus. We show that PbHiT coupled with gRNA sequencing robustly recapitulates known knockout mutant phenotypes in pooled transfections. Furthermore, we provide an online resource of knockout and tagging designs to target the entire P. berghei genome and scale-up vector production using a pooled ligation approach. This work presents for the first time a tool for high-throughput CRISPR screens in Plasmodium for studying the parasite's biology at scale.", "doi": "10.1093/nar/gkaf005", "pmid": "39844455", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11754126"}, {"db": "pii", "key": "7973899"}], "notes": [], "created": "2025-11-19T10:27:39.428Z", "modified": "2025-11-24T10:10:45.104Z"}, {"entity": "publication", "iuid": "c00a60f65c6949b7ae95fbd1ea808a22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c00a60f65c6949b7ae95fbd1ea808a22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c00a60f65c6949b7ae95fbd1ea808a22"}}, "title": "Pervasive horizontal transmission of Wolbachia in natural populations of closely related and widespread tropical skipper butterflies.", "authors": [{"family": "Ribeiro", "given": "Pedro", "initials": "P"}, {"family": "Butenko", "given": "Anzhelika", "initials": "A"}, {"family": "Linke", "given": "Daniel", "initials": "D"}, {"family": "Ghanavi", "given": "Hamid Reza", "initials": "HR"}, {"family": "Meier", "given": "Joana Isabel", "initials": "JI"}, {"family": "Wahlberg", "given": "Niklas", "initials": "N"}, {"family": "Matos-Marav\u00ed", "given": "P\u00e1vel", "initials": "P"}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "25", "issue": "1", "pages": "5", "issn-l": "1471-2180"}, "abstract": "The endosymbiotic relationship between Wolbachia bacteria and insects has been of interest for many years due to their diverse types of host reproductive phenotypic manipulation and potential role in the host's evolutionary history and population dynamics. Even though infection rates are high in Lepidoptera and specifically in butterflies, and reproductive manipulation is present in these taxa, less attention has been given to understanding how Wolbachia is acquired and maintained in their natural populations, across and within species having continental geographical distributions.\n\nWe used whole genome sequencing data to investigate the phylogenetics, demographic history, and infection rate dynamics of Wolbachia in four species of the Spicauda genus of skipper butterflies (Lepidoptera: Hesperiidae), a taxon that presents sympatric and often syntopic distribution, with drastic variability in species abundance in the Neotropical region. We show that infection is maintained by high turnover rates driven mainly by pervasive horizontal transmissions, while also presenting novel cases of double infection by distantly related supergroups of Wolbachia in S. simplicius.\n\nOur results suggest that Wolbachia population dynamics is host species-specific, with genetic cohesiveness across wide geographical distributions. We demonstrate that low coverage whole genome sequencing data can be used for an exhaustive assessment of Wolbachia infection in natural populations of butterflies, as well as its dynamics in closely related host species. This ultimately leads to a better understanding of the endosymbiotic population dynamics of Wolbachia and its effects on the host's biology and evolution.", "doi": "10.1186/s12866-024-03719-1", "pmid": "39773184", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11706079"}, {"db": "pii", "key": "10.1186/s12866-024-03719-1"}], "notes": [], "created": "2025-11-21T13:17:30.064Z", "modified": "2025-11-21T13:17:30.067Z"}, {"entity": "publication", "iuid": "626dde82bebd4d8bb7880ecc0a2237e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/626dde82bebd4d8bb7880ecc0a2237e0"}}, "title": "Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.", "authors": [{"family": "Kaldhusdal", "given": "Vilde", "initials": "V"}, {"family": "Boger", "given": "Mathias Franzen", "initials": "MF"}, {"family": "Tjernlund", "given": "Annelie", "initials": "A"}, {"family": "Burgener", "given": "Adam D", "initials": "AD"}, {"family": "Bradley", "given": "Frideborg", "initials": "F", "orcid": "0000-0003-3006-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d51eaeb949e94bd39ab3605d495dc647.json"}}, {"family": "Lajoie", "given": "Julie", "initials": "J"}, {"family": "Omollo", "given": "Kenneth", "initials": "K"}, {"family": "Kimani", "given": "Joshua", "initials": "J"}, {"family": "Fowke", "given": "Keith", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Broliden", "given": "Kristina", "initials": "K", "orcid": "0000-0003-2224-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/95346da4e5984d48bbb50032797155e5.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "1014"}, "abstract": "The injectable contraceptive, depot medroxyprogesterone acetate (DMPA), is associated with compromised cervical mucosal barriers. High-resolution spatial transcriptomics is applied here to reveal the spatial localization of these altered molecular markers. Ectocervical tissue samples from Kenyan sex workers using DMPA, or non-hormonal contraceptives, underwent spatial transcriptomics and gene set enrichment analyses. Integrated systemic estradiol levels and bulk tissue gene expression data from a larger cohort enhanced the study's scope. Unsupervised clustering unveiled four epithelial and seven submucosal layers, showcasing spatially restricted and diverse functional epithelial responses, and a less structured submucosal spatial ordering. DMPA associated with mucosal-wide immunoglobulin gene upregulation, verified by CD20+ B-cell immunostaining, and upregulated immune markers adjacent to the basal membrane. Downregulated genes represented spatially restricted disrupted epithelial barrier integrity and submucosal extracellular matrix dysfunction. The transcriptional profile was associated with markers of estrogen regulation. Collectively, our findings reveal estrogen-modulated distinct ectocervical transcriptional profiles associated with DMPA usage. While upregulation of immunoglobulin genes occurs throughout the mucosa, activation of innate immune responses and dysregulation of barrier integrity markers are spatially restricted. These results extend previous analyses using bulk transcriptomics and provide insights into the molecular landscape influenced by DMPA, shedding light on contraceptive effects and health implications.", "doi": "10.1038/s41598-024-83775-9", "pmid": "39762272", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11704007"}, {"db": "pii", "key": "10.1038/s41598-024-83775-9"}], "notes": [], "created": "2025-01-23T12:51:23.407Z", "modified": "2025-11-19T08:36:34.197Z"}, {"entity": "publication", "iuid": "be2943c4178e4522a7aec07e5c5f5cc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be2943c4178e4522a7aec07e5c5f5cc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be2943c4178e4522a7aec07e5c5f5cc6"}}, "title": "Positive Selection on Mammalian Immune Genes-Effects of Gene Function and Selective Constraint.", "authors": [{"family": "Nandakumar", "given": "Mridula", "initials": "M", "orcid": "0000-0003-4133-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/62b3ae7920a94445baa9c525a56c0973.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Carlsson", "given": "Fredric", "initials": "F", "orcid": "0000-0003-0875-4395", "researcher": {"href": "https://publications.scilifelab.se/researcher/d970f49b801a41eaafe818b724c03cda.json"}}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal article", "published": "2025-01-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "1", "issn-l": "0737-4038"}, "abstract": "Genome-wide analyses of various taxa have repeatedly shown that immune genes are important targets of positive selection. However, little is known about what factors determine which immune genes are under positive selection. To address this question, we here focus on the mammalian immune system and investigate the importance of gene function and other factors such as gene expression, protein-protein interactions, and overall selective constraint as determinants of positive selection. We compiled a list of >1,100 immune genes that were divided into six functional categories and analyzed using data from rodents. Genes encoding proteins that are in direct interactions with pathogens, such as pattern recognition receptors (PRRs), are often expected to be key targets of positive selection. We found that categories containing cytokines, cytokine receptors, and other cell surface proteins involved in, for example, cell-cell interactions were at least as important targets as PRRs, with three times higher rate of positive selection than nonimmune genes. The higher rate of positive selection on cytokines and cell surface proteins was partly an effect of these categories having lower selective constraint. Nonetheless, cytokines had a higher rate of positive selection than nonimmune genes even at a given level of selective constraint, indicating that gene function per se can also be a determinant of positive selection. These results have broad implications for understanding the causes of positive selection on immune genes, specifically the relative importance of host-pathogen coevolution versus other processes.", "doi": "10.1093/molbev/msaf016", "pmid": "39834162", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11783303"}, {"db": "pii", "key": "7965092"}], "notes": [], "created": "2025-11-21T09:29:18.915Z", "modified": "2025-11-21T09:29:19.178Z"}, {"entity": "publication", "iuid": "56f2be4738414a2bb34f30ee5eda8d1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56f2be4738414a2bb34f30ee5eda8d1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56f2be4738414a2bb34f30ee5eda8d1c"}}, "title": "Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia.", "authors": [{"family": "Komic", "given": "Hana", "initials": "H"}, {"family": "Nilsson", "given": "Malin S", "initials": "MS"}, {"family": "Wennstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Bandaru", "given": "Tagore Sanketh", "initials": "TS"}, {"family": "Jaako", "given": "Pekka", "initials": "P"}, {"family": "Hellstrand", "given": "Kristoffer", "initials": "K"}, {"family": "Thor\u00e9n", "given": "Fredrik B", "initials": "FB"}, {"family": "Martner", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2025-01-01", "journal": {"title": "Haematologica", "issn": "1592-8721", "issn-l": "0390-6078", "volume": "110", "issue": "1", "pages": "117-128"}, "abstract": "Hydroxyurea (HU) is frequently used in the early phase of chronic myeloid leukemia (CML) to achieve cytoreduction prior to tyrosine kinase inhibitor therapy. However, its impact on CML stem and progenitor cells (SPC) remains largely unknown. This study utilized targeted proteo-transcriptomic expression data on 596 genes and 51 surface proteins in 60,000 CD14-CD34+ cells from chronic phase CML patients to determine effects of short-term HU treatment (4-19 days) on CML SPC. Peripheral blood and bone marrow samples were obtained from 17 CML patients eligible for short-term HU treatment (3 patients before and after HU, 7 patients before HU and 7 patients after HU) and subjected to single-cell CITE-sequencing and/or flow cytometry analysis. The analysis revealed enhanced frequencies of hemoglobin-expressing (HBA1, HBA2, HBB) erythroid progenitor cells in blood and bone marrow following HU treatment. In addition, there was an accumulation of cell subsets with S/G2/M phase-related gene and protein expression, likely representing cells arrested in, or progressing slowly through, the cell cycle. The increased frequency of cells in S/G2/M phase after HU was observed already among the most immature leukemic stem cells (LSC), and patients with a large fraction of LSC in the S/G2/M phase showed poor responsiveness to tyrosine kinase inhibitor treatment. We conclude that short-term HU treatment entails differentiation of erythroid progenitor cells and alters the characteristics of LSC in CML. The results imply that studies of LSC and progenitor populations in CML should take effects of initial HU therapy into account.", "doi": "10.3324/haematol.2024.285071", "pmid": "39157872", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC11694111"}], "notes": [], "created": "2025-02-03T07:42:24.770Z", "modified": "2025-02-28T08:05:18.309Z"}, {"entity": "publication", "iuid": "a748b4d74c7342cc95cfa6d89417bef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a748b4d74c7342cc95cfa6d89417bef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a748b4d74c7342cc95cfa6d89417bef1"}}, "title": "Dark carbon fixation is a common process in the water column of stratified boreal lakes.", "authors": [{"family": "Martin", "given": "Ga\u00ebtan", "initials": "G"}, {"family": "Rissanen", "given": "Antti J", "initials": "AJ"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Peura", "given": "Sari", "initials": "S"}], "type": "journal article", "published": "2025-01-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "958", "pages": "177433", "issn-l": "0048-9697"}, "abstract": "CO2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water.", "doi": "10.1016/j.scitotenv.2024.177433", "pmid": "39522777", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)07590-9"}], "notes": [], "created": "2025-01-02T10:28:48.083Z", "modified": "2025-11-28T10:44:31.434Z"}, {"entity": "publication", "iuid": "fb69b51e8faf4e51bbfd8e7f2a4a3e4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb69b51e8faf4e51bbfd8e7f2a4a3e4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb69b51e8faf4e51bbfd8e7f2a4a3e4c"}}, "title": "Phthalate esters in baltic lagoons: Spatial distribution, ecological risks, and novel insights into their fate using transcriptomics.", "authors": [{"family": "Lorre", "given": "Elise", "initials": "E"}, {"family": "Bianchi", "given": "Federica", "initials": "F"}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}, {"family": "Samuilovien\u0117", "given": "Aurelija", "initials": "A"}, {"family": "Wo\u017aniczka", "given": "Adam", "initials": "A"}, {"family": "Zilius", "given": "Mindaugas", "initials": "M"}], "type": "journal article", "published": "2024-12-20", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "957", "pages": "177526", "issn-l": "0048-9697"}, "abstract": "Plasticizers such as phthalate esters (PAEs) are organic compounds widely used in various consumer and industrial products, raising strong environmental concerns due to their pervasive presence and potential adverse effects. Lagoon ecosystems are particularly vulnerable to PAE pollution as they are semi-enclosed and receive high loads of organic materials. The present study investigates the distribution of seven common PAEs in three large European lagoons (Curonian, Vistula and Szczecin) in the southern Baltic Sea. The concentration levels of PAEs in the water column, encompassing both the dissolved and particulate-bound phases, and in sediments were assessed to elucidate distribution patterns and potential ecological risks within these lagoon ecosystems. The average concentration of total PAEs in the water column ranged from 0.03 to 1.45 \u03bcg L-1, whereas sediment concentration varied from 0.008 to 1.06 \u03bcg g-1, levels comparable to or lower than those found in other European coastal areas. Distribution patterns of PAEs in sediment showed notable similarity across all three lagoons, whereas variations were observed in the water column. Notably, di(2-ethylhexyl) phthalate (DEHP), di-n-octyl phthalate (DOP) and dimethyl phthalate (DMP) emerged as the most concerning congeners in studied lagoons, all of which pose a moderate risk to aquatic organisms. This study applied shotgun transcriptomic analysis to field samples, revealing active microbial communities involved in PAEs degradation in the Baltic lagoons for the first time. The degradation of phthalic acid (PA) into intermediate compounds such as protocatechuate was not identified as a rate-limiting step in the studied environment. The degradation activity was primarily localized in the sediment layers, with Gram-negative bacteria playing a major role, while Gram-positive bacteria appeared incapable of degrading PA. These findings provide valuable insights into the distribution and transformation mechanisms of PAEs in estuarine environments.", "doi": "10.1016/j.scitotenv.2024.177526", "pmid": "39549755", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)07683-6"}], "notes": [], "created": "2025-01-02T10:30:52.543Z", "modified": "2025-04-07T07:29:33.765Z"}, {"entity": "publication", "iuid": "5cb642ba606340c383ccccef9091ae0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cb642ba606340c383ccccef9091ae0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cb642ba606340c383ccccef9091ae0c"}}, "title": "Spatiotemporal single-cell roadmap of human skin wound healing.", "authors": [{"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Bian", "given": "Xiaowei", "initials": "X"}, {"family": "Luo", "given": "Lihua", "initials": "L"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Li", "given": "Li", "initials": "L"}, {"family": "Zhang", "given": "Letian", "initials": "L"}, {"family": "Chen", "given": "Yongjian", "initials": "Y"}, {"family": "Guo", "given": "Lei", "initials": "L"}, {"family": "Gao", "given": "Juan", "initials": "J"}, {"family": "Cao", "given": "Chunyan", "initials": "C"}, {"family": "Wang", "given": "Jiating", "initials": "J"}, {"family": "He", "given": "Wenjun", "initials": "W"}, {"family": "Xiao", "given": "Yunting", "initials": "Y"}, {"family": "Zhu", "given": "Liping", "initials": "L"}, {"family": "Annusver", "given": "Karl", "initials": "K"}, {"family": "Gopee", "given": "Nusayhah Hudaa", "initials": "NH"}, {"family": "Basurto-Lozada", "given": "Daniela", "initials": "D"}, {"family": "Horsfall", "given": "David", "initials": "D"}, {"family": "Bennett", "given": "Clare L", "initials": "CL"}, {"family": "Kasper", "given": "Maria", "initials": "M"}, {"family": "Haniffa", "given": "Muzlifah", "initials": "M"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Li", "given": "Dongqing", "initials": "D"}, {"family": "Land\u00e9n", "given": "Ning Xu", "initials": "NX"}], "type": "journal article", "published": "2024-12-18", "journal": {"title": "Cell Stem Cell", "issn": "1875-9777", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Wound healing is vital for human health, yet the details of cellular dynamics and coordination in human wound repair remain largely unexplored. To address this, we conducted single-cell multi-omics analyses on human skin wound tissues through inflammation, proliferation, and remodeling phases of wound repair from the same individuals, monitoring the cellular and molecular dynamics of human skin wound healing at an unprecedented spatiotemporal resolution. This singular roadmap reveals the cellular architecture of the wound margin and identifies FOSL1 as a critical driver of re-epithelialization. It shows that pro-inflammatory macrophages and fibroblasts sequentially support keratinocyte migration like a relay race across different healing stages. Comparison with single-cell data from venous and diabetic foot ulcers uncovers a link between failed keratinocyte migration and impaired inflammatory response in chronic wounds. Additionally, comparing human and mouse acute wound transcriptomes underscores the indispensable value of this roadmap in bridging basic research with clinical innovations.", "doi": "10.1016/j.stem.2024.11.013", "pmid": "39729995", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1934-5909(24)00412-0"}], "notes": [], "created": "2025-01-02T10:30:31.039Z", "modified": "2025-01-20T13:20:10.129Z"}, {"entity": "publication", "iuid": "13600136596f4b84869a1e2d85c6a40e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13600136596f4b84869a1e2d85c6a40e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13600136596f4b84869a1e2d85c6a40e"}}, "title": "Multi-omics analysis detail a submicroscopic inv(15)(q14q15) generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency.", "authors": [{"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Soller", "given": "Maria Johansson", "initials": "MJ"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-12-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "30343", "issn-l": "2045-2322"}, "abstract": "Inversions are balanced structural variants that often remain undetected in genetic diagnostics. We present a female proband with a de novo Chromosome 15 paracentric inversion, disrupting MEIS2 and NUSAP1. The inversion was detected by short-read genome sequencing and confirmed with adaptive long-read sequencing. The breakpoint junction analysis revealed a 96 bp (bp) deletion and an 18 bp insertion in the two junctions, suggesting that the rearrangement arose through a replicative error. Transcriptome sequencing of cultured fibroblasts revealed normal MEIS2 levels and 0.61-fold decreased expression of NUSAP1. Furthermore, three fusion transcripts were detected and confirmed by Sanger sequencing. Heterozygous loss of MEIS2 (MIM# 600987) is associated with a cleft palate, heart malformations, and intellectual impairment, which overlap with the clinical symptoms observed in the proband. The observed fusion transcripts are likely non-functional, and MEIS2 haploinsufficiency is the likely disease causative mechanism. Altogether, this study's findings illustrate the importance of including inversions in rare disease diagnostic testing and highlight the value of long read sequencing for the validation and characterization of such variants.", "doi": "10.1038/s41598-024-81507-7", "pmid": "39639090", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Long read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11621304"}, {"db": "pii", "key": "10.1038/s41598-024-81507-7"}], "notes": [], "created": "2025-01-02T10:32:21.284Z", "modified": "2025-11-18T20:49:45.019Z"}, {"entity": "publication", "iuid": "45dd1cb1d3e747509d50c4a91ee6b891", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45dd1cb1d3e747509d50c4a91ee6b891.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45dd1cb1d3e747509d50c4a91ee6b891"}}, "title": "Metagenomic characterization of viruses in the serum of children with newly diagnosed cancer.", "authors": [{"family": "Leijonhufvud", "given": "Gustaf", "initials": "G"}, {"family": "Soratto", "given": "Tatiany Aparecida Teixeira", "initials": "TAT"}, {"family": "Matos", "given": "Gabriel Machado", "initials": "GM"}, {"family": "Bajalan", "given": "Amanj", "initials": "A"}, {"family": "Eichler-Jonsson", "given": "Claudia", "initials": "C"}, {"family": "Gustafsson", "given": "Britt", "initials": "B"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "J. Clin. Virol.", "issn": "1873-5967", "volume": "175", "pages": "105736", "issn-l": "1386-6532"}, "abstract": "A large cohort of pediatric patients with various forms of childhood cancer was investigated for the presence of viruses using metagenomics. A total of 476 patient samples, collected between 1989 and 2018, were analyzed, representing various pediatric oncological diagnoses and a control group of non-malignant diagnoses.\n\nThe study was carried out using metagenomic sequencing of serum samples. Viruses were identified and analyzed using bioinformatics methods, followed by Polymerase chain reaction (PCR) confirmation RESULTS: The results indicate that a wide range of viruses can be detected in the bloodstream of children with newly diagnosed cancer. Nine viral genomes were identified: Human Pegivirus (HPgV), Hepatitis C virus, Parechovirus 1, Rhinovirus C, Human papillomavirus 116, Human polyomavirus 10, Parvovirus B19, and different variants of Torque Teno Virus (TTV). In this study, a previously unknown virus was found belonging to the Iflavirdae family in the order Picornavirales. HPGV was significantly more common in patients with leukemia compared to other conditions.\n\nThese results highlight the abundance of systemic virus infections in children, and the value of metagenomic sequencing for hypothesis forming regarding the associations between virus infections and cancer.", "doi": "10.1016/j.jcv.2024.105736", "pmid": "39405634", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S1386-6532(24)00098-2"}], "notes": [], "created": "2024-10-31T12:39:54.775Z", "modified": "2025-11-18T20:44:18.394Z"}, {"entity": "publication", "iuid": "d487b33890704e89aab5b9f9c9f53fd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d487b33890704e89aab5b9f9c9f53fd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d487b33890704e89aab5b9f9c9f53fd8"}}, "title": "A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce.", "authors": [{"family": "Stojkovi\u010d", "given": "Katja", "initials": "K"}, {"family": "Canovi", "given": "Camilla", "initials": "C"}, {"family": "Le", "given": "Kim-Cuong", "initials": "KC"}, {"family": "Ahmad", "given": "Iftikhar", "initials": "I"}, {"family": "Gaboreanu", "given": "Ioana", "initials": "I"}, {"family": "Johansson", "given": "Sofie", "initials": "S"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Egertsdotter", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-0696-4279", "researcher": {"href": "https://publications.scilifelab.se/researcher/577fc164af6842379fbbcb57c8b02986.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Plant J.", "issn": "1365-313X", "issn-l": "0960-7412", "volume": "120", "issue": "5", "pages": "2238-2252"}, "abstract": "Somatic embryogenesis (SE) is a powerful model system for studying embryo development and an important method for scaling up availability of elite and climate-adapted genetic material of Norway spruce (Picea abies L. Karst). However, there are several steps during the development of the somatic embryo (Sem) that are suboptimal compared to zygotic embryo (Zem) development. These differences are poorly understood and result in substantial yield losses during plant production, which limits cost-effective large-scale production of SE plants. This study presents a comprehensive data resource profiling gene expression during zygotic and somatic embryo development to support studies aiming to advance understanding of gene regulatory programmes controlling embryo development. Transcriptome expression patterns were analysed during zygotic embryogenesis (ZE) in Norway spruce, including separated samples of the female gametophytes and Zem, and at multiple stages during SE. Expression data from eight developmental stages of SE, starting with pro-embryogenic masses (PEMs) up until germination, revealed extensive modulation of the transcriptome between the early and mid-stage maturing embryos and at the transition of desiccated embryos to germination. Comparative analysis of gene expression changes during ZE and SE identified differences in the pattern of gene expression changes and functional enrichment of these provided insight into the associated biological processes. Orthologs of transcription factors known to regulate embryo development in angiosperms were differentially regulated during Zem and Sem development and in the different zygotic embryo tissues, providing clues to the differences in development observed between Zem and Sem. This resource represents the most comprehensive dataset available for exploring embryo development in conifers.", "doi": "10.1111/tpj.17087", "pmid": "39462439", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11629735"}], "notes": [], "created": "2024-11-25T10:28:06.952Z", "modified": "2025-02-28T14:20:52.731Z"}, {"entity": "publication", "iuid": "a8e13d829b924977b538b6c4cd583673", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8e13d829b924977b538b6c4cd583673.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8e13d829b924977b538b6c4cd583673"}}, "title": "A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera.", "authors": [{"family": "Cangren", "given": "Patrik", "initials": "P"}, {"family": "Bertrand", "given": "Yann J K", "initials": "YJK"}, {"family": "Braverman", "given": "John M", "initials": "JM"}, {"family": "Gilfillan", "given": "Gregor Duncan", "initials": "GD"}, {"family": "Hamilton", "given": "Matthew B", "initials": "MB"}, {"family": "Oxelman", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Data Brief", "issn": "2352-3409", "volume": "57", "pages": "111094", "issn-l": "2352-3409"}, "abstract": "A dataset of 40 assembled and annotated transcriptomes from 34 different species sampled from phylogenetically diverse parts of the flowering plant genus Silene (Caryophyllaceae) and the related genera Agrostemma, Atocion, Eudianthe, Heliosperma, Petrocoptis and Viscaria. RNA extracted from roots, stems, leaves, buds and flowers were sequenced using paired end reads on the Illumina Hiseq platform. A total of 716 million raw reads were produced and assembled into 2.67 million isogroups (\"genes\"). Contigs from all samples were annotated using UniProt/SwissProt and assigned with GO-terms. A total of 974274 annotations were made (per sample average 24357, stdev 7034), giving an annotation proportion of 37% (per sample average 39%, stdev 9.75%). 741087 of the annotations had taxonomic identities within Magnoliopsida (per sample average 18527, stdev 3931), resulting in assignment of 4519488 GO-terms (per sample average 112987, stdev 22536). The data set can be further utilized for biological research and phylogenetic studies, evolutionary questions, functional analyses of genes, polyploidy as well as for marker development.", "doi": "10.1016/j.dib.2024.111094", "pmid": "39633972", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11615531"}, {"db": "pii", "key": "S2352-3409(24)01056-4"}], "notes": [], "created": "2025-01-02T10:31:13.246Z", "modified": "2025-01-02T10:31:13.250Z"}, {"entity": "publication", "iuid": "35169fcfafb34d33808c4bcb778a2f58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35169fcfafb34d33808c4bcb778a2f58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35169fcfafb34d33808c4bcb778a2f58"}}, "title": "Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote.", "authors": [{"family": "Sayers", "given": "Claire", "initials": "C"}, {"family": "Pandey", "given": "Vikash", "initials": "V"}, {"family": "Balakrishnan", "given": "Arjun", "initials": "A"}, {"family": "Michie", "given": "Katharine", "initials": "K"}, {"family": "Svedberg", "given": "Dennis", "initials": "D", "orcid": "0000-0001-5799-4075", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9273749dce544ee85e251fab9edbb70.json"}}, {"family": "Hunziker", "given": "Mirjam", "initials": "M", "orcid": "0000-0002-2912-4993", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f021733485045d8ad5ba2eb9c206525.json"}}, {"family": "Pardo", "given": "Mercedes", "initials": "M"}, {"family": "Choudhary", "given": "Jyoti", "initials": "J"}, {"family": "Berntsson", "given": "Ronnie", "initials": "R", "orcid": "0000-0001-6848-322X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e78d8a69e46241bc8a79ede3df38ebdf.json"}}, {"family": "Billker", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1716-168X", "researcher": {"href": "https://publications.scilifelab.se/researcher/baa3de453a8047688800db0d5a14e291.json"}}], "type": "journal article", "published": "2024-11-20", "journal": {"title": "Cell Syst", "issn": "2639-5460", "volume": "15", "issue": "11", "pages": "1075-1091.e6", "issn-l": "2405-4712"}, "abstract": "Sexual reproduction in malaria parasites is essential for their transmission to mosquitoes and offers a divergent eukaryote model to understand the evolution of sex. Through a panel of genetic screens in Plasmodium berghei, we identify 348 sex and transmission-related genes and define roles for unstudied genes as putative targets for transmission-blocking interventions. The functional data provide a deeper understanding of female metabolic reprogramming, meiosis, and the axoneme. We identify a complex of a SUN domain protein (SUN1) and a putative allantoicase (ALLC1) that is essential for male fertility by linking the microtubule organizing center to the nuclear envelope and enabling mitotic spindle formation during male gametogenesis. Both proteins have orthologs in mouse testis, and the data raise the possibility of an ancient role for atypical SUN domain proteins in coupling the nucleus and axoneme. Altogether, our data provide an unbiased picture of the molecular processes that underpin malaria parasite transmission. A record of this paper's transparent peer review process is included in the supplemental information.", "doi": "10.1016/j.cels.2024.10.008", "pmid": "39541984", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S2405-4712(24)00305-3"}], "notes": [], "created": "2025-01-02T10:30:05.533Z", "modified": "2025-04-07T07:30:42.201Z"}, {"entity": "publication", "iuid": "7dc1eec982f6407b9279d515c64d5013", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7dc1eec982f6407b9279d515c64d5013.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7dc1eec982f6407b9279d515c64d5013"}}, "title": "Transcriptomic profiling of the oocyte-cumulus-granulosa cell complex from estrogen receptor \u03b2 knockout mice.", "authors": [{"family": "T\u00f6h\u00f6nen", "given": "Virpi", "initials": "V"}, {"family": "Antonson", "given": "Per", "initials": "P"}, {"family": "Boggavarapu", "given": "Nageswara Rao", "initials": "NR"}, {"family": "Ali", "given": "Heba", "initials": "H"}, {"family": "Motaholi", "given": "Leticia Apolinario", "initials": "LA"}, {"family": "Gustafsson", "given": "Jan-\u00c5ke", "initials": "J\u00c5"}, {"family": "Varshney", "given": "Mukesh", "initials": "M"}, {"family": "Rodriguez-Wallberg", "given": "Kenny A", "initials": "KA"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Nalvarte", "given": "Ivan", "initials": "I"}, {"family": "Inzunza", "given": "Jose", "initials": "J"}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "F S Sci", "issn": "2666-335X", "volume": "5", "issue": "4", "pages": "306-317", "issn-l": null}, "abstract": "To study the role of estrogen receptor \u03b2 in follicle development and maturation and the response to gonadotropin stimulation aiming at superovulation.\n\nExperimental study and transcriptomic analysis.\n\nKarolinka Institutet, medical university.\n\nHealthy wild-type (WT) and estrogen receptor \u03b2 knockout (Esr2-KO) female mice undergoing superovulation at 4 weeks, 7 weeks, and 6 months of age.\n\nNot applicable.\n\nOocyte yield after superovulation, transcriptomic profiling of cumulus-granulosa cell complexes and oocytes, and immunohistochemical analyses.\n\nSuperovulation of estrogen receptor \u03b2 (ER\u03b2) knockout mice resulted in reduced oocyte yield at 6 months of age compared with WT mice, but younger mice had similar yields. RNA-seq analysis of cumulus cells from superovulated WT and Esr2-KO mice identified genes and pathways associated with among others adhesion, proliferation, Wnt-signaling, and placed ER\u03b2 in bipotential granulosa cell cluster. Loss of ER\u03b2 increased expression of the other estrogen receptors Esr1 and Gper1.\n\nOur results show that ER\u03b2 has an important role in regulating ovulation in response to exogenous gonadotropins in 6-month-old mice, but not in younger mice. Our transcriptomic and immunohistochemical observations suggest a dysregulation of the granulosa cell communication and lack of tight coordination between granulosa cell replication and antrum expansion. A significant upregulation of other estrogen receptors may support a compensatory mechanism sustaining fertility during younger age in Esr2-KO mice.", "doi": "10.1016/j.xfss.2024.08.004", "pmid": "39168303", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S2666-335X(24)00056-9"}], "notes": [], "created": "2025-09-03T12:06:32.682Z", "modified": "2025-09-03T12:06:32.731Z"}, {"entity": "publication", "iuid": "381cfb2387214c1dbb73fda59a55709f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/381cfb2387214c1dbb73fda59a55709f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/381cfb2387214c1dbb73fda59a55709f"}}, "title": "Local climate, air quality and leaf litter cover shape foliar fungal communities on an urban tree.", "authors": [{"family": "Faticov", "given": "Maria", "initials": "M", "orcid": "0000-0001-8206-9332", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd00e5ee400e440ba76d1010f5cbe7d9.json"}}, {"family": "Amorim", "given": "Jorge H", "initials": "JH"}, {"family": "Abdelfattah", "given": "Ahmed", "initials": "A"}, {"family": "van Dijk", "given": "Laura J A", "initials": "LJA"}, {"family": "Carvalho", "given": "Ana Cristina", "initials": "AC"}, {"family": "Laforest-Lapointe", "given": "Isabelle", "initials": "I"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Ambio", "issn": "1654-7209", "volume": "53", "issue": "11", "pages": "1673-1685", "issn-l": "0044-7447"}, "abstract": "Foliar fungi on urban trees are important for tree health, biodiversity and ecosystem functioning. Yet, we lack insights into how urbanization influences foliar fungal communities. We created detailed maps of Stockholm region's climate and air quality and characterized foliar fungi from mature oaks (Quercus robur) across climatic, air quality and local habitat gradients. Fungal richness was higher in locations with high growing season relative humidity, and fungal community composition was structured by growing season maximum temperature, NO2 concentration and leaf litter cover. The relative abundance of mycoparasites and endophytes increased with temperature. The relative abundance of pathogens was lowest with high concentrations of NO2 and particulate matter (PM2.5), while saprotrophs increased with leaf litter cover. Our findings show that urbanization influences foliar fungi, providing insights for developing management guidelines to promote tree health, prevent disease outbreaks and maintain biodiversity within urban landscapes.", "doi": "10.1007/s13280-024-02041-4", "pmid": "38871928", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11436615"}, {"db": "pii", "key": "10.1007/s13280-024-02041-4"}], "notes": [], "created": "2024-08-15T12:12:43.082Z", "modified": "2025-02-28T14:11:15.200Z"}, {"entity": "publication", "iuid": "62243f04b6c04fa1889cea0d14f2fad5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62243f04b6c04fa1889cea0d14f2fad5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62243f04b6c04fa1889cea0d14f2fad5"}}, "title": "Examining the liver-pancreas crosstalk reveals a role for the molybdenum cofactor in \u03b2-cell regeneration.", "authors": [{"family": "Karampelias", "given": "Christos", "initials": "C", "orcid": "0000-0002-9990-5760", "researcher": {"href": "https://publications.scilifelab.se/researcher/509894ee3f0e41eeaf57eb2febc18c70.json"}}, {"family": "B\u0103loiu", "given": "Bianca", "initials": "B", "orcid": "0009-0001-8047-3515", "researcher": {"href": "https://publications.scilifelab.se/researcher/9da7b4065fe84b5885d203adc2aaada2.json"}}, {"family": "Rathkolb", "given": "Birgit", "initials": "B"}, {"family": "da Silva-Buttkus", "given": "Patricia", "initials": "P", "orcid": "0000-0003-4705-3399", "researcher": {"href": "https://publications.scilifelab.se/researcher/324af17801cc42e799681595b27c86d5.json"}}, {"family": "Bachar-Wikstr\u00f6m", "given": "Etty", "initials": "E", "orcid": "0000-0002-3283-6721", "researcher": {"href": "https://publications.scilifelab.se/researcher/388692a214e44e9ea7497b397d237bc0.json"}}, {"family": "Marschall", "given": "Susan", "initials": "S"}, {"family": "Fuchs", "given": "Helmut", "initials": "H"}, {"family": "Gailus-Durner", "given": "Valerie", "initials": "V"}, {"family": "Chu", "given": "Lianhe", "initials": "L"}, {"family": "Hrab\u011b de Angelis", "given": "Martin", "initials": "M"}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f796ff515c95491e9cd47018e02220c0.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "7", "issue": "11", "pages": "e202402771"}, "abstract": "Regeneration of insulin-producing \u03b2-cells is an alternative avenue to manage diabetes, and it is crucial to unravel this process in vivo during physiological responses to the lack of \u03b2-cells. Here, we aimed to characterize how hepatocytes can contribute to \u03b2-cell regeneration, either directly or indirectly via secreted proteins or metabolites, in a zebrafish model of \u03b2-cell loss. Using lineage tracing, we show that hepatocytes do not directly convert into \u03b2-cells even under extreme \u03b2-cell ablation conditions. A transcriptomic analysis of isolated hepatocytes after \u03b2-cell ablation displayed altered lipid- and glucose-related processes. Based on the transcriptomics, we performed a genetic screen that uncovers a potential role of the molybdenum cofactor (Moco) biosynthetic pathway in \u03b2-cell regeneration and glucose metabolism in zebrafish. Consistently, molybdenum cofactor synthesis 2 (Mocs2) haploinsufficiency in mice indicated dysregulated glucose metabolism and liver function. Together, our study sheds light on the liver-pancreas crosstalk and suggests that the molybdenum cofactor biosynthesis pathway should be further studied in relation to glucose metabolism and diabetes.", "doi": "10.26508/lsa.202402771", "pmid": "39159974", "labels": {"NGI Short read": null, "NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11333758"}, {"db": "pii", "key": "7/11/e202402771"}], "notes": [], "created": "2024-09-30T08:03:57.463Z", "modified": "2025-02-28T14:23:56.417Z"}, {"entity": "publication", "iuid": "405669a21c9d4811a34a94b06e265a98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/405669a21c9d4811a34a94b06e265a98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/405669a21c9d4811a34a94b06e265a98"}}, "title": "Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny \u00c5lesund, Svalbard (79\u00b0N).", "authors": [{"family": "Sipes", "given": "Katie", "initials": "K"}, {"family": "Buongiorno", "given": "Joy", "initials": "J"}, {"family": "Steen", "given": "Andrew D", "initials": "AD"}, {"family": "Abramov", "given": "Andrey A", "initials": "AA"}, {"family": "Abuah", "given": "Chukwufumnanya", "initials": "C"}, {"family": "Peters", "given": "Samantha L", "initials": "SL"}, {"family": "Gianonne", "given": "Richard J", "initials": "RJ"}, {"family": "Hettich", "given": "Robert L", "initials": "RL"}, {"family": "Boike", "given": "Julia", "initials": "J"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Vishnivetskaya", "given": "Tatiana A", "initials": "TA"}, {"family": "Lloyd", "given": "Karen G", "initials": "KG"}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Syst. Appl. Microbiol.", "issn": "1618-0984", "volume": "47", "issue": "6", "pages": "126544", "issn-l": "0723-2020"}, "abstract": "Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny \u00c5lesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5\u00b0C to 5 \u00b0C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding \u03b2 -glucosidase, N-acetyl-\u03b2-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below \u223c6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.", "doi": "10.1016/j.syapm.2024.126544", "pmid": "39303414", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0723-2020(24)00058-4"}], "notes": [], "created": "2024-10-18T07:13:55.740Z", "modified": "2025-02-28T14:13:09.272Z"}, {"entity": "publication", "iuid": "94a6617807b3431a961787b517bc63a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94a6617807b3431a961787b517bc63a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94a6617807b3431a961787b517bc63a0"}}, "title": "Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.", "authors": [{"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Rossini", "given": "Roberto", "initials": "R"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA", "orcid": "0009-0002-8357-5186", "researcher": {"href": "https://publications.scilifelab.se/researcher/5419b796720a47c8aa7a26ca663a96bd.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Bradford", "given": "Tessa M", "initials": "TM", "orcid": "0000-0003-0607-1398", "researcher": {"href": "https://publications.scilifelab.se/researcher/d434c308f143443b864dfb1137c9d549.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df76e7fede64a0294cf68a3ae20a07c.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/424031a0011f4e77bbb6f64a1d369b8b.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}], "type": "journal article", "published": "2024-10-30", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17567", "issn-l": "0962-1083"}, "abstract": "The early evolution of sex chromosomes has remained obscure for more than a century. The Vandiemenella viatica species group of morabine grasshoppers is highly suited for studying the early stages of sex chromosome divergence and degeneration of the Y chromosome. This stems from the fact that neo-XY sex chromosomes have independently evolved multiple times by X-autosome fusions with different autosomes. Here, we generated new chromosome-level assemblies for two chromosomal races representing karyotypes with and without neo-sex chromosomes (P24XY and P24X0), and sequence data of a third chromosomal race with a different neo-XY chromosome system (P25XY). Interestingly, these two neo-XY chromosomal races are formed by different X-autosome fusions (involving chr1 and chrB, respectively), and we found that both neo-Y chromosomes have partly ceased to recombine with their neo-X counterpart. We show that the neo-XY chromosomes have diverged through accumulation of SNPs and structural mutations, and that many neo-Y-linked genes have degenerated since recombination ceased. However, the non-recombining regions of neo-Y chromosomes host non-degenerated genes crucial for sex determination, such as sex-lethal and transformer, alongside genes associated with spermatogenesis, fertility, and reproduction, illustrating their integrative role as a masculinizing supergene. Contrary to expectations, the neo-Y chromosomes showed (slightly) lower density of transposable elements (TEs) compared to other genomic regions. The study reveals the unique dynamics of young sex chromosomes, with evolution of recombination suppression and pronounced decay of (some) neo-sex chromosome genes, and provides a compelling case illustrating how chromosomal fusions and post-fusion mutational processes contribute to the evolution of supergenes.", "doi": "10.1111/mec.17567", "pmid": "39475093", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-31T12:37:22.766Z", "modified": "2024-11-25T10:27:35.236Z"}, {"entity": "publication", "iuid": "62515568135543558aea5335722cb034", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62515568135543558aea5335722cb034.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62515568135543558aea5335722cb034"}}, "title": "Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.", "authors": [{"family": "Shafighi", "given": "Shadi", "initials": "S"}, {"family": "Geras", "given": "Agnieszka", "initials": "A"}, {"family": "Jurzysta", "given": "Barbara", "initials": "B"}, {"family": "Sahaf Naeini", "given": "Alireza", "initials": "A"}, {"family": "Filipiuk", "given": "Igor", "initials": "I"}, {"family": "Ra Czkowska", "given": "Alicja", "initials": "A"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Koperski", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Nowis", "given": "Dominika", "initials": "D", "orcid": "0000-0003-2748-9523", "researcher": {"href": "https://publications.scilifelab.se/researcher/7645c7bdbd1b436bbb1c218b8e0ce355.json"}}, {"family": "Carbone", "given": "Alessandra", "initials": "A", "orcid": "0000-0003-2098-5743", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e13fee16a84747a22b438ce26facf7.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}, {"family": "Szczurek", "given": "Ewa", "initials": "E", "orcid": "0000-0002-1320-6695", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca6b8a8caa7494aaec1b0cab3270a31.json"}}], "type": "journal article", "published": "2024-10-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9343", "issn-l": "2041-1723"}, "abstract": "Spatial and genomic heterogeneity of tumors are crucial factors influencing cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on somatic point mutations is lacking. Here, we propose Tumoroscope, the first probabilistic model that accurately infers cancer clones and their localization in close to single-cell resolution by integrating pathological images, whole exome sequencing, and spatial transcriptomics data. In contrast to previous methods, Tumoroscope explicitly addresses the problem of deconvoluting the proportions of clones in spatial transcriptomics spots. Applied to a reference prostate cancer dataset and a newly generated breast cancer dataset, Tumoroscope reveals spatial patterns of clone colocalization and mutual exclusion in sub-areas of the tumor tissue. We further infer clone-specific gene expression levels and the most highly expressed genes for each clone. In summary, Tumoroscope enables an integrated study of the spatial, genomic, and phenotypic organization of tumors.", "doi": "10.1038/s41467-024-53374-3", "pmid": "39472583", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11522407"}, {"db": "pii", "key": "10.1038/s41467-024-53374-3"}], "notes": [], "created": "2024-10-31T12:37:56.764Z", "modified": "2025-02-28T14:14:34.895Z"}, {"entity": "publication", "iuid": "704c6abb74634b1aab41f82f95856143", "links": {"self": {"href": "https://publications.scilifelab.se/publication/704c6abb74634b1aab41f82f95856143.json"}, "display": {"href": "https://publications.scilifelab.se/publication/704c6abb74634b1aab41f82f95856143"}}, "title": "Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors.", "authors": [{"family": "Bian", "given": "Xiaowei", "initials": "X", "orcid": "0000-0001-8999-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0cad0181bff479bb4a04d047bd9bd35.json"}}, {"family": "Piipponen", "given": "Minna", "initials": "M"}, {"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Luo", "given": "Lihua", "initials": "L", "orcid": "0000-0002-2129-4226", "researcher": {"href": "https://publications.scilifelab.se/researcher/b541fd2e348741ff8dfaad99a0ce453c.json"}}, {"family": "Geara", "given": "Jennifer", "initials": "J"}, {"family": "Chen", "given": "Yongjian", "initials": "Y"}, {"family": "Sangsuwan", "given": "Traimate", "initials": "T"}, {"family": "Maselli", "given": "Monica", "initials": "M"}, {"family": "Diaz", "given": "Candice", "initials": "C"}, {"family": "Bain", "given": "Connor A", "initials": "CA"}, {"family": "Eenjes", "given": "Evelien", "initials": "E"}, {"family": "Genander", "given": "Maria", "initials": "M", "orcid": "0000-0002-2428-8040", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee0b27ddbb154eadbf3293d090720481.json"}}, {"family": "Crichton", "given": "Michael", "initials": "M"}, {"family": "Cash", "given": "Jenna L", "initials": "JL"}, {"family": "Archambault", "given": "Louis", "initials": "L"}, {"family": "Haghdoost", "given": "Siamak", "initials": "S"}, {"family": "Fradette", "given": "Julie", "initials": "J"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Halle", "given": "Martin", "initials": "M", "orcid": "0000-0002-6222-956X", "researcher": {"href": "https://publications.scilifelab.se/researcher/789d6dc42b2d45fd98574075ee17ee73.json"}}, {"family": "Xu Land\u00e9n", "given": "Ning", "initials": "N", "orcid": "0000-0003-4868-3798", "researcher": {"href": "https://publications.scilifelab.se/researcher/c55a2caeb6cd4858aa3326b6e92d09c6.json"}}], "type": "journal article", "published": "2024-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "9286", "issn-l": "2041-1723"}, "abstract": "Radiotherapy (RT), a common cancer treatment, unintentionally harms surrounding tissues, including the skin, and hinders wound healing years after treatment. This study aims to understand the mechanisms behind these late-onset adverse effects. We compare skin biopsies from previously irradiated (RT+) and non-irradiated (RT-) sites in breast cancer survivors who underwent RT years ago. Here we show that the RT+ skin has compromised healing capacity and fibroblast functions. Using ATAC-seq, we discover altered chromatin landscapes in RT+ fibroblasts, with THBS1 identified as a crucial epigenetically primed wound repair-related gene. This is further confirmed by single-cell RNA-sequencing and spatial transcriptomic analysis of human wounds. Notably, fibroblasts in both murine and human post-radiation wound models show heightened and sustained THBS1 expression, impairing fibroblast motility and contractility. Treatment with anti-THBS1 antibodies promotes ex vivo wound closure in RT+ skin from breast cancer survivors. Our findings suggest that fibroblasts retain a long-term radiation memory in the form of epigenetic changes. Targeting this maladaptive epigenetic memory could mitigate RT's late-onset adverse effects, improving the quality of life for cancer survivors.", "doi": "10.1038/s41467-024-53295-1", "pmid": "39468077", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11519383"}, {"db": "pii", "key": "10.1038/s41467-024-53295-1"}], "notes": [], "created": "2024-10-31T12:36:31.716Z", "modified": "2024-11-25T10:18:20.060Z"}, {"entity": "publication", "iuid": "18d0685c91fc415fa2aba0d0458ce0cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18d0685c91fc415fa2aba0d0458ce0cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18d0685c91fc415fa2aba0d0458ce0cb"}}, "title": "ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation.", "authors": [{"family": "Karlstr\u00f6m", "given": "Victor", "initials": "V"}, {"family": "Sagredo", "given": "Eduardo A", "initials": "EA", "orcid": "0000-0001-9984-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dfefa432364269b33bbe8a4075de65.json"}}, {"family": "Planells", "given": "Jordi", "initials": "J"}, {"family": "Welinder", "given": "Charlotte", "initials": "C"}, {"family": "Jungfleisch", "given": "Jennifer", "initials": "J"}, {"family": "Barrera-Conde", "given": "Andrea", "initials": "A"}, {"family": "Engfors", "given": "Linus", "initials": "L"}, {"family": "Daniel", "given": "Chammiran", "initials": "C"}, {"family": "Gebauer", "given": "F\u00e1tima", "initials": "F", "orcid": "0000-0001-7563-0013", "researcher": {"href": "https://publications.scilifelab.se/researcher/18de8bace209425782ab115e16b1f61b.json"}}, {"family": "Visa", "given": "Neus", "initials": "N", "orcid": "0000-0003-3145-3953", "researcher": {"href": "https://publications.scilifelab.se/researcher/e376022ceae148bf9581dc24113875dd.json"}}, {"family": "\u00d6hman", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2024-10-28", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "19", "pages": "12021-12038", "issn-l": "0305-1048"}, "abstract": "ADAR3 is a catalytically inactive member of the family of adenosine deaminases acting on RNA (ADARs). Here we have investigated its function in the context of the developing mouse brain. The expression of ADAR3 gradually increases throughout embryogenesis and drops after birth. Using primary cortical neurons, we show that ADAR3 is only expressed in a subpopulation of in vitro differentiated neurons, which suggests specific functions rather than being a general regulator of ADAR editing in the brain. The analysis of the ADAR3 interactome suggested a role in mRNA stability and translation, and we show that expression of ADAR3 in a neuronal cell line that is otherwise ADAR3-negative changes the expression and stability of a large number of mRNAs. Notably, we show that ADAR3 associates with polysomes and inhibits translation. We propose that ADAR3 binds to target mRNAs and stabilizes them in non-productive polysome complexes. Interestingly, the expression of ADAR3 downregulates genes related to neuronal differentiation and inhibits neurofilament outgrowth in vitro. In summary, we propose that ADAR3 negatively regulates neuronal differentiation, and that it does so by regulating mRNA stability and translation in an editing-independent manner.", "doi": "10.1093/nar/gkae753", "pmid": "39217468", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11514483"}, {"db": "pii", "key": "7747201"}], "notes": [], "created": "2024-09-30T07:54:21.398Z", "modified": "2024-11-25T10:25:41.612Z"}, {"entity": "publication", "iuid": "f3f9c692b94547f3bdebed945926aff5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3f9c692b94547f3bdebed945926aff5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3f9c692b94547f3bdebed945926aff5"}}, "title": "Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial.", "authors": [{"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Arefaine", "given": "Bethlehem", "initials": "B"}, {"family": "Begum", "given": "Neelu", "initials": "N"}, {"family": "Stamouli", "given": "Marilena", "initials": "M"}, {"family": "Witherden", "given": "Elizabeth", "initials": "E"}, {"family": "Mohamad", "given": "Merianne", "initials": "M"}, {"family": "Harzandi", "given": "Azadeh", "initials": "A"}, {"family": "Zamalloa", "given": "Ane", "initials": "A"}, {"family": "Cai", "given": "Haizhuang", "initials": "H"}, {"family": "Williams", "given": "Roger", "initials": "R"}, {"family": "Curtis", "given": "Mike", "initials": "M"}, {"family": "Edwards", "given": "Lindsey A", "initials": "LA"}, {"family": "Chokshi", "given": "Shilpa", "initials": "S"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Proctor", "given": "Gordon", "initials": "G"}, {"family": "Moyes", "given": "David", "initials": "D"}, {"family": "McPhail", "given": "Mark J", "initials": "MJ"}, {"family": "Shawcross", "given": "Debbie L", "initials": "DL"}, {"family": "Uhlen", "given": "Mathias", "initials": "M"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Patel", "given": "Vishal C", "initials": "VC"}], "type": "journal article", "published": "2024-10-22", "journal": {"title": "J Hepatol", "issn": "1600-0641", "issn-l": null}, "abstract": "Cirrhosis complications are often triggered by bacterial infections with multidrug-resistant organisms. Alterations in the gut and oral microbiome in decompensated cirrhosis (DC) influence clinical outcomes. We interrogated: (i) gut and oral microbiome community structures, (ii) virulence factors (VFs) and antimicrobial resistance genes (ARGs) and (iii) oral-gut microbial overlap in patients with differing cirrhosis severity.\n\n15 healthy controls (HC), 26 stable cirrhosis (SC), 46 DC, 14 acute-on-chronic liver failure (ACLF) and 14 with severe infection without cirrhosis (NLS) participated. Metagenomic sequencing was undertaken on paired saliva (S) and faecal (F) samples. 'Salivatypes' and 'enterotypes' based on genera clustering were assessed against cirrhosis severity and clinical parameters. VFs and ARGs were evaluated in oral and gut niches, and distinct resistotypes identified.\n\nSalivatypes and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity and hyperammonaemia. Increasing overlap between oral and gut microbiome communities was observed in DC and ACLF vs SC and HCs, independent of antimicrobial, beta-blocker and acid suppressant therapies. Two distinct gut microbiome clusters [ENT2/ENT3] harboured genes encoding for the phosphoenolpyruvate:sugar phosphotransferase system (PTS) system and other VFs in DC and ACLF. Substantial ARGs (oral: 1,218 and gut: 672) were detected [575 common to both sites]. The cirrhosis resistome was distinct, with three oral and four gut resistotypes identified, respectively.\n\nThe degree of oral-gut microbial community overlap, frequency of VFs and ARGs all increment significantly with cirrhosis severity, with progressive dominance of pathobionts and loss of commensals. Despite similar antimicrobial exposure, patients with DC and ACLF have reduced microbial richness compared to NLS, supporting the additive pathobiological effect of cirrhosis.\n\nThis research underscores the crucial role of microbiome alterations in the progression of cirrhosis in an era of escalating multidrug resistant infections, highlighting the association and potential impact of increased oral-gut microbial overlap, virulence factors, and antimicrobial resistance genes on clinical outcomes. These findings are particularly significant for patients with decompensated cirrhosis and acute-on-chronic liver failure, as they reveal the intricate relationship between microbiome alterations and cirrhosis complications. This is relevant in the context of multidrug-resistant organisms and reduced oral-gut microbial diversity that exacerbate cirrhosis severity, drive hepatic decompensation and complicate treatment. For practical applications, these insights could guide for cirrhosis patients the development of targeted microbiome-based therapeutics and personalised antimicrobial regimens to mitigate infectious complications to improve their clinical outcomes.", "doi": "10.1016/j.jhep.2024.09.046", "pmid": "39447963", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0168-8278(24)02635-7"}], "notes": [], "created": "2024-10-31T12:39:39.977Z", "modified": "2024-11-25T10:14:02.230Z"}, {"entity": "publication", "iuid": "c03c4c5c56a14045971dc3d0630bfac5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c03c4c5c56a14045971dc3d0630bfac5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c03c4c5c56a14045971dc3d0630bfac5"}}, "title": "Persistent effects of di-n-butyl phthalate on liver transcriptome: impaired energy and lipid metabolic pathways.", "authors": [{"family": "Theodoropoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Pierozan", "given": "Paula", "initials": "P"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Karlsson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2024-10-21", "journal": {"title": "Chemosphere", "issn": "1879-1298", "pages": "143605", "issn-l": "0045-6535"}, "abstract": "The environmental contaminant dibutyl phthalate (DBP) is reported to be hepatotoxic, but the underlying molecular pathways and pathological processes remain unclear. Here we used RNA-sequencing to characterize persistent hepatic transcriptional effects one week after the conclusion of five weeks oral exposure to 10 mg/kg/day or 100 mg/kg/day DBP in male mice. The exploratory transcriptome analysis demonstrated five differentially expressed genes (DEGs) in the 10 mg/kg/day group and thirteen in the 100 mg/kg/day group. Gene Set Enrichment Analysis (GSEA), which identifies affected biological pathways rather than focusing solely on individual genes, revealed nine significantly enriched Reactome pathways shared by both DBP treatment groups. Additionally, we found 54 upregulated and one downregulated Reactome pathways in the 10 mg/kg/day DBP group, and 29 upregulated and 13 downregulated pathways in the 100 mg/kg/day DBP group. According to the DEGs and the GSEA findings DBP exposure disrupts several key biological processes, including protein translation, protein folding, apoptosis, hedgehog signaling, degradation of extracellular matrix and alterations in the energy/lipid metabolism. Subsequent liver tissue analysis corroborated these findings, showing that DBP exposure induced tissue disorganization, oxidative stress, lipid accumulation, increased TNF-\u03b1, ATP and glucokinase levels. In addition, several proteins central for the metabolic system were affected, mostly in a dose-response pattern. Taken together the results show that DBP can cause hepatic stress and damage and suggest a potential role for DBP in the development of non-alcoholic fat liver disease, the most prevalent liver disease worldwide.", "doi": "10.1016/j.chemosphere.2024.143605", "pmid": "39442571", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0045-6535(24)02505-0"}], "notes": [], "created": "2024-10-31T12:34:26.795Z", "modified": "2024-11-25T10:12:32.978Z"}, {"entity": "publication", "iuid": "2a14fd27a1034c0a88a19ff85f785d19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a14fd27a1034c0a88a19ff85f785d19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a14fd27a1034c0a88a19ff85f785d19"}}, "title": "Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting.", "authors": [{"family": "Frisk", "given": "Christoffer", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Hage", "given": "Camilla", "initials": "C"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Persson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2024-10-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "938", "issn-l": "1471-2164"}, "abstract": "Epicardial adipose tissue (EAT) surrounds the heart and is hypothesised to play a role in the development of heart failure (HF). In this study, we first investigated the differences in gene expression between epicardial adipose tissue (EAT) and subcutaneous adipose tissue (SAT) in patients undergoing elective coronary artery bypass graft (CABG) surgery (n = 21; 95% male). Secondly, we examined the association between EAT and SAT in patients at risk for HF stage A (n = 12) and in pre-HF patients, who show signs but not symptoms of HF, stage B (n = 9).\n\nThe study confirmed a distinct separation between EAT and SAT. In EAT 17 clusters of genes were present, of which several novel gene modules are associated with characteristics of HF. Notably, seven gene modules showed significant correlation to measures of HF, such as end diastolic left ventricular posterior wall thickness, e'mean, deceleration time and BMI. One module was particularly distinct in EAT when compared to SAT, featuring key genes such as FLT4, SEMA3A, and PTX3, which are implicated in angiogenesis, inflammation regulation, and tissue repair, suggesting a unique role in EAT linked to left ventricular dysfunction. Genetic expression was compared in EAT across all pre-HF and normal phenotypes, revealing small genetic changes in the form of 18 differentially expressed genes in ACC/AHA Stage A vs. Stage B.\n\nThe roles of subcutaneous and epicardial fat are clearly different. We highlight the gene expression difference in search of potential modifiers of HF progress. The true implications of our findings should be corroborated in other studies since HF ACC/AHA stage B patients are common and carry a considerable risk for progression to symptomatic HF.", "doi": "10.1186/s12864-024-10851-9", "pmid": "39375631", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11457432"}, {"db": "pii", "key": "10.1186/s12864-024-10851-9"}], "notes": [], "created": "2024-10-31T12:36:52.295Z", "modified": "2025-02-28T14:22:11.481Z"}, {"entity": "publication", "iuid": "88fdebe09a364acd8a3d8b6f9e56465e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88fdebe09a364acd8a3d8b6f9e56465e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88fdebe09a364acd8a3d8b6f9e56465e"}}, "title": "The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.", "authors": [{"family": "Li", "given": "Dongqing", "initials": "D", "orcid": "0000-0003-0588-9390", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d51ff81e8ec4cc5a429dd095a0c315f.json"}}, {"family": "Liu", "given": "Zhuang", "initials": "Z"}, {"family": "Zhang", "given": "Letian", "initials": "L"}, {"family": "Bian", "given": "Xiaowei", "initials": "X", "orcid": "0000-0001-8999-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0cad0181bff479bb4a04d047bd9bd35.json"}}, {"family": "Wu", "given": "Jianmin", "initials": "J", "orcid": "0000-0002-8223-1667", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8b209cc41384aefa1fb3d70e564e3f3.json"}}, {"family": "Li", "given": "Li", "initials": "L"}, {"family": "Chen", "given": "Yongjian", "initials": "Y"}, {"family": "Luo", "given": "Lihua", "initials": "L", "orcid": "0000-0002-2129-4226", "researcher": {"href": "https://publications.scilifelab.se/researcher/b541fd2e348741ff8dfaad99a0ce453c.json"}}, {"family": "Pan", "given": "Ling", "initials": "L"}, {"family": "Kong", "given": "Lingzhuo", "initials": "L"}, {"family": "Xiao", "given": "Yunting", "initials": "Y"}, {"family": "Wang", "given": "Jiating", "initials": "J"}, {"family": "Zhang", "given": "Xiya", "initials": "X"}, {"family": "Wang", "given": "Wang", "initials": "W"}, {"family": "Toma", "given": "Maria", "initials": "M", "orcid": "0000-0002-4766-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/80f80639a3774c5bb5007d1f9af63a0e.json"}}, {"family": "Piipponen", "given": "Minna", "initials": "M"}, {"family": "Sommar", "given": "Pehr", "initials": "P"}, {"family": "Xu Land\u00e9n", "given": "Ning", "initials": "N", "orcid": "0000-0003-4868-3798", "researcher": {"href": "https://publications.scilifelab.se/researcher/c55a2caeb6cd4858aa3326b6e92d09c6.json"}}], "type": "journal article", "published": "2024-10-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8637", "issn-l": "2041-1723"}, "abstract": "The cell transition from an inflammatory phase to a subsequent proliferative phase is crucial for wound healing, yet the driving mechanism remains unclear. By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identify SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. Snhg26-deficient mice exhibit impaired wound repair characterized by delayed re-epithelization accompanied by exacerbated inflammation. Single-cell transcriptome analysis combined with gain-of-function and loss-of-function of SNHG26 in vitro and ex vivo reveals its specific role in facilitating inflammatory-to-proliferative state transition of keratinocyte progenitors. A mechanistic study unravels that SNHG26 interacts with and relocates the transcription factor ILF2 from inflammatory genomic loci, such as JUN, IL6, IL8, and CCL20, to the genomic locus of LAMB3. Collectively, our findings suggest that lncRNAs play cardinal roles in expediting tissue repair and regeneration and may constitute an invaluable reservoir of therapeutic targets in reparative medicine.", "doi": "10.1038/s41467-024-52783-8", "pmid": "39366968", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Spatial omics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11452505"}, {"db": "pii", "key": "10.1038/s41467-024-52783-8"}], "notes": [], "created": "2024-10-18T07:13:08.010Z", "modified": "2025-02-28T14:14:23.292Z"}, {"entity": "publication", "iuid": "9b81114066764b15946e9e8731fac1e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b81114066764b15946e9e8731fac1e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b81114066764b15946e9e8731fac1e5"}}, "title": "The single-cell transcriptomic atlas iPain identifies senescence of nociceptors as a therapeutical target for chronic pain treatment.", "authors": [{"family": "Techameena", "given": "Prach", "initials": "P", "orcid": "0009-0005-9380-2428", "researcher": {"href": "https://publications.scilifelab.se/researcher/835cc139cbbd4e08afd433a817f74ac6.json"}}, {"family": "Feng", "given": "Xiaona", "initials": "X"}, {"family": "Zhang", "given": "Kaiwen", "initials": "K", "orcid": "0009-0001-0790-1616", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1880c8da747467795a011858ca2c9bf.json"}}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}], "type": "journal article", "published": "2024-10-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8585", "issn-l": "2041-1723"}, "abstract": "Chronic pain remains a significant medical challenge with complex underlying mechanisms, and an urgent need for new treatments. Our research built and utilized the iPain single-cell atlas to study chronic pain progression in dorsal root and trigeminal ganglia. We discovered that senescence of a small subset of pain-sensing neurons may be a driver of chronic pain. This mechanism was observed in animal models after nerve injury and in human patients diagnosed with chronic pain or diabetic painful neuropathy. Notably, treatment with senolytics, drugs that remove senescent cells, reversed pain symptoms in mice post-injury. These findings highlight the role of cellular senescence in chronic pain development, demonstrate the therapeutic potential of senolytic treatments, and underscore the value of the iPain atlas for future pain research.", "doi": "10.1038/s41467-024-52052-8", "pmid": "39362841", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11450014"}, {"db": "pii", "key": "10.1038/s41467-024-52052-8"}], "notes": [], "created": "2024-10-16T12:42:25.382Z", "modified": "2024-11-25T10:17:57.934Z"}, {"entity": "publication", "iuid": "e6f61bc7ac194957a549772ddd3a7942", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6f61bc7ac194957a549772ddd3a7942.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6f61bc7ac194957a549772ddd3a7942"}}, "title": "The Population History of Domestic Sheep Revealed by Paleogenomes.", "authors": [{"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Ata\u011f", "given": "G\u00f6zde", "initials": "G", "orcid": "0000-0001-6173-3126", "researcher": {"href": "https://publications.scilifelab.se/researcher/e478e5f000ce44a090ccd7fad904bf36.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P", "orcid": "0000-0001-7678-9691", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a48ddd9e9b491ea55ec2ac0bd4328f.json"}}, {"family": "Akbaba", "given": "Ali", "initials": "A", "orcid": "0000-0001-6755-6546", "researcher": {"href": "https://publications.scilifelab.se/researcher/757adfca411c4168a0a51c5765852aa9.json"}}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E", "orcid": "0000-0002-8194-0277", "researcher": {"href": "https://publications.scilifelab.se/researcher/c319bee9c36a4e6a88dee29c8edc9d0d.json"}}, {"family": "Buluktaev", "given": "Aleksey", "initials": "A", "orcid": "0000-0002-2329-465X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d47b67dc6dcf4570ae0797c7a9c57f86.json"}}, {"family": "Abazari", "given": "Mohammad Foad", "initials": "MF", "orcid": "0000-0002-3383-8526", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b0029d4a8554ba396ff443d06dd5724.json"}}, {"family": "Yorulmaz", "given": "Sevgi", "initials": "S", "orcid": "0000-0002-9592-6310", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ac25b5dcc84758b3f852d81133cac6.json"}}, {"family": "Kazanc\u0131", "given": "Duygu Deniz", "initials": "DD", "orcid": "0000-0002-8333-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f28aea0bd7e4bb7b6ac3d8843cae17f.json"}}, {"family": "K\u00fc\u00e7\u00fckakda\u011f Do\u011fu", "given": "Ay\u00e7a", "initials": "A", "orcid": "0000-0001-6208-4092", "researcher": {"href": "https://publications.scilifelab.se/researcher/5599e1dd0d34404cb490ae2da3213b17.json"}}, {"family": "\u00c7akan", "given": "Yasin G\u00f6khan", "initials": "YG", "orcid": "0000-0002-4919-7129", "researcher": {"href": "https://publications.scilifelab.se/researcher/957fecf5337744e890d2f09e9fc4caeb.json"}}, {"family": "\u00d6zbal", "given": "Rana", "initials": "R", "orcid": "0000-0001-6765-2765", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad960fa098e477eac6f367ce0e659c9.json"}}, {"family": "Gerritsen", "given": "Fokke", "initials": "F", "orcid": "0000-0002-6665-1928", "researcher": {"href": "https://publications.scilifelab.se/researcher/d447abfa3d8b42bd85d56693a1c9cbb0.json"}}, {"family": "De Cupere", "given": "Bea", "initials": "B", "orcid": "0000-0001-7559-8965", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7eee394cf44406ea73df88535d1f025.json"}}, {"family": "Duru", "given": "Refik", "initials": "R"}, {"family": "Umurtak", "given": "G\u00fcls\u00fcn", "initials": "G", "orcid": "0000-0003-0493-1868", "researcher": {"href": "https://publications.scilifelab.se/researcher/797ff752aeb54d4f9ea67dc624e25380.json"}}, {"family": "Arbuckle", "given": "Benjamin S", "initials": "BS", "orcid": "0000-0002-5445-5516", "researcher": {"href": "https://publications.scilifelab.se/researcher/36815e3b09264f84a86736d94af24854.json"}}, {"family": "Baird", "given": "Douglas", "initials": "D", "orcid": "0000-0001-8651-5272", "researcher": {"href": "https://publications.scilifelab.se/researcher/da109d91ead140d8a61f649d9de10cdd.json"}}, {"family": "\u00c7evik", "given": "\u00d6zlem", "initials": "\u00d6", "orcid": "0000-0001-5442-3744", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbb50dfe46c4ed4b3a2894df441dee4.json"}}, {"family": "B\u0131\u00e7ak\u00e7\u0131", "given": "Erhan", "initials": "E", "orcid": "0000-0002-8945-3481", "researcher": {"href": "https://publications.scilifelab.se/researcher/347f652e1c46403ba545385dfe368357.json"}}, {"family": "G\u00fcndem", "given": "Can Yumni", "initials": "CY", "orcid": "0000-0002-6369-0913", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa5c7727305b41c9bbb661977ca6f3b3.json"}}, {"family": "Pi\u015fkin", "given": "Evangelia", "initials": "E", "orcid": "0000-0001-7727-3013", "researcher": {"href": "https://publications.scilifelab.se/researcher/a753df2d8dd54c3d8ec3144b1613dc82.json"}}, {"family": "Hachem", "given": "Lamys", "initials": "L", "orcid": "0000-0001-8543-4673", "researcher": {"href": "https://publications.scilifelab.se/researcher/b61b4a7a26eb442bba0104bb90e919af.json"}}, {"family": "Canpolat", "given": "Kayra", "initials": "K", "orcid": "0009-0002-6783-7959", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9b915528c9f4cf6adb8e9a1adf9affb.json"}}, {"family": "Fakhari", "given": "Zohre", "initials": "Z", "orcid": "0000-0002-9774-5249", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cf41456b026401489693ab2bf88f402.json"}}, {"family": "Ochir-Goryaeva", "given": "Maria", "initials": "M", "orcid": "0000-0002-0210-7595", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f76ba2d2bb24e57bd57c8c2f88cfc13.json"}}, {"family": "Kukanova", "given": "Viktoria", "initials": "V", "orcid": "0000-0002-7696-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/892f68b502b24952a1152c75399e7c6e.json"}}, {"family": "Valipour", "given": "Hamid Reza", "initials": "HR", "orcid": "0009-0009-7757-7151", "researcher": {"href": "https://publications.scilifelab.se/researcher/686157eec2ae449db018349010b24761.json"}}, {"family": "Hoseinzadeh", "given": "Javad", "initials": "J", "orcid": "0000-0002-1954-8389", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0da85200b66457d93c08a09e2d416a7.json"}}, {"family": "K\u00fc\u00e7\u00fck Balo\u011flu", "given": "Fatma", "initials": "F"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Hadjisterkotis", "given": "Eleftherios", "initials": "E", "orcid": "0000-0002-3168-4674", "researcher": {"href": "https://publications.scilifelab.se/researcher/d606145f22b5409aa15cb3c21ab84e12.json"}}, {"family": "Grange", "given": "Thierry", "initials": "T", "orcid": "0000-0001-8700-3092", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b118d3bd3a94e3a9ff5b9ad274078b8.json"}}, {"family": "Geigl", "given": "Eva-Maria", "initials": "EM", "orcid": "0000-0001-6376-2094", "researcher": {"href": "https://publications.scilifelab.se/researcher/40dc9d0284134a2d93b6589017a5b2fd.json"}}, {"family": "Togan", "given": "\u0130nci Z", "initials": "\u0130Z", "orcid": "0009-0003-6150-8078", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe18c9497384cbeba7b3d52ed92bc53.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}], "type": "journal article", "published": "2024-10-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "41", "issue": "10", "issn-l": "0737-4038"}, "abstract": "Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons. We find that Neolithic European, as well as domestic sheep breeds, are genetically closer to the Anatolian Epipaleolithic sheep and the present-day Anatolian and Cyprian Mouflon than to the Iranian Mouflon. This supports a Central Anatolian source for domestication, presenting strong evidence for a domestication event in SW Asia outside the Fertile Crescent, although we cannot rule out multiple domestication events also within the Neolithic Fertile Crescent. We further find evidence for multiple admixture and replacement events, including one that parallels the Pontic Steppe-related ancestry expansion in Europe, as well as a post-Bronze Age event that appears to have further spread Asia-related alleles across global sheep breeds. Our findings mark the dynamism of past domestic sheep populations in their potential for dispersal and admixture, sometimes being paralleled by their shepherds and in other cases not.", "doi": "10.1093/molbev/msae158", "pmid": "39437846", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service", "Ancient DNA": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11495565"}, {"db": "pii", "key": "7826489"}], "notes": [], "created": "2024-10-31T12:38:18.188Z", "modified": "2024-11-10T12:21:05.378Z"}, {"entity": "publication", "iuid": "05d86f8a7fb74d428015995eeda36e63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05d86f8a7fb74d428015995eeda36e63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05d86f8a7fb74d428015995eeda36e63"}}, "title": "Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.", "authors": [{"family": "Meng", "given": "Lingqi", "initials": "L"}, {"family": "Jin", "given": "Han", "initials": "H"}, {"family": "Yulug", "given": "Burak", "initials": "B"}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X"}, {"family": "Hanoglu", "given": "Lutfu", "initials": "L"}, {"family": "Cankaya", "given": "Seyda", "initials": "S"}, {"family": "Coskun", "given": "Ebru", "initials": "E"}, {"family": "Idil", "given": "Ezgi", "initials": "E"}, {"family": "Nogaylar", "given": "Rahim", "initials": "R"}, {"family": "Ozsimsek", "given": "Ahmet", "initials": "A"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2024-10-02", "journal": {"title": "Alzheimers Res Ther", "issn": "1758-9193", "issn-l": null, "volume": "16", "issue": "1", "pages": "213"}, "abstract": "Alzheimer's disease (AD) is a debilitating neurodegenerative disorder with a global impact, yet its pathogenesis remains poorly understood. While age, metabolic abnormalities, and accumulation of neurotoxic substances are potential risk factors for AD, their effects are confounded by other factors. To address this challenge, we first utilized multi-omics data from 87 well phenotyped AD patients and generated plasma proteomics and metabolomics data, as well as gut and saliva metagenomics data to investigate the molecular-level alterations accounting the host-microbiome interactions. Second, we analyzed individual omics data and identified the key parameters involved in the severity of the dementia in AD patients. Next, we employed Artificial Intelligence (AI) based models to predict AD severity based on the significantly altered features identified in each omics analysis. Based on our integrative analysis, we found the clinical relevance of plasma proteins, including SKAP1 and NEFL, plasma metabolites including homovanillate and glutamate, and Paraprevotella clara in gut microbiome in predicting the AD severity. Finally, we validated the predictive power of our AI based models by generating additional multi-omics data from the same group of AD patients by following up for 3 months. Hence, we observed that these results may have important implications for the development of potential diagnostic and therapeutic approaches for AD patients.", "doi": "10.1186/s13195-024-01578-6", "pmid": "39358810", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": null, "Bioinformatics Support for Computational Resources": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11448018"}, {"db": "pii", "key": "10.1186/s13195-024-01578-6"}], "notes": [], "created": "2024-10-18T07:17:02.815Z", "modified": "2025-02-28T14:23:13.693Z"}, {"entity": "publication", "iuid": "04f5f65a41e349288d0990b9a2122f0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04f5f65a41e349288d0990b9a2122f0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04f5f65a41e349288d0990b9a2122f0b"}}, "title": "Ebullition dominates methane emissions in stratified coastal waters.", "authors": [{"family": "Hermans", "given": "Martijn", "initials": "M"}, {"family": "Stranne", "given": "Christian", "initials": "C"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Sokolov", "given": "Alexander", "initials": "A"}, {"family": "Roth", "given": "Florian", "initials": "F"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "M\u00f6rth", "given": "Carl-Magnus", "initials": "CM"}, {"family": "Ten Hietbrink", "given": "Sophie", "initials": "S"}, {"family": "Sun", "given": "Xiaole", "initials": "X"}, {"family": "Gustafsson", "given": "Erik", "initials": "E"}, {"family": "Gustafsson", "given": "Bo G", "initials": "BG"}, {"family": "Norkko", "given": "Alf", "initials": "A"}, {"family": "Jilbert", "given": "Tom", "initials": "T"}, {"family": "Humborg", "given": "Christoph", "initials": "C"}], "type": "journal article", "published": "2024-10-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "945", "pages": "174183", "issn-l": "0048-9697"}, "abstract": "Coastal areas are an important source of methane (CH4). However, the exact origins of CH4 in the surface waters of coastal regions, which in turn drive sea-air emissions, remain uncertain. To gain a comprehensive understanding of the current and future climate change feedbacks, it is crucial to identify these CH4 sources and processes that regulate its formation and oxidation. This study investigated coastal CH4 dynamics by comparing water column data from six stations located in the brackish Tv\u00e4rminne Archipelago, Baltic Sea. The sediment biogeochemistry and microbiology were further investigated at two stations (i.e., nearshore and offshore). These stations differed in terms of stratification, bottom water redox conditions, and organic matter loading. At the nearshore station, CH4 diffusion from the sediment into the water column was negligible, because nearly all CH4 was oxidized within the upper sediment column before reaching the sediment surface. On the other hand, at the offshore station, there was significant benthic diffusion of CH4, albeit the majority underwent oxidation before reaching the sediment-water interface, due to shoaling of the sulfate methane transition zone (SMTZ). The potential contribution of CH4 production in the water column was evaluated and was found to be negligible. After examining the isotopic signatures of \u03b413C-CH4 across the sediment and water column, it became apparent that the surface water \u03b413C-CH4 values observed in areas with thermal stratification could not be explained by diffusion, advective fluxes, nor production in the water column. In fact, these values bore a remarkable resemblance to those detected below the SMTZ. This supports the hypothesis that the source of CH4 in surface waters is more likely to originate from ebullition than diffusion in stratified brackish coastal systems.", "doi": "10.1016/j.scitotenv.2024.174183", "pmid": "38909808", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)04331-6"}], "notes": [], "created": "2024-08-15T12:11:57.538Z", "modified": "2025-02-28T14:12:53.990Z"}, {"entity": "publication", "iuid": "d82774b91b3543f98a71d6c065a62093", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d82774b91b3543f98a71d6c065a62093.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d82774b91b3543f98a71d6c065a62093"}}, "title": "Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice.", "authors": [{"family": "Mantas", "given": "Ioannis", "initials": "I", "orcid": "0000-0001-6288-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/025776ae147144dab1e2f10a5761b9ed.json"}}, {"family": "Flais", "given": "Ivana", "initials": "I"}, {"family": "Masarapu", "given": "Yuvarani", "initials": "Y", "orcid": "0000-0002-3267-2085", "researcher": {"href": "https://publications.scilifelab.se/researcher/055fa17f6cdd490e87182c94c847c440.json"}}, {"family": "Ionescu", "given": "Tudor", "initials": "T"}, {"family": "Frapard", "given": "Sol\u00e8ne", "initials": "S", "orcid": "0000-0002-2649-7225", "researcher": {"href": "https://publications.scilifelab.se/researcher/a336a6a31fae4766afbb5e376a4a12a3.json"}}, {"family": "Jung", "given": "Felix", "initials": "F"}, {"family": "Le Merre", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4205-7411", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba592e9aa93b433cb85ff11a786b0a71.json"}}, {"family": "Saarinen", "given": "Marcus", "initials": "M"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Salmani", "given": "Behzad Yaghmaeian", "initials": "BY", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Zhang", "given": "Xiaoqun", "initials": "X", "orcid": "0000-0002-9461-8682", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f307c88103d43b1b0b893fa59a8e828.json"}}, {"family": "Chergui", "given": "Karima", "initials": "K"}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications.scilifelab.se/researcher/88931dd9e39c48e2820b89080c3945ad.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Hengerer", "given": "Bastian", "initials": "B", "orcid": "0000-0002-7811-9795", "researcher": {"href": "https://publications.scilifelab.se/researcher/2adf2c1fe0954f018f91ebce7d06d945.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}], "type": "journal article", "published": "2024-09-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "8176", "issn-l": "2041-1723"}, "abstract": "The Claustrum/dorsal endopiriform cortex complex (CLA) is an enigmatic brain region with extensive glutamatergic projections to multiple cortical areas. The transcription factor Nurr1 is highly expressed in the CLA, but its role in this region is not understood. By using conditional gene-targeted mice, we show that Nurr1 is a crucial regulator of CLA neuron identity. Although CLA neurons remain intact in the absence of Nurr1, the distinctive gene expression pattern in the CLA is abolished. CLA has been hypothesized to control hallucinations, but little is known of how the CLA responds to hallucinogens. After the deletion of Nurr1 in the CLA, both hallucinogen receptor expression and signaling are lost. Furthermore, functional ultrasound and Neuropixel electrophysiological recordings revealed that the hallucinogenic-receptor agonists' effects on functional connectivity between prefrontal and sensorimotor cortices are altered in Nurr1-ablated mice. Our findings suggest that Nurr1-targeted strategies provide additional avenues for functional studies of the CLA.", "doi": "10.1038/s41467-024-52429-9", "pmid": "39289358", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11408527"}, {"db": "pii", "key": "10.1038/s41467-024-52429-9"}], "notes": [], "created": "2024-10-31T12:38:39.729Z", "modified": "2024-10-31T12:38:39.977Z"}, {"entity": "publication", "iuid": "728698aa891a4159a798b19be431232f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728698aa891a4159a798b19be431232f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728698aa891a4159a798b19be431232f"}}, "title": "Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19.", "authors": [{"family": "Li", "given": "Xuan", "initials": "X", "orcid": "0000-0003-0066-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/23234f8a3b2e4d299405be6a66008435.json"}}, {"family": "Jayaprasad", "given": "Suvratha", "initials": "S"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Cooper", "given": "Steven J B", "initials": "SJB", "orcid": "0000-0002-7843-8438", "researcher": {"href": "https://publications.scilifelab.se/researcher/8df76e7fede64a0294cf68a3ae20a07c.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}], "type": "journal article", "published": "2024-09-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "11", "issue": "1", "pages": "997"}, "abstract": "Morabine grasshoppers in the Vandiemenella viatica species group, which show karyotype diversity, have been studied for their ecological distribution and speciation in relation to their genetic and chromosomal diversity. They are good models for studying sex chromosome evolution as \"old\" and newly emerged sex chromosomes co-exist within the group. Here we present a reference genome for the viatica19 chromosomal race, that possesses the ancestral karyotype within the group. Using PacBio HiFi and Hi-C sequencing, we generated a chromosome-level assembly of 4.09 Gb in span, scaffold N50 of 429 Mb, and complete BUSCO score of 98.1%, containing 10 pseudo-chromosomes. We provide Illumina datasets of males and females, used to identify the X chromosome. The assembly contains 19,034 predicted protein-coding genes, and a total of 75.21% of repetitive DNA sequences. By leveraging HiFi reads, we mapped the genome-wide distribution of methylated bases (5mC and 6 mA). This comprehensive assembly offers a robust reference for morabine grasshoppers and supports further research into speciation and sex chromosome diversification within the group and its related species.", "doi": "10.1038/s41597-024-03858-0", "pmid": "39266578", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Collaborative", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11393057"}, {"db": "pii", "key": "10.1038/s41597-024-03858-0"}], "notes": [], "created": "2024-09-16T19:39:19.961Z", "modified": "2024-11-25T10:20:16.787Z"}, {"entity": "publication", "iuid": "e003f233986343769aeeac993d399bce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e003f233986343769aeeac993d399bce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e003f233986343769aeeac993d399bce"}}, "title": "Immune system adaptation during gender-affirming testosterone treatment", "authors": [{"family": "Tadepally", "given": "Lakshmikanth,", "initials": "L"}, {"family": "Consiglio", "given": "Camila,", "initials": "C"}, {"family": "Sardh", "given": "Fabian,", "initials": "F"}, {"family": "Forlin", "given": "Rickard,", "initials": "R"}, {"family": "Wang", "given": "Jun,", "initials": "J"}, {"family": "Tan", "given": "Zhiyan,", "initials": "Z"}, {"family": "Barcenilla", "given": "Hugo,", "initials": "H"}, {"family": "Rodriguez", "given": "Lucie,", "initials": "L"}, {"family": "Sugrue", "given": "Jamie,", "initials": "J"}, {"family": "Noori", "given": "Peri,", "initials": "P"}, {"family": "Ivanchenko", "given": "Margarita", "initials": "M"}, {"family": "Pi\u00f1ero P\u00e1ez", "given": "Laura,", "initials": "L"}, {"family": "Gonzalez", "given": "Laura,", "initials": "L"}, {"family": "Habimana Mugabo", "given": "Constantin,", "initials": "C"}, {"family": "Johnsson", "given": "Anette,", "initials": "A"}, {"family": "Ryberg", "given": "Henrik,", "initials": "H"}, {"family": "Hallgren", "given": "\u00c5sa,", "initials": "\u00c5"}, {"family": "Pou", "given": "Christian,", "initials": "C"}, {"family": "Chen", "given": "Yang,", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr,", "initials": "J"}, {"family": "James", "given": "Anna,", "initials": "A"}, {"family": "Dahlqvist", "given": "Per,", "initials": "P"}, {"family": "Wahlberg", "given": "Jeanette,", "initials": "J"}, {"family": "Hagelin", "given": "Anders,", "initials": "A"}, {"family": "Holmberg", "given": "Mats,", "initials": "M"}, {"family": "Degerblad", "given": "Marie,", "initials": "M"}, {"family": "Isaksson", "given": "Magnus,", "initials": "M"}, {"family": "Duffy", "given": "Darragh,", "initials": "D"}, {"family": "K\u00e4mpe", "given": "Olle,", "initials": "O"}, {"family": "Landegren", "given": "Nils,", "initials": "N"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": null, "published": "2024-09-04", "journal": {"title": "Nature", "issn": null, "issn-l": null, "volume": "633", "issue": null, "pages": "155-164"}, "abstract": "Infectious, infammatory and autoimmune conditions present diferently in males and females. SARS-CoV-2 infection in naive males is associated with increased risk of death, whereas females are at increased risk of long COVID1, similar to observations\r\nin other infections. Females respond more strongly to vaccines, and adverse reactions are more frequent, like most autoimmune diseases. Immunological sex diferences stem from genetic, hormonal and behavioural factors but their relative importance is only partially understood. In individuals assigned female sex at birth and undergoing gender-affirming testosterone therapy (trans men), hormone concentrations change markedly but the immunological consequences are poorly understood. Here we performed longitudinal systems-level analyses in 23 trans men and found that testosterone modulates a cross-regulated axis between type-I interferon and tumour necrosis factor. This is mediated by functional attenuation of type-I interferon responses in both plasmacytoid dendritic cells and monocytes. Conversely, testosterone potentiates monocyte responses leading to\r\nincreased tumour necrosis factor, interleukin-6 and interleukin-15 production and downstream activation of nuclear factor kappa B-regulated genes and potentiation of interferon-\u03b3 responses, primarily in natural killer cells. These fndings in trans men\r\nare corroborated by sex-divergent responses in public datasets and illustrate the dynamic regulation of human immunity by sex hormones, with implications for the health of individuals undergoing hormone therapy and our understanding of sex-divergent immune responses in cisgender individuals.", "doi": "DOI: 10.1038/s41586-024-07789-z", "pmid": "39232147", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-09-30T07:39:01.962Z", "modified": "2024-09-30T07:49:09.576Z"}, {"entity": "publication", "iuid": "1b9b1f7cd2e24ef1a1ec01582e63e588", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b9b1f7cd2e24ef1a1ec01582e63e588.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b9b1f7cd2e24ef1a1ec01582e63e588"}}, "title": "Temporal dynamics of faster neo-Z evolution in butterflies.", "authors": [{"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L", "orcid": "0000-0003-0104-4796", "researcher": {"href": "https://publications.scilifelab.se/researcher/a45738fda5954b73a28e47430c4b1f20.json"}}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2024-09-03", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "78", "issue": "9", "pages": "1554-1567", "issn-l": "0014-3820"}, "abstract": "The faster-Z/X hypothesis predicts that sex-linked genes should diverge faster than autosomal genes. However, studies across different lineages have shown mixed support for this effect. So far, most analyses have focused on old and well-differentiated sex chromosomes, but less is known about the divergence of more recently acquired neo-sex chromosomes. In Lepidoptera (moths and butterflies), Z-autosome fusions are frequent, but the evolutionary dynamics of neo-Z chromosomes have not been explored in detail. Here, we analyzed the faster-Z effect in Leptidea sinapis, a butterfly with three Z chromosomes. We show that the neo-Z chromosomes have been acquired stepwise, resulting in strata of differentiation and masculinization. While all Z chromosomes showed evidence of the faster-Z effect, selection for genes on the youngest neo-Z chromosome (Z3) appears to have been hampered by a largely intact, homologous neo-W chromosome. However, the intermediately aged neo-Z chromosome (Z2), which lacks W gametologs, showed fewer evolutionary constraints, resulting in particularly fast evolution. Our results therefore support that neo-sex chromosomes can constitute temporary hot-spots of adaptation and divergence. The underlying dynamics are likely causally linked to shifts in selective constraints, evolution of gene expression, and degeneration of W-linked gametologs which gradually expose Z-linked genes to selection.", "doi": "10.1093/evolut/qpae082", "pmid": "38813673", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7685102"}], "notes": [], "created": "2024-08-15T12:10:17.669Z", "modified": "2025-02-28T14:17:36.747Z"}, {"entity": "publication", "iuid": "fd897a24518e497783311e1f8bfd4c40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd897a24518e497783311e1f8bfd4c40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd897a24518e497783311e1f8bfd4c40"}}, "title": "Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon.", "authors": [{"family": "Fernandes", "given": "Alexandre M", "initials": "AM"}, {"family": "Cohn-Haft", "given": "Mario", "initials": "M"}, {"family": "F\u00e1bio Silveira", "given": "Lu\u00eds", "initials": "L"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A"}, {"family": "Nascimento", "given": "Nath\u00e1lia", "initials": "N"}, {"family": "Olsson", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "198", "pages": "108117", "issn-l": "1055-7903"}, "abstract": "The Least Nighthawk Chordeiles pusillus is widespread wherever there are savannas in the South American tropics, often in isolated patches, such as white-sands savannas in the Amazon rainforest realm. Here, we investigate genetic relationships between populations of the Least Nighthawk to understand historical processes leading to its diversification and to determine dispersal routes between northern and southern savannas by way of three hypothesized dispersal corridors by comparing samples from white-sand savannas to samples from other savannas outside of the Amazon rainforest region. We use 32 mtDNA samples from the range of C. pusillus to infer a dated phylogeny. In a subset of 17 samples, we use shotgun sequences to infer a distance-based phylogeny and to estimate individual admixture proportions. We calculate gene flow and shared alleles between white-sand and non-Amazonian populations using the ABBA-BABA test (D statistics), and Principal Component Analysis (PCA) to examine genetic structure within and between lineages. Finally, we use species distribution modelling (SDM) of conditions during the Last Glacial Maximum (LGM), currently, and in the future (2050-2080) to predict potential species occurrence under a climate change scenario. Two main clades (estimated to have diverged around 1.07 million years ago) were recovered with mtDNA sequences and Single Nucleotide Polymorphism (SNPs) and were supported by NGSadmix and PCA: one in the Amazon basin white-sand savannas, the other in the non-Amazonian savannas. Possible allele sharing between these clades was indicated by the D-statistics between northern non-Amazonian populations and the white-sand savanna population, but this was not corroborated by the admixture analyses. Dispersal among northern non-Amazonian populations may have occurred in a dry corridor between the Guianan and the Brazilian Shield, which has since moved eastward. Our data suggest that the lineages separated well before the Last Glacial Maximum, consequently dispersal could have happened at any earlier time during similar climatic conditions. Subsequently, non-Amazonian lineages became more divergent among themselves, possibly connecting and dispersing across the mouth of the Amazon River across Maraj\u00f3 island during favourable climatic conditions in the Pleistocene.", "doi": "10.1016/j.ympev.2024.108117", "pmid": "38852908", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(24)00109-X"}], "notes": [], "created": "2024-08-15T12:12:21.220Z", "modified": "2025-02-28T14:13:45.330Z"}, {"entity": "publication", "iuid": "3ac2338c940e45e6acafb257753df065", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ac2338c940e45e6acafb257753df065.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ac2338c940e45e6acafb257753df065"}}, "title": "Immune system adaptation during gender-affirming testosterone treatment.", "authors": [{"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Consiglio", "given": "Camila", "initials": "C", "orcid": "0000-0002-8901-2328", "researcher": {"href": "https://publications.scilifelab.se/researcher/7df7044aa718438ca370ed90cdd9c282.json"}}, {"family": "Sardh", "given": "Fabian", "initials": "F"}, {"family": "Forlin", "given": "Rikard", "initials": "R"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Barcenilla", "given": "Hugo", "initials": "H", "orcid": "0000-0002-7255-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f0d6085e774a0fbdc1ad8d6eea3c23.json"}}, {"family": "Rodriguez", "given": "Lucie", "initials": "L", "orcid": "0000-0002-3692-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f9c2cfec48e4c4d8e9bc528a02d489b.json"}}, {"family": "Sugrue", "given": "Jamie", "initials": "J"}, {"family": "Noori", "given": "Peri", "initials": "P"}, {"family": "Ivanchenko", "given": "Margarita", "initials": "M"}, {"family": "Pi\u00f1ero P\u00e1ez", "given": "Laura", "initials": "L"}, {"family": "Gonzalez", "given": "Laura", "initials": "L"}, {"family": "Habimana Mugabo", "given": "Constantin", "initials": "C"}, {"family": "Johnsson", "given": "Anette", "initials": "A"}, {"family": "Ryberg", "given": "Henrik", "initials": "H"}, {"family": "Hallgren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Mike\u0161", "given": "Jarom\u00edr", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "James", "given": "Anna", "initials": "A"}, {"family": "Dahlqvist", "given": "Per", "initials": "P", "orcid": "0000-0002-6471-9503", "researcher": {"href": "https://publications.scilifelab.se/researcher/3577b15f446643499c52143174a5e15b.json"}}, {"family": "Wahlberg", "given": "Jeanette", "initials": "J", "orcid": "0000-0003-4061-6830", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3c768cb21cb4d0ca6ed684ad39e9121.json"}}, {"family": "Hagelin", "given": "Anders", "initials": "A"}, {"family": "Holmberg", "given": "Mats", "initials": "M", "orcid": "0000-0003-2884-9981", "researcher": {"href": "https://publications.scilifelab.se/researcher/38b253b834ed4733af1e5a13daac7541.json"}}, {"family": "Degerblad", "given": "Marie", "initials": "M"}, {"family": "Isaksson", "given": "Magnus", "initials": "M"}, {"family": "Duffy", "given": "Darragh", "initials": "D", "orcid": "0000-0002-8875-2308", "researcher": {"href": "https://publications.scilifelab.se/researcher/dce1a0fd17154c73b30f23c2a58bd390.json"}}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "633", "issue": "8028", "pages": "155-164", "issn-l": "0028-0836"}, "abstract": "Infectious, inflammatory and autoimmune conditions present differently in males and females. SARS-CoV-2 infection in naive males is associated with increased risk of death, whereas females are at increased risk of long COVID1, similar to observations in other infections2. Females respond more strongly to vaccines, and adverse reactions are more frequent3, like most autoimmune diseases4. Immunological sex differences stem from genetic, hormonal and behavioural factors5 but their relative importance is only partially understood6-8. In individuals assigned female sex at birth and undergoing gender-affirming testosterone therapy (trans men), hormone concentrations change markedly but the immunological consequences are poorly understood. Here we performed longitudinal systems-level analyses in 23 trans men and found that testosterone modulates a cross-regulated axis between type-I interferon and tumour necrosis factor. This is mediated by functional attenuation of type-I interferon responses in both plasmacytoid dendritic cells and monocytes. Conversely, testosterone potentiates monocyte responses leading to increased tumour necrosis factor, interleukin-6 and interleukin-15 production and downstream activation of nuclear factor kappa B-regulated genes and potentiation of interferon-\u03b3 responses, primarily in natural killer cells. These findings in trans men are corroborated by sex-divergent responses in public datasets and illustrate the dynamic regulation of human immunity by sex hormones, with implications for the health of individuals undergoing hormone therapy and our understanding of sex-divergent immune responses in cisgender individuals.", "doi": "10.1038/s41586-024-07789-z", "pmid": "39232147", "labels": {"Affinity Proteomics Stockholm": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11374716"}, {"db": "pii", "key": "10.1038/s41586-024-07789-z"}], "notes": [], "created": "2024-09-05T12:15:43.557Z", "modified": "2024-11-25T10:19:29.191Z"}, {"entity": "publication", "iuid": "ca128e901f5f4cf484de05f16bcca9cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca128e901f5f4cf484de05f16bcca9cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca128e901f5f4cf484de05f16bcca9cc"}}, "title": "Contemporary intergeneric hybridization and backcrossing among birds-of-paradise.", "authors": [{"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER"}, {"family": "M\u00fcller", "given": "Ingo A", "initials": "IA"}, {"family": "P\u00e4ckert", "given": "Martin", "initials": "M", "orcid": "0000-0001-5045-0139", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b587876461a4066b09d2bd5d3eaffc1.json"}}, {"family": "Frahnert", "given": "Sylke", "initials": "S"}, {"family": "van Grouw", "given": "Hein", "initials": "H"}, {"family": "Kamminga", "given": "Pepijn", "initials": "P"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Evolution Letters", "issn": "2056-3744", "issn-l": "2056-3744", "volume": "8", "issue": "5", "pages": "680-694"}, "abstract": "Despite large differences in morphology, behavior and lek-mating strategies the birds-of-paradise are known to hybridize occasionally, even across different genera. Many of these bird-of-paradise hybrids were originally described as distinct species based on large morphological differences when compared to recognized species. Nowadays, these specimens are generally recognized as hybrids based on morphological assessments. Having fascinated naturalists for centuries, hybrid specimens of birds-of-paradise have been collected and the specimens kept in Natural History Collections. In the present study, we utilize this remarkable resource in a museomics framework and evaluate the genomic composition of most described intergeneric hybrids and some intrageneric hybrids. We show that the majority of investigated specimens are first-generation hybrids and that the parental species, in most cases, are in line with prior morphological assessments. We also identify two specimens that are the result of introgressive hybridization between different genera. Additionally, two specimens exhibit hybrid morphologies but have no identifiable signals of hybridization, which may indicate that minor levels of introgression can have large morphological effects. Our findings provide direct evidence of contemporary introgressive hybridization taking place between genera of birds-of-paradise in nature, despite markedly different morphologies and lek-mating behaviors.", "doi": "10.1093/evlett/qrae023", "pmid": "39328285", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11424083"}, {"db": "pii", "key": "qrae023"}], "notes": [], "created": "2024-10-18T07:14:19.442Z", "modified": "2024-11-25T10:23:13.047Z"}, {"entity": "publication", "iuid": "fb1e8e903950444399072a83edb56f9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb1e8e903950444399072a83edb56f9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb1e8e903950444399072a83edb56f9e"}}, "title": "Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma.", "authors": [{"family": "Olsen", "given": "Thale K", "initials": "TK"}, {"family": "Otte", "given": "J\u00f6rg", "initials": "J"}, {"family": "Mei", "given": "Shenglin", "initials": "S"}, {"family": "Embaie", "given": "Bethel Tesfai", "initials": "BT"}, {"family": "Kameneva", "given": "Polina", "initials": "P"}, {"family": "Cheng", "given": "Huaitao", "initials": "H"}, {"family": "Gao", "given": "Teng", "initials": "T"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Tsea", "given": "Ioanna", "initials": "I"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kryukov", "given": "Emil", "initials": "E"}, {"family": "Hou", "given": "Ziyi", "initials": "Z"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}, {"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Stenman", "given": "Jakob", "initials": "J"}, {"family": "Fard", "given": "Shahrzad Shirazi", "initials": "SS"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Baryawno", "given": "Ninib", "initials": "N"}], "type": "letter", "published": "2024-08-31", "journal": {"title": "Mol. Cancer", "issn": "1476-4598", "issn-l": "1476-4598", "volume": "23", "issue": "1", "pages": "180"}, "abstract": "Neuroblastoma (NB) is a heterogeneous embryonal malignancy and the deadliest tumor of infancy. It is a complex disease that can result in diverse clinical outcomes. In some children, tumors regress spontaneously. Others respond well to existing treatments. But for the high-risk group, which constitutes approximately 40% of all patients, the prognosis remains dire despite collaborative efforts in basic and clinical research. While its exact cellular origin is still under debate, NB is assumed to arise from the neural crest cell lineage including multipotent Schwann cell precursors (SCPs), which differentiate into sympatho-adrenal cell states eventually producing chromaffin cells and sympathoblasts.\r\n\r\nTo investigate clonal development of neuroblastoma cell states, we performed haplotype-specific analysis of human tumor samples using single-cell multi-omics, including joint DNA/RNA sequencing of sorted single cells (DNTR-seq). Samples were also assessed using immunofluorescence stainings and fluorescence in-situ hybridization (FISH).\r\n\r\nBeyond adrenergic tumor cells, we identify subpopulations of aneuploid SCP-like cells, characterized by clonal expansion, whole-chromosome 17 gains, as well as expression programs of proliferation, apoptosis, and a non-immunomodulatory phenotype.\r\n\r\nAneuploid pre-malignant SCP-like cells represent a novel feature of NB. Genetic evidence and tumor phylogeny suggest that these clones and malignant adrenergic populations originate from aneuploidy-prone cells of migrating neural crest or SCP origin, before lineage commitment to sympatho-adrenal cell states. Our findings expand the phenotypic spectrum of NB cell states. Considering the multipotency of SCPs in development, we suggest that the transformation of fetal SCPs may represent one possible mechanism of tumor initiation in NB with chromosome 17 aberrations as a characteristic element.", "doi": "10.1186/s12943-024-02091-y", "pmid": "39217332", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "NGI Single cell": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11365129"}, {"db": "pii", "key": "10.1186/s12943-024-02091-y"}], "notes": [], "created": "2024-11-08T13:34:23.383Z", "modified": "2025-07-18T10:50:14.322Z"}, {"entity": "publication", "iuid": "5581474da4f04b29a9f3762e0739e6d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5581474da4f04b29a9f3762e0739e6d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5581474da4f04b29a9f3762e0739e6d6"}}, "title": "Rapid and robust isolation of microglia and vascular cells from brain subregions for integrative single-cell analyses.", "authors": [{"family": "Preka", "given": "Efthalia", "initials": "E"}, {"family": "Lastra Romero", "given": "Alejandro", "initials": "A"}, {"family": "Sun", "given": "Ying", "initials": "Y"}, {"family": "Onetti Vilalta", "given": "Yara", "initials": "Y"}, {"family": "Seitz", "given": "Thea", "initials": "T"}, {"family": "Fragkopoulou", "given": "Adamantia", "initials": "A"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Osman", "given": "Ahmed M", "initials": "AM"}, {"family": "Blomgren", "given": "Klas", "initials": "K"}], "type": "journal article", "published": "2024-08-30", "journal": {"title": "Heliyon", "issn": "2405-8440", "volume": "10", "issue": "16", "pages": "e35838", "issn-l": "2405-8440"}, "abstract": "Cell isolation protocols from brain tissue include prolonged ex vivo processing durations, rendering them suboptimal for transcriptomic studies. Particularly for microglia and vascular cells, current isolation methods produce lower yields, necessitating addition of an enrichment step, and use of large tissue volumes - in most cases whole brain tissue - to obtain sufficient yields. Here, we developed a simple, rapid, and reproducible cell isolation method for generating single-cell suspensions from micro-dissected brain regions, enriched for microglia and vascular cells, without an enrichment step. Cells isolated using this method are suitable for molecular profiling studies using 10 \u00d7 Genomics Chromium single-cell RNA sequencing with high reproducibility. Our method is valuable for longitudinal unbiased molecular profiling of microglia and vascular cells within different brain regions, spanning multiple time points across physiological development or disease progression.", "doi": "10.1016/j.heliyon.2024.e35838", "pmid": "39211933", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11357767"}, {"db": "pii", "key": "S2405-8440(24)11869-5"}], "notes": [], "created": "2024-10-16T12:38:46.895Z", "modified": "2024-11-25T10:13:13.532Z"}, {"entity": "publication", "iuid": "6ea83c3a932245afb40f6805a42f0311", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ea83c3a932245afb40f6805a42f0311.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ea83c3a932245afb40f6805a42f0311"}}, "title": "Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat.", "authors": [{"family": "Edlund", "given": "Maja", "initials": "M"}, {"family": "Anderson", "given": "Benjamin M", "initials": "BM"}, {"family": "Su", "given": "Huei-Jiun", "initials": "H"}, {"family": "Robison", "given": "Tanner", "initials": "T"}, {"family": "Caraballo-Ortiz", "given": "Marcos A", "initials": "MA"}, {"family": "Der", "given": "Joshua P", "initials": "JP"}, {"family": "Nickrent", "given": "Daniel L", "initials": "DL"}, {"family": "Petersen", "given": "Gitte", "initials": "G"}], "type": "journal article", "published": "2024-08-30", "journal": {"title": "Ann. Bot.", "issn": "1095-8290", "issn-l": "0305-7364", "volume": null, "issue": null, "pages": null}, "abstract": "Biological aspects of haustorial parasitism have significant effects on the configuration of the plastid genome. Approximately half the diversity of haustorial parasites belongs to the order Santalales, where a clearer picture of plastome evolution in relation to parasitism is starting to emerge. However, in previous studies of plastome evolution there is still a notable under-representation of members from non-parasitic and deep-branching hemiparasitic lineages, limiting evolutionary inference around the time of transition to a parasitic lifestyle. To expand taxon sampling relevant to this transition we therefore targeted three families of non-parasites (Erythropalaceae, Strombosiaceae, and Coulaceae), two families of root-feeding hemiparasites (Ximeniaceae and Olacaceae), and two families of uncertain parasitic status (Aptandraceae and Octoknemaceae). With data from these lineages we aimed to explore plastome evolution in relation to evolution of parasitism.\r\n\r\nFrom 29 new samples we sequenced and annotated plastomes and the nuclear ribosomal cistron. We examined phylogenetic patterns, plastome evolution, and patterns of relaxed or intensified selection in plastid genes. Available transcriptome data were analyzed to investigate potential transfer of infA to the nuclear genome.\r\n\r\nPhylogenetic relationships indicate a single functional loss of all plastid ndh genes (ndhA-K) in a clade formed by confirmed parasites and Aptandraceae, and the loss coincides with major size and boundary shifts of the inverted repeat (IR) region. Depending on an autotrophic or heterotrophic lifestyle in Aptandraceae, plastome changes are either correlated with or predate evolution of parasitism. Phylogenetic patterns also indicate repeated loss of infA from the plastome, and based on presence of transcribed sequences with presequences corresponding to thylakoid luminal transit peptides, we infer that the genes were transferred to the nuclear genome.\r\n\r\nExcept for the loss of the ndh complex, relatively few genes have been lost from the plastome in deep-branching root parasites in Santalales. Prior to loss of the ndh genes, they show signs of relaxed selection indicative of their dispensability. To firmly establish a potential correlation between ndh gene loss, plastome instability and evolution of parasitism, it is pertinent to refute or confirm a parasitic lifestyle all Santalales clades.", "doi": "10.1093/aob/mcae145", "pmid": "39213003", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": null}, "xrefs": [{"db": "pii", "key": "7745948"}], "notes": [], "created": "2024-09-30T07:32:28.486Z", "modified": "2024-10-31T12:43:38.872Z"}, {"entity": "publication", "iuid": "1e2bfcb46e6a45fbb3122eedc049ea53", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e2bfcb46e6a45fbb3122eedc049ea53.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e2bfcb46e6a45fbb3122eedc049ea53"}}, "title": "Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Sanchez-Pinto", "given": "Iban", "initials": "I", "orcid": "0000-0001-6805-5567", "researcher": {"href": "https://publications.scilifelab.se/researcher/6afd2d3bc0584ec4a9f2cf2da524e408.json"}}, {"family": "Solaun", "given": "Jos\u00e9 Luis", "initials": "JL"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T", "orcid": "0009-0009-3553-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a32a4e171454874a03920c915d3265f.json"}}, {"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca893ff5227f41a699fa68cca126600e.json"}}, {"family": "P\u00e9rez-Ramallo", "given": "Patxi", "initials": "P", "orcid": "0000-0002-1142-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb111a8997c4fc4a3167bbeabcac042.json"}}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "de Anca Prado", "given": "Violeta", "initials": "V", "orcid": "0000-0003-1845-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf4f1fec38fa4efb801ba17713c26586.json"}}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Herrasti", "given": "Lourdes", "initials": "L", "orcid": "0000-0002-4021-9731", "researcher": {"href": "https://publications.scilifelab.se/researcher/030a255131a84c019ea7c83386e2fbf2.json"}}, {"family": "Azkarate", "given": "Agust\u00edn", "initials": "A"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}], "type": "journal article", "published": "2024-08-30", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "35", "pages": "eadp8625", "issn-l": "2375-2548"}, "abstract": "Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.", "doi": "10.1126/sciadv.adp8625", "pmid": "39196943", "labels": {"Ancient DNA": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11352919"}], "notes": [], "created": "2024-08-29T12:38:46.980Z", "modified": "2024-11-25T10:28:22.603Z"}, {"entity": "publication", "iuid": "09b2174874b74c20886dd68920d6961e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09b2174874b74c20886dd68920d6961e"}}, "title": "Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis.", "authors": [{"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Macedo", "given": "Diego", "initials": "D"}, {"family": "Huppertz", "given": "Frederik", "initials": "F"}, {"family": "Veith", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-1810-8808", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e316fdf93964e89a0606e68da08c336.json"}}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Christ", "given": "Elena", "initials": "E"}, {"family": "Scheytt", "given": "Richard", "initials": "R", "orcid": "0009-0004-1405-6360", "researcher": {"href": "https://publications.scilifelab.se/researcher/3866987412724150b6af427c16dd17cf.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2024-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "7177"}, "abstract": "The Plasmodium falciparum life cycle includes obligate transition between a human and mosquito host. Gametocytes are responsible for transmission from the human to the mosquito vector where gamete fusion followed by meiosis occurs. To elucidate how male and female gametocytes differentiate in the absence of sex chromosomes, we perform FACS-based cell enrichment of a P. falciparum gametocyte reporter line followed by single-cell RNA-seq. In our analyses we define the transcriptional programs and predict candidate driver genes underlying male and female development, including genes from the ApiAP2 family of transcription factors. A motif-driven, gene regulatory network analysis indicates that AP2-G5 specifically modulates male development. Additionally, genes linked to the inner membrane complex, involved in morphological changes, are uniquely expressed in the female lineage. The transcriptional programs of male and female development detailed herein allow for further exploration of the evolution of sex in eukaryotes and provide targets for future development of transmission blocking therapies.", "doi": "10.1038/s41467-024-51201-3", "pmid": "39187486", "labels": {"Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "NGI Short read": null}, "xrefs": [{"db": "pmc", "key": "PMC11347709"}, {"db": "pii", "key": "10.1038/s41467-024-51201-3"}], "notes": [], "created": "2024-11-25T10:17:42.276Z", "modified": "2025-07-18T10:45:32.069Z"}, {"entity": "publication", "iuid": "06092f1c02924d8da8dd7a4929fd5ac3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06092f1c02924d8da8dd7a4929fd5ac3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06092f1c02924d8da8dd7a4929fd5ac3"}}, "title": "Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics.", "authors": [{"family": "Sonavane", "given": "Sumalata", "initials": "S", "orcid": "0000-0002-0728-4822", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c951e7727ce4f1a9dc0abc3b62019f8.json"}}, {"family": "Hassan", "given": "Sameer", "initials": "S"}, {"family": "Chatterjee", "given": "Urmimala", "initials": "U", "orcid": "0000-0002-6681-1696", "researcher": {"href": "https://publications.scilifelab.se/researcher/418ed6f1f8a440efb4df1c0b4f2dd265.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Holm", "given": "Lena", "initials": "L", "orcid": "0000-0002-7717-4370", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b769bc4b7e74ce48c1f26bc5d647e18.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A", "orcid": "0009-0007-0542-0695", "researcher": {"href": "https://publications.scilifelab.se/researcher/64c67099378344c8b7d1ff66a7bfdc48.json"}}, {"family": "Greco", "given": "Gabriele", "initials": "G", "orcid": "0000-0003-3356-7081", "researcher": {"href": "https://publications.scilifelab.se/researcher/924046db702c424f8296265c8d6599fd.json"}}, {"family": "Fereydouni", "given": "Noah", "initials": "N", "orcid": "0000-0002-1786-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc54e88c9a724eecb2a2c68e9f025a97.json"}}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Churcher", "given": "Allison", "initials": "A", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Johansson", "given": "Jan", "initials": "J"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Rising", "given": "Anna", "initials": "A", "orcid": "0000-0002-1872-1207", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f120d653e7c47d7833be7a44c21dbaa.json"}}], "type": "journal article", "published": "2024-08-16", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "10", "issue": "33", "pages": "eadn0597"}, "abstract": "Spiders produce nature's toughest fiber using renewable components at ambient temperatures and with water as solvent, making it highly interesting to replicate for the materials industry. Despite this, much remains to be understood about the bioprocessing and composition of spider silk fibers. Here, we identify 18 proteins that make up the spiders' strongest silk type, the major ampullate fiber. Single-cell RNA sequencing and spatial transcriptomics revealed that the secretory epithelium of the gland harbors six cell types. These cell types are confined to three distinct glandular zones that produce specific combinations of silk proteins. Image analysis of histological sections showed that the secretions from the three zones do not mix, and proteomics analysis revealed that these secretions form layers in the final fiber. Using a multi-omics approach, we provide substantial advancements in the understanding of the structure and function of the major ampullate silk gland as well as of the architecture and composition of the fiber it produces.", "doi": "10.1126/sciadv.adn0597", "pmid": "39141739", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Spatial omics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11323941"}], "notes": [], "created": "2024-08-15T12:15:23.174Z", "modified": "2024-11-25T10:28:17.415Z"}, {"entity": "publication", "iuid": "53f9468fbc74451191f9dcfd1c77d21f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53f9468fbc74451191f9dcfd1c77d21f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53f9468fbc74451191f9dcfd1c77d21f"}}, "title": "Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.", "authors": [{"family": "Biswas", "given": "Twinkle", "initials": "T", "orcid": "0000-0001-6106-0611", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e4bf354cc1240edbec52c1478249950.json"}}, {"family": "Vogel", "given": "Heiko", "initials": "H", "orcid": "0000-0001-9821-7731", "researcher": {"href": "https://publications.scilifelab.se/researcher/a64cd168fc814737830d2d01bacc78d6.json"}}, {"family": "Biedermann", "given": "Peter H W", "initials": "PHW", "orcid": "0000-0003-4234-5659", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cbd5bd2cf0445ca996d99377179272c.json"}}, {"family": "Lehenberger", "given": "Maximilian", "initials": "M", "orcid": "0000-0001-9097-9715", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5b54a1d9485441a9512d310f5025680.json"}}, {"family": "Yuvaraj", "given": "Jothi Kumar", "initials": "JK", "orcid": "0000-0002-5702-3751", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e338cdc27804e5795dfab4f8763424f.json"}}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}], "type": "journal article", "published": "2024-08-06", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "764", "issn-l": "1471-2164"}, "abstract": "Chemoreception is crucial for insect fitness, underlying for instance food-, host-, and mate finding. Chemicals in the environment are detected by receptors from three divergent gene families: odorant receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs). However, how the chemoreceptor gene families evolve in parallel with ecological specializations remains poorly understood, especially in the order Coleoptera. Hence, we sequenced the genome and annotated the chemoreceptor genes of the specialised ambrosia beetle Trypodendron lineatum (Coleoptera, Curculionidae, Scolytinae) and compared its chemoreceptor gene repertoires with those of other scolytines with different ecological adaptations, as well as a polyphagous cerambycid species.\n\nWe identified 67 ORs, 38 GRs, and 44 IRs in T. lineatum ('Tlin'). Across gene families, T. lineatum has fewer chemoreceptors compared to related scolytines, the coffee berry borer Hypothenemus hampei and the mountain pine beetle Dendroctonus ponderosae, and clearly fewer receptors than the polyphagous cerambycid Anoplophora glabripennis. The comparatively low number of chemoreceptors is largely explained by the scarcity of large receptor lineage radiations, especially among the bitter taste GRs and the 'divergent' IRs, and the absence of alternatively spliced GR genes. Only one non-fructose sugar receptor was found, suggesting several sugar receptors have been lost. Also, we found no orthologue in the 'GR215 clade', which is widely conserved across Coleoptera. Two TlinORs are orthologous to ORs that are functionally conserved across curculionids, responding to 2-phenylethanol (2-PE) and green leaf volatiles (GLVs), respectively.\n\nTrypodendron lineatum reproduces inside the xylem of decaying conifers where it feeds on its obligate fungal mutualist Phialophoropsis ferruginea. Like previous studies, our results suggest that stenophagy correlates with small chemoreceptor numbers in wood-boring beetles; indeed, the few GRs may be due to its restricted fungal diet. The presence of TlinORs orthologous to those detecting 2-PE and GLVs in other species suggests these compounds are important for T. lineatum. Future functional studies should test this prediction, and chemoreceptor annotations should be conducted on additional ambrosia beetle species to investigate whether few chemoreceptors is a general trait in this specialized group of beetles.", "doi": "10.1186/s12864-024-10678-4", "pmid": "39107741", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11302349"}, {"db": "pii", "key": "10.1186/s12864-024-10678-4"}], "notes": [], "created": "2024-08-15T12:16:43.573Z", "modified": "2024-11-25T10:30:07.491Z"}, {"entity": "publication", "iuid": "eb29b09a66a84e1081cbd8cf6eb5333a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb29b09a66a84e1081cbd8cf6eb5333a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb29b09a66a84e1081cbd8cf6eb5333a"}}, "title": "Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.", "authors": [{"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7855-9539", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c626e0c08ca449899cebece751e79cf.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Papetti", "given": "Chiara", "initials": "C", "orcid": "0000-0002-4567-459X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a151631ac04ec0bfd9f952781bc973.json"}}, {"family": "Gislason", "given": "Astthor", "initials": "A"}, {"family": "Glenner", "given": "Henrik", "initials": "H"}, {"family": "Cartes", "given": "Joan E", "initials": "JE"}, {"family": "Blanco-Bercial", "given": "Leocadio", "initials": "L", "orcid": "0000-0003-0658-7183", "researcher": {"href": "https://publications.scilifelab.se/researcher/5077c59ccfe8496eb534c1ef6d725e06.json"}}, {"family": "Eriksen", "given": "Elena", "initials": "E"}, {"family": "Meyer", "given": "Bettina", "initials": "B", "orcid": "0000-0001-6804-9896", "researcher": {"href": "https://publications.scilifelab.se/researcher/9347bf907b1c4b258495153b5550f3dc.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}], "type": "journal article", "published": "2024-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "6297"}, "abstract": "Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.", "doi": "10.1038/s41467-024-50239-7", "pmid": "39090106", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11294593"}, {"db": "pii", "key": "10.1038/s41467-024-50239-7"}], "notes": [], "created": "2024-08-02T12:21:47.326Z", "modified": "2024-11-25T10:17:04.308Z"}, {"entity": "publication", "iuid": "3bf46273f014498b80752db1b270c250", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bf46273f014498b80752db1b270c250.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bf46273f014498b80752db1b270c250"}}, "title": "Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album).", "authors": [{"family": "Schneider", "given": "Katharina", "initials": "K", "orcid": "0009-0004-7727-594X", "researcher": {"href": "https://publications.scilifelab.se/researcher/27ac69b83e6e4a70ab1473838d162f61.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MdlP"}, {"family": "Janz", "given": "Niklas", "initials": "N", "orcid": "0000-0002-6379-7905", "researcher": {"href": "https://publications.scilifelab.se/researcher/addc1292f6db4eeeacee907b4a534f52.json"}}, {"family": "Moberg", "given": "Dick", "initials": "D", "orcid": "0000-0001-5704-3915", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f9df1ca5bd343cdb148d7c8fbfc6f46.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/68d7f780ed30472eb2af408b0762c14d.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "33", "issue": "16", "pages": "e17479"}, "abstract": "Generalist plant-feeding insects are characterised by a broad host repertoire that can comprise several families or even different orders of plants. The genetic and physiological mechanisms underlying the use of such a wide host range are still not fully understood. Earlier studies indicate that the consumption of different host plants is associated with host-specific gene expression profiles. It remained, however, unclear if and how larvae can alter these profiles in the case of a changing host environment. Using the polyphagous comma butterfly (Polygonia c-album) we show that larvae can adjust their transcriptional profiles in response to a new host plant. The switch to some of the host plants, however, resulted in a larger transcriptional response and, thus, seems to be more challenging. At a physiological level, no correspondence for these patterns could be found in larval performance. This suggests that a high transcriptional but also phenotypic flexibility are essential for the use of a broad and diverse host range. We furthermore propose that host switch tests in the laboratory followed by transcriptomic investigations can be a valuable tool to examine not only plasticity in host use but also subtle and/or transient trade-offs in the evolution of host plant repertoires.", "doi": "10.1111/mec.17479", "pmid": "39036890", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T19:50:29.574Z", "modified": "2025-01-02T12:19:27.670Z"}, {"entity": "publication", "iuid": "15068cccc8704f1789179c51b4f175eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15068cccc8704f1789179c51b4f175eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15068cccc8704f1789179c51b4f175eb"}}, "title": "Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.", "authors": [{"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P"}, {"family": "Stanicek", "given": "Laura", "initials": "L"}, {"family": "Sagredo", "given": "Eduardo A", "initials": "EA", "orcid": "0000-0001-9984-2985", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dfefa432364269b33bbe8a4075de65.json"}}, {"family": "Widmark", "given": "Albin", "initials": "A"}, {"family": "Doukoumopoulos", "given": "Evangelos", "initials": "E"}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "42", "issue": "8", "pages": "1296-1302"}, "abstract": "MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.", "doi": "10.1038/s41587-023-01951-0", "pmid": "37735263", "labels": {"National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11324520"}, {"db": "pii", "key": "10.1038/s41587-023-01951-0"}], "notes": [], "created": "2023-10-19T13:55:15.412Z", "modified": "2024-11-25T10:19:39.688Z"}, {"entity": "publication", "iuid": "c1686601bc6b4c808ba31fbb6c6d93d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c1686601bc6b4c808ba31fbb6c6d93d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c1686601bc6b4c808ba31fbb6c6d93d3"}}, "title": "A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis.", "authors": [{"family": "Pahlevan Kakhki", "given": "Majid", "initials": "M", "orcid": "0000-0002-5407-3147", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f376c85cfbe4711ae41d9ee5ade8f09.json"}}, {"family": "Giordano", "given": "Antonino", "initials": "A"}, {"family": "Starvaggi Cucuzza", "given": "Chiara", "initials": "C", "orcid": "0000-0002-9088-7658", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ead2e8f98754d1586891eda5adb9e1a.json"}}, {"family": "Venkata S Badam", "given": "Tejaswi", "initials": "T"}, {"family": "Samudyata", "given": "Samudyata", "initials": "S"}, {"family": "Lem\u00e9e", "given": "Marianne Victoria", "initials": "MV", "orcid": "0000-0002-4897-0722", "researcher": {"href": "https://publications.scilifelab.se/researcher/361e3a91dc5245e587309759769414c8.json"}}, {"family": "Stridh", "given": "Pernilla", "initials": "P", "orcid": "0000-0003-4855-0039", "researcher": {"href": "https://publications.scilifelab.se/researcher/613e86be4685423093de57bb83be261b.json"}}, {"family": "Gkogka", "given": "Asimenia", "initials": "A"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Harroud", "given": "Adil", "initials": "A", "orcid": "0000-0003-2616-7274", "researcher": {"href": "https://publications.scilifelab.se/researcher/91a769f610fb430e89258c1c30cbd23b.json"}}, {"family": "Gyllenberg", "given": "Alexandra", "initials": "A"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Boddul", "given": "Sanjaykumar", "initials": "S"}, {"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Sorosina", "given": "Melissa", "initials": "M"}, {"family": "Filippi", "given": "Massimo", "initials": "M", "orcid": "0000-0002-5485-0479", "researcher": {"href": "https://publications.scilifelab.se/researcher/8878f32c07334124b8e3bce42c94c076.json"}}, {"family": "Esposito", "given": "Federica", "initials": "F"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9633-677X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a34df8186ba24df3b14fe9743cf546b4.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}, {"family": "Casaccia", "given": "Patrizia", "initials": "P", "orcid": "0000-0002-4785-9264", "researcher": {"href": "https://publications.scilifelab.se/researcher/e62a7dde40bd454e9072ff43fff8a2ea.json"}}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Sellgren", "given": "Carl M", "initials": "CM", "orcid": "0000-0001-9103-2785", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c0740ddfd6d4c98988b2a19096a9814.json"}}, {"family": "Golzio", "given": "Christelle", "initials": "C"}, {"family": "Kular", "given": "Lara", "initials": "L", "orcid": "0000-0002-2907-6071", "researcher": {"href": "https://publications.scilifelab.se/researcher/09563004a20543dc934dd4d3b1ceebd7.json"}}, {"family": "Jagodic", "given": "Maja", "initials": "M", "orcid": "0000-0003-0756-889X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b651ef39c6b0436992e2305f425eba72.json"}}], "type": "journal article", "published": "2024-07-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6419", "issn-l": "2041-1723"}, "abstract": "Multiple Sclerosis (MS) is a heterogeneous inflammatory and neurodegenerative disease with an unpredictable course towards progressive disability. Treating progressive MS is challenging due to limited insights into the underlying mechanisms. We examined the molecular changes associated with primary progressive MS (PPMS) using a cross-tissue (blood and post-mortem brain) and multilayered data (genetic, epigenetic, transcriptomic) from independent cohorts. In PPMS, we found hypermethylation of the 1q21.1 locus, controlled by PPMS-specific genetic variations and influencing the expression of proximal genes (CHD1L, PRKAB2) in the brain. Evidence from reporter assay and CRISPR/dCas9 experiments supports a causal link between methylation and expression and correlation network analysis further implicates these genes in PPMS brain processes. Knock-down of CHD1L in human iPSC-derived neurons and knock-out of chd1l in zebrafish led to developmental and functional deficits of neurons. Thus, several lines of evidence suggest a distinct genetic-epigenetic-transcriptional interplay in the 1q21.1 locus potentially contributing to PPMS pathogenesis.", "doi": "10.1038/s41467-024-50794-z", "pmid": "39079955", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11289459"}, {"db": "pii", "key": "10.1038/s41467-024-50794-z"}], "notes": [], "created": "2024-08-15T12:14:24.965Z", "modified": "2024-11-25T10:17:37.116Z"}, {"entity": "publication", "iuid": "d28325d47fdb47cda393a1e60d677055", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d28325d47fdb47cda393a1e60d677055.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d28325d47fdb47cda393a1e60d677055"}}, "title": "Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.", "authors": [{"family": "Mandolesi", "given": "Marco", "initials": "M", "orcid": "0000-0003-2927-7831", "researcher": {"href": "https://publications.scilifelab.se/researcher/29e6c31be1704c97a2853aca0833f6b0.json"}}, {"family": "Das", "given": "Hrishikesh", "initials": "H", "orcid": "0000-0001-7495-7065", "researcher": {"href": "https://publications.scilifelab.se/researcher/b150c8ccf1164aaab678a9f6c1acd97b.json"}}, {"family": "de Vries", "given": "Liset", "initials": "L", "orcid": "0000-0002-4797-086X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6b05b7eec7c4120b4bee2ff15ac8035.json"}}, {"family": "Yang", "given": "Yiqiu", "initials": "Y"}, {"family": "Kim", "given": "Changil", "initials": "C"}, {"family": "Dhinakaran", "given": "Manojj", "initials": "M", "orcid": "0000-0003-2536-8699", "researcher": {"href": "https://publications.scilifelab.se/researcher/de859a6247424dd285f56b841dc23a36.json"}}, {"family": "Castro Dopico", "given": "Xaquin", "initials": "X", "orcid": "0000-0002-9005-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1d266d61654951a684193993ca53b1.json"}}, {"family": "Fischbach", "given": "Julian", "initials": "J", "orcid": "0000-0001-9411-9181", "researcher": {"href": "https://publications.scilifelab.se/researcher/20e4fea1f9f54727b1bf3ef1cb8f81a4.json"}}, {"family": "Kim", "given": "Sungyong", "initials": "S"}, {"family": "Guryleva", "given": "Mariia V", "initials": "MV"}, {"family": "\u00c0dori", "given": "Monika", "initials": "M"}, {"family": "Chernyshev", "given": "Mark", "initials": "M", "orcid": "0000-0003-1622-9240", "researcher": {"href": "https://publications.scilifelab.se/researcher/678134399edb44afac5e7eacc8622fcb.json"}}, {"family": "St\u00e5lmarck", "given": "Aron", "initials": "A"}, {"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "McInerney", "given": "Gerald M", "initials": "GM", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-0227-5636", "researcher": {"href": "https://publications.scilifelab.se/researcher/6105f3617cdf4241bf335299ac957ee5.json"}}, {"family": "Corcoran", "given": "Martin", "initials": "M"}, {"family": "H\u00e4llberg", "given": "B Martin", "initials": "BM", "orcid": "0000-0002-6781-0345", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b7e4327d0ac48288afd6061f149156d.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}}], "type": "journal article", "published": "2024-07-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "6338", "issn-l": "2041-1723"}, "abstract": "The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.", "doi": "10.1038/s41467-024-50286-0", "pmid": "39068149", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11283548"}, {"db": "pii", "key": "10.1038/s41467-024-50286-0"}], "notes": [], "created": "2024-10-14T13:07:16.627Z", "modified": "2024-11-25T10:17:09.411Z"}, {"entity": "publication", "iuid": "d8db2ba0f09244fb8155dd659af8ce6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8db2ba0f09244fb8155dd659af8ce6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8db2ba0f09244fb8155dd659af8ce6d"}}, "title": "Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system.", "authors": [{"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Christidis", "given": "Les", "initials": "L"}, {"family": "Benz", "given": "Brett W", "initials": "BW"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2024-07-19", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "27", "issue": "7", "pages": "110300", "issn-l": "2589-0042"}, "abstract": "Sexual selection can directly contribute to reproductive isolation and is an important mechanism that can lead to speciation. Lek-mating is one of the most extreme forms of sexual selection, but surprisingly does not seem to preclude occasional hybridization in nature. However, hybridization among lekking species may still be trivial if selection against offspring with intermediate phenotypes prohibits introgression. Here we investigate this further by sequencing the genomes of nearly all bird-of-paradise (Paradisaeidae) species and 10 museum specimens of putative hybrid origin. We find that intergeneric hybridization indeed still takes place despite extreme differentiation in form, plumage, and behavior. In parallel, the genomes of contemporary species contain widespread signatures of past introgression, demonstrating that hybridization has repeatedly resulted in shared genetic variation despite strong sexual isolation. Our study raises important questions about extrinsic factors that modulate hybridization probability and the evolutionary consequences of introgressive hybridization between lekking species.", "doi": "10.1016/j.isci.2024.110300", "pmid": "39055907", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11269930"}, {"db": "pii", "key": "S2589-0042(24)01525-6"}], "notes": [], "created": "2024-08-15T12:16:05.868Z", "modified": "2024-11-25T10:13:34.840Z"}, {"entity": "publication", "iuid": "6982c09dce1341eaab59a3af9f9874d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6982c09dce1341eaab59a3af9f9874d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6982c09dce1341eaab59a3af9f9874d7"}}, "title": "Temporal dynamics of woolly mammoth genome erosion prior to extinction.", "authors": [{"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Kanellidou", "given": "Foteini", "initials": "F"}, {"family": "Muller", "given": "H\u00e9lo\u00efse", "initials": "H"}, {"family": "Plotnikov", "given": "Valerii", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Danilov", "given": "Gleb K", "initials": "GK"}, {"family": "Giann\u00ec", "given": "Maddalena", "initials": "M"}, {"family": "van der Sluis", "given": "Laura", "initials": "L"}, {"family": "Higham", "given": "Tom", "initials": "T"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2024-07-11", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "187", "issue": "14", "pages": "3531-3540.e13", "issn-l": "0092-8674"}, "abstract": "A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.", "doi": "10.1016/j.cell.2024.05.033", "pmid": "38942016", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)00577-4"}], "notes": [], "created": "2024-08-15T12:13:21.650Z", "modified": "2025-02-28T14:11:50.850Z"}, {"entity": "publication", "iuid": "a7701b730ae64100a1a1c05e7d0ac0ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7701b730ae64100a1a1c05e7d0ac0ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7701b730ae64100a1a1c05e7d0ac0ac"}}, "title": "Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.", "authors": [{"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Bengtsson", "given": "Jesse D", "initials": "JD"}, {"family": "Du", "given": "Haowei", "initials": "H", "orcid": "0000-0001-9052-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c66b32c1f0f497c8652ac2ec9a9cbe8.json"}}, {"family": "Gandhi", "given": "Mira", "initials": "M"}, {"family": "Lun", "given": "Ming Yin", "initials": "MY"}, {"family": "Mehaffey", "given": "Michele G", "initials": "MG"}, {"family": "Park", "given": "KyungHee", "initials": "K"}, {"family": "H\u00f6ps", "given": "Wolfram", "initials": "W"}, {"family": "Benito", "given": "Eva", "initials": "E"}, {"family": "Hasenfeld", "given": "Patrick", "initials": "P"}, {"family": "Korbel", "given": "Jan O", "initials": "JO"}, {"family": "Mahmoud", "given": "Medhat", "initials": "M", "orcid": "0000-0002-2553-4231", "researcher": {"href": "https://publications.scilifelab.se/researcher/e05f2f3025d34f1e940334615a912e1e.json"}}, {"family": "Paulin", "given": "Luis F", "initials": "LF", "orcid": "0000-0003-2567-3773", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e25b0a91ea84c54af6407fead39e2e7.json"}}, {"family": "Jhangiani", "given": "Shalini N", "initials": "SN"}, {"family": "Hwang", "given": "James Paul", "initials": "JP"}, {"family": "Bhamidipati", "given": "Sravya V", "initials": "SV"}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Fatih", "given": "Jawid M", "initials": "JM"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1356-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82176147e434163a72c946839708743.json"}}, {"family": "Pendleton", "given": "Matthew", "initials": "M", "orcid": "0000-0002-7465-4459", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf7bfd1f8b6492396f3354447413ea3.json"}}, {"family": "Harrington", "given": "Eoghan", "initials": "E"}, {"family": "Juul", "given": "Sissel", "initials": "S"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Sedlazeck", "given": "Fritz J", "initials": "FJ", "orcid": "0000-0001-6040-2691", "researcher": {"href": "https://publications.scilifelab.se/researcher/28f940f4fb8b47ec8acb7ba04ca3890b.json"}}, {"family": "Pehlivan", "given": "Davut", "initials": "D", "orcid": "0000-0001-5788-0270", "researcher": {"href": "https://publications.scilifelab.se/researcher/161dfab97b5b4438a16506714d94e751.json"}}, {"family": "Lupski", "given": "James R", "initials": "JR", "orcid": "0000-0001-9907-9246", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dd1dee9767489aaf25865670feb7b7.json"}}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "4", "issue": "7", "pages": "100590", "issn-l": null}, "abstract": "The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of \u223c2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.", "doi": "10.1016/j.xgen.2024.100590", "pmid": "38908378", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11293582"}, {"db": "pii", "key": "S2666-979X(24)00174-5"}], "notes": [], "created": "2024-08-15T12:10:53.870Z", "modified": "2024-11-27T09:00:48.437Z"}, {"entity": "publication", "iuid": "92172550f1414171b256c572edd291a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92172550f1414171b256c572edd291a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92172550f1414171b256c572edd291a1"}}, "title": "Unravelling reference bias in ancient DNA datasets.", "authors": [{"family": "Dolenz", "given": "Stephanie", "initials": "S"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/165a756337e8489f9621bbaa73fd4f7b.json"}}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J"}, {"family": "Sharif", "given": "Muhammad Bilal", "initials": "MB"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}], "type": "journal article", "published": "2024-07-01", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "40", "issue": "7", "issn-l": "1367-4803"}, "abstract": "The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.\n\nFor these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.\n\nAMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).", "doi": "10.1093/bioinformatics/btae436", "pmid": "38960861", "labels": {"Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11254355"}, {"db": "pii", "key": "7705522"}], "notes": [], "created": "2024-11-25T10:22:52.302Z", "modified": "2025-02-28T14:17:04.861Z"}, {"entity": "publication", "iuid": "56af984b6a0d491285345060f91242cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56af984b6a0d491285345060f91242cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56af984b6a0d491285345060f91242cf"}}, "title": "Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice.", "authors": [{"family": "Holl", "given": "Daniel", "initials": "D"}, {"family": "Hau", "given": "Wing Fung", "initials": "WF", "orcid": "0009-0007-2761-5418", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f74d99ab034701b26c96076630090e.json"}}, {"family": "Julien", "given": "Anais", "initials": "A"}, {"family": "Banitalebi", "given": "Shervin", "initials": "S"}, {"family": "Kalkitsas", "given": "Jannis", "initials": "J"}, {"family": "Savant", "given": "Soniya", "initials": "S"}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications.scilifelab.se/researcher/3144601c466246cfa70acbe8c7ee00ee.json"}}, {"family": "Herault", "given": "Yann", "initials": "Y", "orcid": "0000-0001-7049-6900", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6aedf7c13e6402f8260f8a58853538e.json"}}, {"family": "Pavlovic", "given": "Guillaume", "initials": "G", "orcid": "0000-0001-9122-4592", "researcher": {"href": "https://publications.scilifelab.se/researcher/55785234582d43dc89bbc6d53a9240b7.json"}}, {"family": "Amiry-Moghaddam", "given": "Mahmood", "initials": "M", "orcid": "0000-0003-1071-1247", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d84e29408b47cfb4a2babdb383bcd3.json"}}, {"family": "Dias", "given": "David Oliveira", "initials": "DO", "orcid": "0000-0002-2144-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/e234830ba9004cc8aaecfeebe37cb297.json"}}, {"family": "G\u00f6ritz", "given": "Christian", "initials": "C", "orcid": "0000-0003-0799-766X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3358941841740db8d22fd49e14bdea2.json"}}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "27", "issue": "7", "pages": "1285-1298", "issn-l": "1097-6256"}, "abstract": "Fibrotic scar tissue formation occurs in humans and mice. The fibrotic scar impairs tissue regeneration and functional recovery. However, the origin of scar-forming fibroblasts is unclear. Here, we show that stromal fibroblasts forming the fibrotic scar derive from two populations of perivascular cells after spinal cord injury (SCI) in adult mice of both sexes. We anatomically and transcriptionally identify the two cell populations as pericytes and perivascular fibroblasts. Fibroblasts and pericytes are enriched in the white and gray matter regions of the spinal cord, respectively. Both cell populations are recruited in response to SCI and inflammation. However, their contribution to fibrotic scar tissue depends on the location of the lesion. Upon injury, pericytes and perivascular fibroblasts become activated and transcriptionally converge on the generation of stromal myofibroblasts. Our results show that pericytes and perivascular fibroblasts contribute to the fibrotic scar in a region-dependent manner.", "doi": "10.1038/s41593-024-01678-4", "pmid": "38849523", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Integrated Microscopy Technologies Stockholm": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11239523"}, {"db": "pii", "key": "10.1038/s41593-024-01678-4"}], "notes": [], "created": "2024-06-15T18:54:16.128Z", "modified": "2024-10-16T13:39:42.660Z"}, {"entity": "publication", "iuid": "7061bf38c8d54081964a055cf5acd308", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7061bf38c8d54081964a055cf5acd308.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7061bf38c8d54081964a055cf5acd308"}}, "title": "A combination of long- and short-read genomics reveals frequent p-arm breakpoints within chromosome 21 complex genomic rearrangements.", "authors": [{"family": "Schuy", "given": "Jakob", "initials": "J"}, {"family": "S\u00e6ther", "given": "Kristine Bilgrav", "initials": "KB"}, {"family": "Lisfeld", "given": "Jasmin", "initials": "J"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Lun", "given": "Ming Yin", "initials": "MY"}, {"family": "Hastie", "given": "Alex", "initials": "A"}, {"family": "Rudolph", "given": "Susanne", "initials": "S"}, {"family": "Fuchs", "given": "Sigrid", "initials": "S"}, {"family": "Neveling", "given": "Kornelia", "initials": "K"}, {"family": "Hempel", "given": "Maja", "initials": "M"}, {"family": "Hoischen", "given": "Alexander", "initials": "A"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2024-06-28", "journal": {"title": "Genetics in Medicine Open", "issn": "2949-7744", "issn-l": null, "volume": "2", "issue": null, "pages": "101863"}, "abstract": "Although chromosome 21 is the smallest human chromosome, it is highly relevant in the pathogenicity of both cancer and congenital diseases, including Alzheimer disease and trisomy 21 (Down syndrome). In addition, cases with rare structural variants (SVs) of chromosome 21 have been reported. These events vary in size and include large chromosomal events, such as ring chromosomes and small partial aneuploidies. The p-arm of the acrocentric chromosome 21 was devoid of reference genomic sequence in GRCh37 and GRCh38, which hampered our ability to solve genomic rearrangements and find the mechanism of formation of disease-causing SVs. We hypothesize that conserved satellite structures and segmental duplications located on the p-arm play an important role in the formation of complex SVs involving chromosome 21.\n\nThree cases with complex chromosome 21 rearrangements were studied with a combination of short-read and long-read genome sequencing, as well as optical genome mapping. The data were aligned to the T2T-CHM13 assembly.\n\nWe were able to resolve all 3 complex chromosome 21 rearrangements in which 15, 8, and 26 breakpoints were identified, respectively. By comparing the identified SV breakpoints, we were able to pinpoint a region between 21p13 and 21p12 that appears to be frequently involved in chromosome 21 rearrangements. Importantly, we observed acrocentric satellite DNA at several breakpoint junctions suggesting an important role for those elements in the formation of complex SVs.\n\nTaken together, our results provide further insights into the architecture and underlying mechanisms of complex rearrangements on acrocentric chromosomes.", "doi": "10.1016/j.gimo.2024.101863", "pmid": "39669604", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11613786"}, {"db": "pii", "key": "S2949-7744(24)01009-4"}], "notes": [], "created": "2024-08-02T12:03:46.047Z", "modified": "2025-12-04T19:37:09.934Z"}, {"entity": "publication", "iuid": "106fa6369b824a5fa743a8aa918a5652", "links": {"self": {"href": "https://publications.scilifelab.se/publication/106fa6369b824a5fa743a8aa918a5652.json"}, "display": {"href": "https://publications.scilifelab.se/publication/106fa6369b824a5fa743a8aa918a5652"}}, "title": "Climate change induces shifts in coastal Baltic Sea surface water microorganism stress and photosynthesis gene expression.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K"}, {"family": "Forsman", "given": "Anders", "initials": "A"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2024-06-07", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "15", "pages": "1393538", "issn-l": "1664-302X"}, "abstract": "The world's oceans are challenged by climate change linked warming with typically highly populated coastal areas being particularly susceptible to these effects. Many studies of climate change on the marine environment use large, short-term temperature manipulations that neglect factors such as long-term adaptation and seasonal cycles. In this study, a Baltic Sea 'heated' bay influenced by thermal discharge since the 1970s from a nuclear reactor (in relation to an unaffected nearby 'control' bay) was used to investigate how elevated temperature impacts surface water microbial communities and activities. 16S rRNA gene amplicon based microbial diversity and population structure showed no difference in alpha diversity in surface water microbial communities, while the beta diversity showed a dissimilarity between the bays. Amplicon sequencing variant relative abundances between the bays showed statistically higher values for, e.g., Ilumatobacteraceae and Burkholderiaceae in the heated and control bays, respectively. RNA transcript-derived activities followed a similar pattern in alpha and beta diversity with no effect on Shannon's H diversity but a significant difference in the beta diversity between the bays. The RNA data further showed more elevated transcript counts assigned to stress related genes in the heated bay that included heat shock protein genes dnaKJ, the co-chaperonin groS, and the nucleotide exchange factor heat shock protein grpE. The RNA data also showed elevated oxidative phosphorylation transcripts in the heated (e.g., atpHG) compared to control (e.g., atpAEFB) bay. Furthermore, genes related to photosynthesis had generally higher transcript numbers in the control bay, such as photosystem I (psaAC) and II genes (psbABCEH). These increased stress gene responses in the heated bay will likely have additional cascading effects on marine carbon cycling and ecosystem services.", "doi": "10.3389/fmicb.2024.1393538", "pmid": "38912348", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11190084"}], "notes": [], "created": "2024-08-15T12:10:01.944Z", "modified": "2024-11-25T10:33:14.816Z"}, {"entity": "publication", "iuid": "df880e2368024d3186c599e61cf01f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df880e2368024d3186c599e61cf01f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df880e2368024d3186c599e61cf01f8a"}}, "title": "ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers.", "authors": [{"family": "Zhang", "given": "Yi", "initials": "Y"}, {"family": "Xie", "given": "Guojia", "initials": "G", "orcid": "0000-0002-8250-6157", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec90bde6e0a474f927615602734cd4c.json"}}, {"family": "Lee", "given": "Ji-Eun", "initials": "JE", "orcid": "0000-0002-3768-7016", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b9ee3b2ab77440c80566ad35fc02924.json"}}, {"family": "Zandian", "given": "Mohamad", "initials": "M", "orcid": "0000-0002-4967-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f81558cc5d546f0bbb8b9db1456bc14.json"}}, {"family": "Sudarshan", "given": "Deepthi", "initials": "D"}, {"family": "Estavoyer", "given": "Benjamin", "initials": "B"}, {"family": "Benz", "given": "Caroline", "initials": "C", "orcid": "0000-0002-5166-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/86628e15252f4dd98f08759d59fad848.json"}}, {"family": "Viita", "given": "Tiina", "initials": "T"}, {"family": "Asgaritarghi", "given": "Golareh", "initials": "G"}, {"family": "Lachance", "given": "Catherine", "initials": "C"}, {"family": "Messmer", "given": "Cl\u00e9mence", "initials": "C"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Sinha", "given": "Vikrant Kumar", "initials": "VK"}, {"family": "Lambert", "given": "Jean-Philippe", "initials": "JP", "orcid": "0000-0002-0833-1221", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea53138c672d469295549d26672f2e26.json"}}, {"family": "Chen", "given": "Yu-Wen", "initials": "YW"}, {"family": "Wang", "given": "Shu-Ping", "initials": "SP", "orcid": "0000-0002-5895-1269", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd9023a2623140319f7e298758b186e1.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}, {"family": "Affar", "given": "El Bachir", "initials": "EB", "orcid": "0000-0002-6374-3683", "researcher": {"href": "https://publications.scilifelab.se/researcher/1acebd04acd94e199bebe57a10db34ff.json"}}, {"family": "C\u00f4t\u00e9", "given": "Jacques", "initials": "J", "orcid": "0000-0001-6751-555X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4db696aa49342a0b1d9c0efb38c899c.json"}}, {"family": "Ge", "given": "Kai", "initials": "K"}, {"family": "Kutateladze", "given": "Tatiana G", "initials": "TG", "orcid": "0000-0001-7375-6990", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f6b888607504d27b88684a37f4087b9.json"}}], "type": "journal article", "published": "2024-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "4883", "issn-l": "2041-1723"}, "abstract": "The human methyltransferase and transcriptional coactivator MLL4 and its paralog MLL3 are frequently mutated in cancer. MLL4 and MLL3 monomethylate histone H3K4 and contain a set of uncharacterized PHD fingers. Here, we report a novel function of the PHD2 and PHD3 (PHD2/3) fingers of MLL4 and MLL3 that bind to ASXL2, a component of the Polycomb repressive H2AK119 deubiquitinase (PR-DUB) complex. The structure of MLL4 PHD2/3 in complex with the MLL-binding helix (MBH) of ASXL2 and mutational analyses reveal the molecular mechanism which is conserved in homologous ASXL1 and ASXL3. The native interaction of the Trithorax MLL3/4 complexes with the PR-DUB complex in vivo depends solely on MBH of ASXL1/2, coupling the two histone modifying activities. ChIP-seq analysis in embryonic stem cells demonstrates that MBH of ASXL1/2 is required for the deubiquitinase BAP1 recruitment to MLL4-bound active enhancers. Our findings suggest an ASXL1/2-dependent functional link between the MLL3/4 and PR-DUB complexes.", "doi": "10.1038/s41467-024-49391-x", "pmid": "38849395", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11161652"}, {"db": "pii", "key": "10.1038/s41467-024-49391-x"}], "notes": [], "created": "2024-08-15T12:13:00.466Z", "modified": "2024-10-01T09:33:16.920Z"}, {"entity": "publication", "iuid": "791e1f95c2e443d09b14d0136e94cb09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/791e1f95c2e443d09b14d0136e94cb09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/791e1f95c2e443d09b14d0136e94cb09"}}, "title": "MLL4 binds TET3.", "authors": [{"family": "Becht", "given": "Dustin C", "initials": "DC"}, {"family": "Mohid", "given": "Sk Abdul", "initials": "SA"}, {"family": "Lee", "given": "Ji-Eun", "initials": "JE"}, {"family": "Zandian", "given": "Mohamad", "initials": "M"}, {"family": "Benz", "given": "Caroline", "initials": "C"}, {"family": "Biswas", "given": "Soumi", "initials": "S"}, {"family": "Sinha", "given": "Vikrant Kumar", "initials": "VK"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}, {"family": "Ge", "given": "Kai", "initials": "K"}, {"family": "Zhang", "given": "Yi", "initials": "Y"}, {"family": "Kutateladze", "given": "Tatiana G", "initials": "TG"}], "type": "journal article", "published": "2024-06-06", "journal": {"title": "Structure", "issn": "1878-4186", "volume": "32", "issue": "6", "pages": "706-714.e3", "issn-l": "0969-2126"}, "abstract": "Human mixed lineage leukemia 4 (MLL4), also known as KMT2D, regulates cell type specific transcriptional programs through enhancer activation. Along with the catalytic methyltransferase domain, MLL4 contains seven less characterized plant homeodomain (PHD) fingers. Here, we report that the sixth PHD finger of MLL4 (MLL4PHD6) binds to the hydrophobic motif of ten-eleven translocation 3 (TET3), a dioxygenase that converts methylated cytosine into oxidized derivatives. The solution NMR structure of the TET3-MLL4PHD6 complex and binding assays show that, like histone H4 tail, TET3 occupies the hydrophobic site of MLL4PHD6, and that this interaction is conserved in the seventh PHD finger of homologous MLL3 (MLL3PHD7). Analysis of genomic localization of endogenous MLL4 and ectopically expressed TET3 in mouse embryonic stem cells reveals a high degree overlap on active enhancers and suggests a potential functional relationship of MLL4 and TET3.", "doi": "10.1016/j.str.2024.03.005", "pmid": "38579707", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1979275"}, {"db": "pmc", "key": "PMC11162309"}, {"db": "pii", "key": "S0969-2126(24)00087-X"}], "notes": [], "created": "2024-04-26T08:54:40.761Z", "modified": "2025-02-28T14:13:04.213Z"}, {"entity": "publication", "iuid": "df8fde700de34a3aaee98c266abd7265", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df8fde700de34a3aaee98c266abd7265.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df8fde700de34a3aaee98c266abd7265"}}, "title": "Spatial Transcriptomics in a Case of Follicular Thyroid Carcinoma Reveals Clone-Specific Dysregulation of Genes Regulating Extracellular Matrix in the Invading Front.", "authors": [{"family": "Condello", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4569-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/09be613118f743bd992bba237b61ceb4.json"}}, {"family": "Paulsson", "given": "Johan O", "initials": "JO", "orcid": "0000-0003-0390-6740", "researcher": {"href": "https://publications.scilifelab.se/researcher/762d22bad5b7462dbba2a87c9b3221a0.json"}}, {"family": "Zedenius", "given": "Jan", "initials": "J", "orcid": "0000-0003-2833-3758", "researcher": {"href": "https://publications.scilifelab.se/researcher/319fe27b84674ea3829d2e0c0e0ab966.json"}}, {"family": "N\u00e4sman", "given": "Anders", "initials": "A", "orcid": "0000-0003-4602-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/368352486dc54915b6873ad1aae59ea2.json"}}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Endocr. Pathol.", "issn": "1559-0097", "volume": "35", "issue": "2", "pages": "122-133", "issn-l": "1046-3976"}, "abstract": "Follicular thyroid carcinoma (FTC) is recognized by its ability to invade the tumor capsule and blood vessels, although the exact molecular signals orchestrating this phenotype remain elusive. In this study, the spatial transcriptional landscape of an FTC is detailed with comparisons between the invasive front and histologically indolent central core tumor areas. The Visium spatial gene expression platform allowed us to interrogate and visualize the whole transcriptome in 2D across formalin-fixated paraffin-embedded (FFPE) tissue sections. Four different 6 \u00d7 6 mm areas of an FTC were scrutinized, including regions with capsular and vascular invasion, capsule-near area without invasion, and a central core area of the tumor. Following successful capturing and sequencing, several expressional clusters were identified with regional variation. Most notably, invasive tumor cell clusters were significantly over-expressing genes associated with pathways interacting with the extracellular matrix (ECM) remodeling and epithelial-to-mesenchymal transition (EMT). Subsets of these genes (POSTN and DPYSL3) were additionally validated using immunohistochemistry in an independent cohort of follicular thyroid tumors showing a clear gradient pattern from the core to the periphery of the tumor. Moreover, the reconstruction of the evolutionary tree identified the invasive clones as late events in follicular thyroid tumorigenesis. To our knowledge, this is one of the first 2D global transcriptional mappings of FTC using this platform to date. Invasive FTC clones develop in a stepwise fashion and display significant dysregulation of genes associated with the ECM and EMT - thus highlighting important molecular crosstalk for further investigations.", "doi": "10.1007/s12022-024-09798-0", "pmid": "38280140", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Spatial omics": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11176252"}, {"db": "pii", "key": "10.1007/s12022-024-09798-0"}], "notes": [], "created": "2024-02-13T07:46:50.221Z", "modified": "2024-11-25T10:11:30.955Z"}, {"entity": "publication", "iuid": "5eb6b1800bd74ca9b4bb50dc8675adab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eb6b1800bd74ca9b4bb50dc8675adab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eb6b1800bd74ca9b4bb50dc8675adab"}}, "title": "Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees.", "authors": [{"family": "L\u00e4hteenaro", "given": "Meri", "initials": "M"}, {"family": "Benda", "given": "Daniel", "initials": "D"}, {"family": "Straka", "given": "Jakub", "initials": "J"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "pages": "108068", "volume": "195", "issn-l": "1055-7903"}, "abstract": "Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.", "doi": "10.1016/j.ympev.2024.108068", "pmid": "38554985", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(24)00060-5"}], "notes": [], "created": "2024-04-09T12:37:01.446Z", "modified": "2025-02-28T14:13:39.851Z"}, {"entity": "publication", "iuid": "ad7858d5972e4eebb3327e5c45183267", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad7858d5972e4eebb3327e5c45183267.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad7858d5972e4eebb3327e5c45183267"}}, "title": "Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support.", "authors": [{"family": "Amoedo-Leite", "given": "Catarina", "initials": "C", "orcid": "0000-0002-7556-4826", "researcher": {"href": "https://publications.scilifelab.se/researcher/09c63612668841df817c18ab93d6f4e4.json"}}, {"family": "Parv", "given": "Kristel", "initials": "K"}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Herrera-Hidalgo", "given": "Carmen", "initials": "C"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Giraud", "given": "Antoine", "initials": "A", "orcid": "0000-0002-8559-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0d7d5e9c90a4dc8b798c366ce4aa6a7.json"}}, {"family": "Malaquias", "given": "Marta", "initials": "M"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Holl", "given": "Daniel", "initials": "D"}, {"family": "Seignez", "given": "Cedric", "initials": "C"}, {"family": "G\u00f6ritz", "given": "Christian", "initials": "C", "orcid": "0000-0003-0799-766X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3358941841740db8d22fd49e14bdea2.json"}}, {"family": "Christoffersson", "given": "Gustaf", "initials": "G"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "3", "issue": "6", "pages": "685-700", "issn-l": null}, "abstract": "Sterile inflammation after injury is important for tissue restoration. In injured human and mouse tissues, macrophages were recently found to accumulate perivascularly. This study investigates if macrophages adopt a mural cell phenotype important for restoration after ischemic injury. Single-cell RNA sequencing of fate-mapped macrophages from ischemic mouse muscles demonstrates a macrophage-toward-mural cell switch of a subpopulation of macrophages with downregulated myeloid cell genes and upregulated mural cell genes, including PDGFR\u03b2. This observation was further strengthened when including unspliced transcripts in the analysis. The macrophage switch was proven functionally relevant, as induction of macrophage-specific PDGFR\u03b2 deficiency prevented their perivascular macrophage phenotype, impaired vessel maturation and increased vessel leakiness, which ultimately reduced limb function. In conclusion, macrophages in adult ischemic tissue were demonstrated to undergo a cellular program to morphologically, transcriptomically and functionally resemble mural cells while weakening their macrophage identity. The macrophage-to-mural cell-like phenotypic switch is crucial for restoring tissue function and warrants further exploration as a potential target for immunotherapies to enhance healing.", "doi": "10.1038/s44161-024-00478-0", "pmid": "39196227", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11358018"}, {"db": "pii", "key": "10.1038/s44161-024-00478-0"}], "notes": [], "created": "2024-10-16T12:27:59.619Z", "modified": "2024-11-12T20:14:44.444Z"}, {"entity": "publication", "iuid": "af19706f7c38424598b494c199cfa069", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af19706f7c38424598b494c199cfa069.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af19706f7c38424598b494c199cfa069"}}, "title": "Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).", "authors": [{"family": "M\u00fcller", "given": "Ingo A", "initials": "IA", "orcid": "0000-0002-8812-9313", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a64e79dc2214694b6fe09447161d115.json"}}, {"family": "Th\u00f6rn", "given": "Filip", "initials": "F", "orcid": "0000-0002-8173-7877", "researcher": {"href": "https://publications.scilifelab.se/researcher/e272339ca04d4daf935b708b04c5c53e.json"}}, {"family": "Rajan", "given": "Samyuktha", "initials": "S"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Dumbacher", "given": "John P", "initials": "JP", "orcid": "0000-0001-8942-1554", "researcher": {"href": "https://publications.scilifelab.se/researcher/6221be035944462989353d66f126a5c5.json"}}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2024-05-23", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "5", "pages": "e0293715", "issn-l": "1932-6203"}, "abstract": "The family Melampittidae is endemic to New Guinea and consists of two monotypic genera: Melampitta lugubris (Lesser Melampitta) and Megalampitta gigantea (Greater Melampitta). Both Melampitta species have scattered and disconnected distributions across New Guinea in the central mountain range and in some of the outlying ranges. While M. lugubris is common and found in most montane regions of the island, M. gigantaea is elusive and known from only six localities in isolated pockets on New Guinea with very specific habitats of limestone and sinkholes. In this project, we apply museomics to determine the population structure and demographic history of these two species. We re-sequenced the genomes of all seven known M. gigantaea samples housed in museum collections as well as 24 M. lugubris samples from across its distribution. By comparing population structure between the two species, we investigate to what extent habitat dependence, such as in M. gigantaea, may affect population connectivity. Phylogenetic and population genomic analyses, as well as acoustic variation revealed that M. gigantaea consists of a single population in contrast to M. lugubris that shows much stronger population structure across the island. We suggest a recent collapse of M. gigantaea into its fragmented habitats as an explanation to its unexpected low diversity and lack of population structure. The deep genetic divergences between the M. lugubris populations on the Vogelkop region, in the western central range and the eastern central range, respectively, suggests that these three populations should be elevated to full species level. This work sheds new light on the mechanisms that have shaped the intriguing distribution of the two species within this family and is a prime example of the importance of museum collections for genomic studies of poorly known and rare species.", "doi": "10.1371/journal.pone.0293715", "pmid": "38781204", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11115331"}, {"db": "pii", "key": "PONE-D-23-33496"}], "notes": [], "created": "2024-06-03T08:57:15.775Z", "modified": "2024-11-25T10:31:56.366Z"}, {"entity": "publication", "iuid": "f6948a9aff764db1be4bc43190fb3fa6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6948a9aff764db1be4bc43190fb3fa6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6948a9aff764db1be4bc43190fb3fa6"}}, "title": "Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae.", "authors": [{"family": "Thureborn", "given": "Olle", "initials": "O", "orcid": "0000-0002-9609-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e3d14e6d70a454babea2bbc6e0f9fc2.json"}}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG"}, {"family": "Rydin", "given": "Catarina", "initials": "C", "orcid": "0000-0002-3347-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/70fff179e5b549c182dd7929b20f2e22.json"}}], "type": "journal article", "published": "2024-05-20", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "5", "pages": "e0302365", "issn-l": "1932-6203"}, "abstract": "In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.", "doi": "10.1371/journal.pone.0302365", "pmid": "38768140", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11104678"}, {"db": "pii", "key": "PONE-D-23-18658"}], "notes": [], "created": "2024-06-03T08:56:47.806Z", "modified": "2024-10-01T09:26:05.774Z"}, {"entity": "publication", "iuid": "9aa0722104fb4d088f7b2eed26775252", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9aa0722104fb4d088f7b2eed26775252.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9aa0722104fb4d088f7b2eed26775252"}}, "title": "Defining the contribution of Troy-positive progenitor cells to the mouse esophageal epithelium.", "authors": [{"family": "Grommisch", "given": "David", "initials": "D"}, {"family": "Wang", "given": "Menghan", "initials": "M"}, {"family": "Eenjes", "given": "Evelien", "initials": "E"}, {"family": "Svetli\u010di\u010d", "given": "Maja", "initials": "M"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Giselsson", "given": "Pontus", "initials": "P"}, {"family": "Genander", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2024-05-20", "journal": {"title": "Dev. Cell", "issn": "1878-1551", "volume": "59", "issue": "10", "pages": "1269-1283.e6", "issn-l": "1534-5807"}, "abstract": "Progenitor cells adapt their behavior in response to tissue demands. However, the molecular mechanisms controlling esophageal progenitor decisions remain largely unknown. Here, we demonstrate the presence of a Troy (Tnfrsf19)-expressing progenitor subpopulation localized to defined regions along the mouse esophageal axis. Lineage tracing and mathematical modeling demonstrate that Troy-positive progenitor cells are prone to undergoing symmetrical fate choices and contribute to esophageal tissue homeostasis long term. Functionally, TROY inhibits progenitor proliferation and enables commitment to differentiation without affecting fate symmetry. Whereas Troy expression is stable during esophageal homeostasis, progenitor cells downregulate Troy in response to tissue stress, enabling proliferative expansion of basal cells refractory to differentiation and reestablishment of tissue homeostasis. Our results demonstrate functional, spatially restricted progenitor heterogeneity in the esophageal epithelium and identify how dynamic regulation of Troy coordinates tissue generation.", "doi": "10.1016/j.devcel.2024.03.011", "pmid": "38565145", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1534-5807(24)00179-5"}], "notes": [], "created": "2024-05-17T09:35:53.304Z", "modified": "2024-11-25T10:12:43.181Z"}, {"entity": "publication", "iuid": "39209205f30a4c179c78c4423bb1e8b3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39209205f30a4c179c78c4423bb1e8b3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39209205f30a4c179c78c4423bb1e8b3"}}, "title": "The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.", "authors": [{"family": "Shi", "given": "Tingting", "initials": "T"}, {"family": "Zhang", "given": "Xinxin", "initials": "X"}, {"family": "Hou", "given": "Yukang", "initials": "Y"}, {"family": "Jia", "given": "Changfu", "initials": "C"}, {"family": "Dan", "given": "Xuming", "initials": "X"}, {"family": "Zhang", "given": "Yulin", "initials": "Y"}, {"family": "Jiang", "given": "Yuanzhong", "initials": "Y"}, {"family": "Lai", "given": "Qiang", "initials": "Q"}, {"family": "Feng", "given": "Jiajun", "initials": "J"}, {"family": "Feng", "given": "Jianju", "initials": "J"}, {"family": "Ma", "given": "Tao", "initials": "T"}, {"family": "Wu", "given": "Jiali", "initials": "J"}, {"family": "Liu", "given": "Shuyu", "initials": "S"}, {"family": "Zhang", "given": "Lei", "initials": "L"}, {"family": "Long", "given": "Zhiqin", "initials": "Z"}, {"family": "Chen", "given": "Liyang", "initials": "L"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Liu", "given": "Jianquan", "initials": "J"}, {"family": "Yin", "given": "Tongming", "initials": "T"}, {"family": "Wang", "given": "Jing", "initials": "J"}], "type": "journal article", "published": "2024-05-06", "journal": {"title": "Mol Plant", "issn": "1752-9867", "volume": "17", "issue": "5", "pages": "725-746", "issn-l": "1674-2052"}, "abstract": "Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a \u223c180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.", "doi": "10.1016/j.molp.2024.03.009", "pmid": "38486452", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "NGI Long read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1674-2052(24)00082-0"}], "notes": [], "created": "2024-03-18T10:01:57.998Z", "modified": "2024-11-25T10:14:12.283Z"}, {"entity": "publication", "iuid": "d70c892fb4af4fec96853063421e84dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d70c892fb4af4fec96853063421e84dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d70c892fb4af4fec96853063421e84dd"}}, "title": "Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.", "authors": [{"family": "Hempel", "given": "Elisabeth", "initials": "E"}, {"family": "Faith", "given": "J Tyler", "initials": "JT"}, {"family": "Preick", "given": "Michaela", "initials": "M"}, {"family": "de Jager", "given": "Deon", "initials": "D"}, {"family": "Barish", "given": "Scott", "initials": "S"}, {"family": "Hartmann", "given": "Stefanie", "initials": "S"}, {"family": "Grau", "given": "Jos\u00e9 H", "initials": "JH"}, {"family": "Moodley", "given": "Yoshan", "initials": "Y"}, {"family": "Gedman", "given": "Gregory", "initials": "G"}, {"family": "Pirovich", "given": "Kathleen Morrill", "initials": "KM"}, {"family": "Bibi", "given": "Faysal", "initials": "F"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC"}, {"family": "Bocklandt", "given": "Sven", "initials": "S"}, {"family": "Lamm", "given": "Ben", "initials": "B"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Westbury", "given": "Michael V", "initials": "MV"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2024-05-06", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "34", "issue": "9", "pages": "2020-2029.e6", "issn-l": "0960-9822"}, "abstract": "Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40\u00d7 nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in \u223cAD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (\u223c1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.", "doi": "10.1016/j.cub.2024.03.051", "pmid": "38614080", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(24)00391-9"}], "notes": [], "created": "2024-04-26T08:52:40.448Z", "modified": "2024-05-17T09:18:01.355Z"}, {"entity": "publication", "iuid": "9d8403031dd949b29cea344fe53b98ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d8403031dd949b29cea344fe53b98ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d8403031dd949b29cea344fe53b98ca"}}, "title": "Meiotic drive against chromosome fusions in butterfly hybrids.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2024-05-04", "journal": {"title": "Chromosome Res.", "issn": "1573-6849", "volume": "32", "issue": "2", "pages": "7", "issn-l": "0967-3849"}, "abstract": "Species frequently differ in the number and structure of chromosomes they harbor, but individuals that are heterozygous for chromosomal rearrangements may suffer from reduced fitness. Chromosomal rearrangements like fissions and fusions can hence serve as a mechanism for speciation between incipient lineages, but their evolution poses a paradox. How can rearrangements get fixed between populations if heterozygotes have reduced fitness? One solution is that this process predominantly occurs in small and isolated populations, where genetic drift can override natural selection. However, fixation is also more likely if a novel rearrangement is favored by a transmission bias, such as meiotic drive. Here, we investigate chromosomal transmission distortion in hybrids between two wood white (Leptidea sinapis) butterfly populations with extensive karyotype differences. Using data from two different crossing experiments, we uncover that there is a transmission bias favoring the ancestral chromosomal state for derived fusions, a result that shows that chromosome fusions actually can fix in populations despite being counteracted by meiotic drive. This means that meiotic drive not only can promote runaway chromosome number evolution and speciation, but also that it can be a conservative force acting against karyotypic change and the evolution of reproductive isolation. Based on our results, we suggest a mechanistic model for why chromosome fusion mutations may be opposed by meiotic drive and discuss factors contributing to karyotype evolution in Lepidoptera.", "doi": "10.1007/s10577-024-09752-0", "pmid": "38702576", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11068667"}, {"db": "pii", "key": "10.1007/s10577-024-09752-0"}], "notes": [], "created": "2024-05-17T09:15:49.658Z", "modified": "2025-02-28T14:10:59.014Z"}, {"entity": "publication", "iuid": "c0da1688f3a74822ac6329a2a61bbfdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0da1688f3a74822ac6329a2a61bbfdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0da1688f3a74822ac6329a2a61bbfdb"}}, "title": "Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Zervakis", "given": "Panagiotis-Ioannis", "initials": "P"}, {"family": "Postel", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0003-0502-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0481ff1051564262af4e5384cbd17ac3.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Losvik", "given": "Aleksandra", "initials": "A"}, {"family": "Mehrabi", "given": "Sara", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Hughes", "given": "P William", "initials": "PW"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Abdelaziz", "given": "Mohamed", "initials": "M"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Arroyo", "given": "Juan", "initials": "J"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2024-05-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "41", "issue": "5", "pages": null}, "abstract": "Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.", "doi": "10.1093/molbev/msae087", "pmid": "38709782", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11114476"}, {"db": "pii", "key": "7665594"}], "notes": [], "created": "2024-05-17T09:14:33.893Z", "modified": "2024-11-15T11:28:42.391Z"}, {"entity": "publication", "iuid": "dceccccd7b74440b9e8f1acfe66fa9a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dceccccd7b74440b9e8f1acfe66fa9a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dceccccd7b74440b9e8f1acfe66fa9a7"}}, "title": "Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque.", "authors": [{"family": "Castro Dopico", "given": "Xaquin", "initials": "X", "orcid": "0000-0002-9005-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1d266d61654951a684193993ca53b1.json"}}, {"family": "Guryleva", "given": "Mariia", "initials": "M", "orcid": "0009-0004-6370-7510", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e8d6837c5fa48e99698c9f465ae1412.json"}}, {"family": "Mandolesi", "given": "Marco", "initials": "M", "orcid": "0000-0003-2927-7831", "researcher": {"href": "https://publications.scilifelab.se/researcher/29e6c31be1704c97a2853aca0833f6b0.json"}}, {"family": "Corcoran", "given": "Martin", "initials": "M", "orcid": "0000-0002-2774-0936", "researcher": {"href": "https://publications.scilifelab.se/researcher/7177b777948c4efa882ffef30764e223.json"}}, {"family": "Coquet", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0002-5967-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b74959951024d6ea9712b55f115652e.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB", "orcid": "0000-0001-7255-9047", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad611ac9c76e44989e585edc4d7ff713.json"}}], "type": "journal article", "published": "2024-05-02", "journal": {"title": "Clin Transl Immunology", "issn": "2050-0068", "volume": "13", "issue": "5", "pages": "e1508", "issn-l": null}, "abstract": "The caecum bridges the small and large intestine and plays a front-line role in discriminating gastrointestinal antigens. Although dysregulated in acute and chronic conditions, the tissue is often overlooked immunologically.\n\nTo address this issue, we applied single-cell transcriptomic-V(D)J sequencing to FACS-isolated CD45+ caecal patch/lamina propria leukocytes from a healthy (5-year-old) female rhesus macaque ex vivo and coupled these data to VDJ deep sequencing reads from haematopoietic tissues.\n\nWe found caecal NK cells and ILC3s to co-exist with a spectrum of effector T cells partially derived from SOX4 + recent thymic emigrants. Tolerogenic V\u03b38V\u03b41-T cells, plastic CD4+ T helper cells and GZMK + EOMES + and TMIGD2 + tissue-resident memory CD8+ T cells were present and differed metabolically. An IL13 + GATA3 + Th2 subset expressing eicosanoid pathway enzymes was accompanied by IL1RL1 + GATA3 + regulatory T cells and a minor proportion of IgE+ plasma cells (PCs), illustrating tightly regulated type 2 immunity devoid of ILC2s. In terms of B lymphocyte lineages, caecal patch antigen-presenting memory B cells sat alongside germinal centre cells undergoing somatic hypermutation and differentiation into IGF1 + PCs. Prototypic gene expression signatures decreased across PC clusters, and notably, expanded IgA clonotypes could be traced in VDJ deep sequencing reads from additional compartments, including the bone marrow, supporting that these cells contribute a steady stream of systemic antibodies.\n\nThe data advance our understanding of caecal immunological function, revealing processes involved in barrier maintenance and molecular networks relevant to disease.", "doi": "10.1002/cti2.1508", "pmid": "38707998", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11063928"}, {"db": "pii", "key": "CTI21508"}], "notes": [], "created": "2024-10-14T13:07:00.500Z", "modified": "2025-02-28T14:09:49.646Z"}, {"entity": "publication", "iuid": "5f59c6ab918f4a4f90bbc3fd52f5804d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f59c6ab918f4a4f90bbc3fd52f5804d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f59c6ab918f4a4f90bbc3fd52f5804d"}}, "title": "Male-transmitted transgenerational effects of the herbicide linuron on DNA methylation profiles in Xenopus tropicalis brain and testis.", "authors": [{"family": "Roza", "given": "Mauricio", "initials": "M"}, {"family": "Eriksson", "given": "Andreas N M", "initials": "ANM"}, {"family": "Svanholm", "given": "Sofie", "initials": "S"}, {"family": "Berg", "given": "Cecilia", "initials": "C"}, {"family": "Karlsson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2024-05-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "923", "pages": "170949", "issn-l": "0048-9697"}, "abstract": "The herbicide linuron can cause endocrine disrupting effects in Xenopus tropicalis frogs, including offspring that were never exposed to the contaminant. The mechanisms by which these effects are transmitted across generations need to be further investigated. Here, we examined transgenerational alterations of brain and testis DNA methylation profiles paternally inherited from grandfathers developmentally exposed to an environmentally relevant concentration of linuron. Reduced representation bisulfite sequencing (RRBS) revealed numerous differentially methylated regions (DMRs) in brain (3060 DMRs) and testis (2551 DMRs) of the adult male F2 generation. Key genes in the brain involved in somatotropic (igfbp4) and thyrotropic signaling (dio1 and tg) were differentially methylated and correlated with phenotypical alterations in body size, weight, hind limb length and plasma glucose levels, indicating that these methylation changes could be potential mediators of the transgenerational effects of linuron. Testis DMRs were found in genes essential for spermatogenesis, meiosis and germ cell development (piwil1, spo11 and tdrd9) and their methylation levels were correlated with the number of germ cells nests per seminiferous tubule, an endpoint of disrupted spermatogenesis. DMRs were also identified in several genes central for the machinery that regulates the epigenetic landscape including DNA methylation (dnmt3a and mbd2) and histone acetylation (hdac8, ep300, elp3, kat5 and kat14), which may at least partly drive the linuron-induced transgenerational effects. The results from this genome-wide DNA methylation profiling contribute to better understanding of potential transgenerational epigenetic inheritance mechanisms in amphibians.", "doi": "10.1016/j.scitotenv.2024.170949", "pmid": "38365020", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)01088-X"}], "notes": [], "created": "2024-03-14T11:04:40.191Z", "modified": "2025-02-28T14:12:48.896Z"}, {"entity": "publication", "iuid": "33f0eb0f11f04f6e97e94329b239557e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f0eb0f11f04f6e97e94329b239557e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f0eb0f11f04f6e97e94329b239557e"}}, "title": "Chromatin accessibility during human first-trimester neurodevelopment.", "authors": [{"family": "Mannens", "given": "Camiel C A", "initials": "CCA", "orcid": "0000-0002-1318-2603", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8d4a5ffd743424fab0d3798a8778715.json"}}, {"family": "Hu", "given": "Lijuan", "initials": "L", "orcid": "0000-0003-1869-0372", "researcher": {"href": "https://publications.scilifelab.se/researcher/49a35358ad6e4b5eaec60d97504102ae.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Schipper", "given": "Marijn", "initials": "M", "orcid": "0000-0002-5170-2796", "researcher": {"href": "https://publications.scilifelab.se/researcher/458e0ee2185d4473bd9bbdd5a9f48e25.json"}}, {"family": "Reagor", "given": "Caleb C", "initials": "CC", "orcid": "0000-0002-8304-1267", "researcher": {"href": "https://publications.scilifelab.se/researcher/981d5cb61a7946f6843e4270576993e9.json"}}, {"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "He", "given": "Xiaoling", "initials": "X", "orcid": "0009-0004-1002-8418", "researcher": {"href": "https://publications.scilifelab.se/researcher/aef7b6a77efd410bb696cf988926f4c4.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}, {"family": "Posthuma", "given": "Danielle", "initials": "D", "orcid": "0000-0001-7582-2365", "researcher": {"href": "https://publications.scilifelab.se/researcher/406e98180d174e8ca087f50074c025c9.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}], "type": "journal article", "published": "2024-05-01", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836"}, "abstract": "The human brain develops through a tightly organized cascade of patterning events, induced by transcription factor expression and changes in chromatin accessibility. Although gene expression across the developing brain has been described at single-cell resolution1, similar atlases of chromatin accessibility have been primarily focused on the forebrain2-4. Here we describe chromatin accessibility and paired gene expression across the entire developing human brain during the first trimester (6-13 weeks after conception). We defined 135 clusters and used multiomic measurements to link candidate cis-regulatory elements to gene expression. The number of accessible regions increased both with age and along neuronal differentiation. Using a convolutional neural network, we identified putative functional transcription factor-binding sites in enhancers characterizing neuronal subtypes. We applied this model to cis-regulatory elements linked to ESRRB to elucidate its activation mechanism in the Purkinje cell lineage. Finally, by linking disease-associated single nucleotide polymorphisms to cis-regulatory elements, we validated putative pathogenic mechanisms in several diseases and identified midbrain-derived GABAergic neurons as being the most vulnerable to major depressive disorder-related mutations. Our findings provide a more detailed view of key gene regulatory mechanisms underlying the emergence of brain cell types during the first trimester and a comprehensive reference for future studies related to human neurodevelopment.", "doi": "10.1038/s41586-024-07234-1", "pmid": "38693260", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-024-07234-1"}], "notes": [], "created": "2024-05-17T09:16:14.715Z", "modified": "2024-05-17T09:16:15.854Z"}, {"entity": "publication", "iuid": "76cdc855f0d04222a6710b42396306db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/76cdc855f0d04222a6710b42396306db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/76cdc855f0d04222a6710b42396306db"}}, "title": "Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting.", "authors": [{"family": "Westenius", "given": "E", "initials": "E", "orcid": "0000-0001-7674-8101", "researcher": {"href": "https://publications.scilifelab.se/researcher/713cc4b0c1044218a26803fefb43522f.json"}}, {"family": "Conner", "given": "P", "initials": "P"}, {"family": "Pettersson", "given": "M", "initials": "M"}, {"family": "Sahlin", "given": "E", "initials": "E"}, {"family": "Papadogiannakis", "given": "N", "initials": "N"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Iwarsson", "given": "E", "initials": "E", "orcid": "0000-0002-3827-0263", "researcher": {"href": "https://publications.scilifelab.se/researcher/d626860f8ce14c6eaa79f9d1b7d76c0b.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Ultrasound Obstet Gynecol", "issn": "1469-0705", "volume": "63", "issue": "5", "pages": "658-663", "issn-l": null}, "abstract": "To investigate the diagnostic yield of trio whole-genome sequencing (WGS) in fetuses with various congenital malformations referred to a tertiary center for prenatal diagnosis.\n\nIn this prospective study, 50 pregnancies with different congenital malformations, negative for trisomies and causative copy-number variants, were analyzed further with fetal-parental trio WGS analysis. Parents were eligible for inclusion if they accepted further investigation following the detection of isolated or multiple malformations on prenatal ultrasound. Cases with isolated increased nuchal translucency, gamete donation or multiple pregnancy were excluded. WGS with the Illumina Inc. 30\u00d7 polymerase-chain-reaction-free short-read sequencing included analysis of single-nucleotide variants, insertions and deletions, structural variants, short tandem repeats and copy-number identification of SMN1 and SMN2 genes.\n\nA molecular diagnosis was achieved in 13/50 (26%) cases. Causative sequence variants were identified in 12 genes: FGFR3 (n = 2), ACTA1 (n = 1), CDH2 (n = 1), COL1A2 (n = 1), DHCR7 (n = 1), EYA1 (n = 1), FBXO11 (n = 1), FRAS1 (n = 1), L1CAM (n = 1), OFD1 (n = 1), PDHA1 (n = 1) and SOX9 (n = 1). The phenotypes of the cases were divided into different groups, with the following diagnostic yields: skeletal malformation (4/9 (44%)), multisystem malformation (3/7 (43%)), central nervous system malformation (5/15 (33%)) and thoracic malformation (1/10 (10%)). Additionally, two cases carried variants that were considered potentially clinically relevant, even though they were assessed as variants of uncertain significance, according to the guidelines provided by the American College of Medical Genetics and Genomics. Overall, we identified a causative or potentially clinically relevant variant in 15/50 (30%) cases.\n\nWe demonstrate a diagnostic yield of 26% with clinical WGS in prenatally detected congenital malformations. This study emphasizes the benefits that WGS can bring to the diagnosis of fetal structural anomalies. It is important to note that causative chromosomal aberrations were excluded from our cohort before WGS. As chromosomal aberrations are a well-known cause of prenatally detected congenital malformations, future studies using WGS as a primary diagnostic test, including assessment of chromosomal aberrations, may show that the detection rate exceeds the diagnostic yield of this study. WGS can add clinically relevant information, explaining the underlying cause of the fetal anomaly, which will provide information concerning the specific prognosis of the condition, as well as estimate the risk of recurrence. A genetic diagnosis can also provide more reproductive choice for future pregnancies. \u00a9 2024 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.", "doi": "10.1002/uog.27592", "pmid": "38268232", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2024-04-22T21:15:15.421Z", "modified": "2025-01-02T10:36:22.668Z"}, {"entity": "publication", "iuid": "8883d2bc3ccc4c31855099b8bd1968f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8883d2bc3ccc4c31855099b8bd1968f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8883d2bc3ccc4c31855099b8bd1968f8"}}, "title": "Ruxolitinib: A new hope for ventilator-induced diaphragm dysfunction.", "authors": [{"family": "Addinsall", "given": "Alex B", "initials": "AB"}, {"family": "Cacciani", "given": "Nicola", "initials": "N"}, {"family": "Moruzzi", "given": "Noah", "initials": "N"}, {"family": "Akkad", "given": "Hazem", "initials": "H"}, {"family": "Maestri", "given": "Alice", "initials": "A"}, {"family": "Berggren", "given": "Per-Olof", "initials": "PO"}, {"family": "Widegren", "given": "Anna", "initials": "A"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Tchkonia", "given": "Tamara", "initials": "T"}, {"family": "Kirkland", "given": "James L", "initials": "JL"}, {"family": "Larsson", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Acta Physiol (Oxf)", "issn": "1748-1716", "volume": "240", "issue": "5", "pages": "e14128", "issn-l": "1748-1708"}, "abstract": "Mechanical ventilation (MV) results in diminished diaphragm size and strength, termed ventilator-induced diaphragm dysfunction (VIDD). VID increases dependence, prolongs weaning, and increases discharge mortality rates. The Janus kinase (JAK)/Signal Transducer and Activator of Transcription (STAT) pathway is implicated in VIDD, upregulated following MV. JAK/STAT inhibition alleviates chronic muscle wasting conditions. This study aimed to explore the therapeutic potential of Ruxolitinib, an FDA approved JAK1/2 inhibitor (JI) for the treatment of VIDD.\n\nRats were subjected to 5 days controlled MV (CMV) with and without daily Ruxolitinib gavage. Muscle fiber size and function were assessed. RNAseq, mitochondrial morphology, respirometry, and mass spectrometry were determined.\n\nCMV significantly reduced diaphragm size and specific force by 45% (p < 0.01), associated with a two-fold P-STAT3 upregulation (p < 0.001). CMV disrupted mitochondrial content and reduced the oxygen consumption rate (p < 0.01). Expression of the motor protein myosin was unaffected, however CMV alters myosin function via post-translational modifications (PTMs). Daily administration of JI increased animal survival (40% vs. 87%; p < 0.05), restricted P-STAT3 (p < 0.001), and preserved diaphragm size and specific force. JI was associated with preserved mitochondrial content and respiratory function (p < 0.01), and the reversal or augmentation of myosin deamidation PTMs of the rod and head region.\n\nJI preserved diaphragm function, leading to increased survival in an experimental model of VIDD. Functional enhancement was associated with maintenance of mitochondrial content and respiration and the reversal of ventilator-induced PTMs of myosin. These results demonstrate the potential of repurposing Ruxolitinib for treatment of VIDD.", "doi": "10.1111/apha.14128", "pmid": "38551103", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-15T11:12:56.537Z", "modified": "2024-10-15T11:12:56.545Z"}, {"entity": "publication", "iuid": "39c1e0f1407f4ace92e2703314862fba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39c1e0f1407f4ace92e2703314862fba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39c1e0f1407f4ace92e2703314862fba"}}, "title": "Head-to-head comparison of relevant cell sources of small extracellular vesicles for cardiac repair: Superiority of embryonic stem cells.", "authors": [{"family": "Gonz\u00e1lez-King", "given": "Hern\u00e1n", "initials": "H", "orcid": "0000-0003-4344-9484", "researcher": {"href": "https://publications.scilifelab.se/researcher/58cbb7a64622479f97f2df3e955bed91.json"}}, {"family": "Rodrigues", "given": "Patricia G", "initials": "PG"}, {"family": "Albery", "given": "Tamsin", "initials": "T"}, {"family": "Tangruksa", "given": "Benyapa", "initials": "B"}, {"family": "Gurrapu", "given": "Ramya", "initials": "R"}, {"family": "Silva", "given": "Andreia M", "initials": "AM", "orcid": "0000-0001-6365-1407", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fc6fd2af138446ba9ccb7b529cbd04d.json"}}, {"family": "Musa", "given": "Gentian", "initials": "G"}, {"family": "Kardasz", "given": "Dominika", "initials": "D"}, {"family": "Liu", "given": "Kai", "initials": "K"}, {"family": "Kull", "given": "Bengt", "initials": "B"}, {"family": "\u00c5vall", "given": "Karin", "initials": "K"}, {"family": "Ryd\u00e9n-Markinhuhta", "given": "Katarina", "initials": "K"}, {"family": "Incitti", "given": "Tania", "initials": "T"}, {"family": "Sharma", "given": "Nitin", "initials": "N"}, {"family": "Graneli", "given": "Cecilia", "initials": "C"}, {"family": "Valadi", "given": "Hadi", "initials": "H", "orcid": "0000-0003-3482-2451", "researcher": {"href": "https://publications.scilifelab.se/researcher/630e0bcbae2f42b8bf7e6185c306b607.json"}}, {"family": "Petkevicius", "given": "Kasparas", "initials": "K"}, {"family": "Carracedo", "given": "Miguel", "initials": "M"}, {"family": "Tejedor", "given": "Sandra", "initials": "S"}, {"family": "Ivanova", "given": "Alena", "initials": "A"}, {"family": "Heydarkhan-Hagvall", "given": "Sepideh", "initials": "S"}, {"family": "Menasch\u00e9", "given": "Phillipe", "initials": "P"}, {"family": "Synnergren", "given": "Jane", "initials": "J"}, {"family": "Dekker", "given": "Niek", "initials": "N"}, {"family": "Wang", "given": "Qing-Dong", "initials": "QD"}, {"family": "Jennbacken", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "volume": "13", "issue": "5", "pages": "e12445", "issn-l": "2001-3078"}, "abstract": "Small extracellular vesicles (sEV) derived from various cell sources have been demonstrated to enhance cardiac function in preclinical models of myocardial infarction (MI). The aim of this study was to compare different sources of sEV for cardiac repair and determine the most effective one, which nowadays remains limited. We comprehensively assessed the efficacy of sEV obtained from human primary bone marrow mesenchymal stromal cells (BM-MSC), human immortalized MSC (hTERT-MSC), human embryonic stem cells (ESC), ESC-derived cardiac progenitor cells (CPC), human ESC-derived cardiomyocytes (CM), and human primary ventricular cardiac fibroblasts (VCF), in in vitro models of cardiac repair. ESC-derived sEV (ESC-sEV) exhibited the best pro-angiogenic and anti-fibrotic effects in vitro. Then, we evaluated the functionality of the sEV with the most promising performances in vitro, in a murine model of MI-reperfusion injury (IRI) and analysed their RNA and protein compositions. In vivo, ESC-sEV provided the most favourable outcome after MI by reducing adverse cardiac remodelling through down-regulating fibrosis and increasing angiogenesis. Furthermore, transcriptomic, and proteomic characterizations of sEV derived from hTERT-MSC, ESC, and CPC revealed factors in ESC-sEV that potentially drove the observed functions. In conclusion, ESC-sEV holds great promise as a cell-free treatment for promoting cardiac repair following MI.", "doi": "10.1002/jev2.12445", "pmid": "38711334", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11074624"}], "notes": [], "created": "2024-05-17T09:11:39.130Z", "modified": "2024-05-17T09:11:39.663Z"}, {"entity": "publication", "iuid": "e63ad63a204e42faba50c1c6ff2181a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e63ad63a204e42faba50c1c6ff2181a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e63ad63a204e42faba50c1c6ff2181a6"}}, "title": "Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.", "authors": [{"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Linderholm", "given": "Anna", "initials": "A"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "BioTechniques", "issn": "1940-9818", "volume": "76", "issue": "5", "pages": "216-223", "issn-l": "0736-6205"}, "abstract": "Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.", "doi": "10.2144/btn-2023-0107", "pmid": "38530148", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-04-26T08:57:15.257Z", "modified": "2025-02-28T14:23:35.440Z"}, {"entity": "publication", "iuid": "4c8011797b384556b77dc6f719cf9763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c8011797b384556b77dc6f719cf9763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c8011797b384556b77dc6f719cf9763"}}, "title": "Population genomic history of the endangered Anatolian and Cyprian mouflons in relation to worldwide wild, feral and domestic sheep lineages.", "authors": [{"family": "Ata\u011f", "given": "G\u00f6zde", "initials": "G", "orcid": "0000-0001-6173-3126", "researcher": {"href": "https://publications.scilifelab.se/researcher/e478e5f000ce44a090ccd7fad904bf36.json"}}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Mereu", "given": "Paolo", "initials": "P"}, {"family": "Pirastru", "given": "Monica", "initials": "M"}, {"family": "Barbato", "given": "Mario", "initials": "M"}, {"family": "Leoni", "given": "Giovanni Giuseppe", "initials": "GG"}, {"family": "G\u00fcler", "given": "Merve N", "initials": "MN"}, {"family": "Er", "given": "Tu\u011f\u00e7e", "initials": "T"}, {"family": "Eker", "given": "Elifnaz", "initials": "E"}, {"family": "Yaz\u0131c\u0131", "given": "Tunca Deniz", "initials": "TD"}, {"family": "K\u0131l\u0131\u00e7", "given": "Muhammed S\u0131dd\u0131k", "initials": "MS"}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE"}, {"family": "\u00c7elik", "given": "Ecem Ay\u015fe", "initials": "EA"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Floridia", "given": "Viviana", "initials": "V"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Bilgin", "given": "C Can", "initials": "CC"}, {"family": "Togan", "given": "\u0130nci", "initials": "\u0130"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Hadjisterkotis", "given": "Eleftherios", "initials": "E"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}], "type": "journal article", "published": "2024-04-27", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653"}, "abstract": "Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the IUCN. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them to eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (Ovis gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity (ROH) blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne as well as mutation load estimates are lower in Cyprian compared to Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages, and a limited consistency between viability metrics and IUCN conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.", "doi": "10.1093/gbe/evae090", "pmid": "38670119", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "7658889"}], "notes": [], "created": "2024-05-17T09:15:15.975Z", "modified": "2024-05-17T09:15:16.133Z"}, {"entity": "publication", "iuid": "6f056c7d9f1f4538bce79a48ffd96515", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f056c7d9f1f4538bce79a48ffd96515.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f056c7d9f1f4538bce79a48ffd96515"}}, "title": "Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa).", "authors": [{"family": "Tsardakas Renhuldt", "given": "Nikos", "initials": "N"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Marmon", "given": "Sofia", "initials": "S"}, {"family": "Sirijovski", "given": "Nick", "initials": "N"}], "type": "journal article", "published": "2024-04-26", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "15", "pages": "1358490", "issn-l": "1664-462X"}, "abstract": "In an ethyl methanesulfonate oat (Avena sativa) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1. The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.", "doi": "10.3389/fpls.2024.1358490", "pmid": "38736447", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11082396"}], "notes": [], "created": "2024-05-17T09:09:43.657Z", "modified": "2025-02-28T14:24:28.465Z"}, {"entity": "publication", "iuid": "8acfeb033c3c459a9cff10bf8bb576c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8acfeb033c3c459a9cff10bf8bb576c9"}}, "title": "High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.", "authors": [{"family": "Zhang", "given": "Ning", "initials": "N"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Verron", "given": "Quentin", "initials": "Q"}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Bellomo", "given": "Sara E", "initials": "SE"}, {"family": "Longo", "given": "Gabriel M C", "initials": "GMC", "orcid": "0000-0003-2028-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/2afe47a108d0451ebaf8269a0f18eb84.json"}}, {"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Su", "given": "Peng", "initials": "P"}, {"family": "Han", "given": "Bo", "initials": "B"}, {"family": "Wang", "given": "Wanzhong", "initials": "W"}, {"family": "Onorato", "given": "Sofia", "initials": "S"}, {"family": "Grassini", "given": "Dora", "initials": "D"}, {"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Giordano", "given": "Silvia", "initials": "S", "orcid": "0000-0003-1854-1086", "researcher": {"href": "https://publications.scilifelab.se/researcher/7072fc7ce1d44d0392b4ba3da82a16fb.json"}}, {"family": "Yang", "given": "Qifeng", "initials": "Q"}, {"family": "Sapino", "given": "Anna", "initials": "A", "orcid": "0000-0003-3542-9571", "researcher": {"href": "https://publications.scilifelab.se/researcher/b77045e1832b4267b330df154cbe80db.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Alkass", "given": "Kanar", "initials": "K"}, {"family": "Druid", "given": "Henrik", "initials": "H", "orcid": "0000-0002-9198-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bb7f9c706b451f9813bae017e0fad7.json"}}, {"family": "Roukos", "given": "Vassilis", "initials": "V", "orcid": "0000-0002-5065-3937", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5da3165b15741ff967e77618bd96cc1.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-04-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3475", "issn-l": "2041-1723"}, "abstract": "Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.", "doi": "10.1038/s41467-024-47664-z", "pmid": "38658552", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11043350"}, {"db": "pii", "key": "10.1038/s41467-024-47664-z"}], "notes": [], "created": "2024-05-17T09:16:39.558Z", "modified": "2024-11-25T10:16:43.449Z"}, {"entity": "publication", "iuid": "73186db56e264ccba504d9a715c478d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73186db56e264ccba504d9a715c478d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73186db56e264ccba504d9a715c478d9"}}, "title": "Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.", "authors": [{"family": "Ten Berk de Boer", "given": "Esmee", "initials": "E"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-04-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "9000", "issn-l": "2045-2322"}, "abstract": "Long-read genome sequencing (lrGS) is a promising method in genetic diagnostics. Here we investigate the potential of lrGS to detect a disease-associated chromosomal translocation between 17p13 and the 19 centromere. We constructed two sets of phased and non-phased de novo assemblies; (i) based on lrGS only and (ii) hybrid assemblies combining lrGS with optical mapping using lrGS reads with a median coverage of 34X. Variant calling detected both structural variants (SVs) and small variants and the accuracy of the small variant calling was compared with those called with short-read genome sequencing (srGS). The de novo and hybrid assemblies had high quality and contiguity with N50 of 62.85 Mb, enabling a near telomere to telomere assembly with less than a 100 contigs per haplotype. Notably, we successfully identified the centromeric breakpoint of the translocation. A concordance of 92% was observed when comparing small variant calling between srGS and lrGS. In summary, our findings underscore the remarkable potential of lrGS as a comprehensive and accurate solution for the analysis of SVs and small variants. Thus, lrGS could replace a large battery of genetic tests that were used for the diagnosis of a single symptomatic translocation carrier, highlighting the potential of lrGS in the realm of digital karyotyping.", "doi": "10.1038/s41598-024-59683-3", "pmid": "38637641", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11026446"}, {"db": "pii", "key": "10.1038/s41598-024-59683-3"}], "notes": [], "created": "2024-04-26T08:52:09.946Z", "modified": "2024-11-25T10:21:08.824Z"}, {"entity": "publication", "iuid": "dc68e741d0514c0997fc05f42b34228a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc68e741d0514c0997fc05f42b34228a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc68e741d0514c0997fc05f42b34228a"}}, "title": "Effects of bottom trawling and environmental factors on benthic bacteria, meiofauna and macrofauna communities and benthic ecosystem processes.", "authors": [{"family": "Bradshaw", "given": "Clare", "initials": "C"}, {"family": "Iburg", "given": "Sven", "initials": "S"}, {"family": "Morys", "given": "Claudia", "initials": "C"}, {"family": "Sk\u00f6ld", "given": "Mattias", "initials": "M"}, {"family": "Pusceddu", "given": "Antonio", "initials": "A"}, {"family": "Ennas", "given": "Claudia", "initials": "C"}, {"family": "Jonsson", "given": "Patrik", "initials": "P"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2024-04-15", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "921", "pages": "171076", "issn-l": "0048-9697"}, "abstract": "Soft sediment marine benthic ecosystems comprise a diverse community of bacteria, meiofauna and macrofauna, which together support a range of ecosystem processes such as biogeochemical cycling. These ecosystems are also fishing grounds for demersal species that are often caught using bottom trawling. This fishing method can have deleterious effects on benthic communities by causing injury or mortality, and through alteration of sediment properties that in turn influence community structure. Although the impacts of bottom trawling on macrofauna are relatively well studied, less is known about the responses of meiofauna and bacteria to such disturbances, or how bottom trawling impacts benthic ecosystem processes. Quantifying trawling impacts against a background of natural environmental variability is also a challenge. To address these questions, we examined effects of bottom trawling and a range of environmental variables (e.g. water chemistry and physical and biochemical surface sediment properties) on a) bacterial, meiofaunal and macrofaunal community structure and b) benthic ecosystem processes (nutrient fluxes, extracellular enzyme activities and carbon turnover and degradation rates). We also investigated the link between the benthic macrofauna community and the same ecosystem processes. While there was a significant effect of bottom trawling intensity on macrofaunal community structure, the same was not seen for bacterial or meiofaunal community composition, which were more affected by environmental factors, such as surface sediment properties. The labile component of the surface sediment carbon pool was higher at highly trawled sites. Carbon degradation rates, extracellular enzyme activities, oxygen fluxes and some nutrient fluxes were significantly affected by trawling, but ecosystem processes were also strongly linked to the abundance of key bioturbators (Macoma balthica, Halicryptus spinulosus, Scoloplos armiger and Pontoporeia femorata). Although benthic ecosystems were affected by a combination of trawling and natural variability, disentangling these showed that the anthropogenic effects were clearest on the larger component of the community, i.e. macrofauna composition, and on ecosystem processes related to sedimentary carbon.", "doi": "10.1016/j.scitotenv.2024.171076", "pmid": "38382611", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)01215-4"}], "notes": [], "created": "2024-03-14T11:09:09.535Z", "modified": "2024-03-14T11:09:09.539Z"}, {"entity": "publication", "iuid": "036d938b353a4b6084fc027f2a6fc9d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/036d938b353a4b6084fc027f2a6fc9d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/036d938b353a4b6084fc027f2a6fc9d6"}}, "title": "Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes.", "authors": [{"family": "Abdel-Fattah", "given": "Wael R", "initials": "WR"}, {"family": "Carlsson", "given": "Mattias", "initials": "M"}, {"family": "Hu", "given": "Guo-Zhen", "initials": "G"}, {"family": "Singh", "given": "Ajeet", "initials": "A"}, {"family": "Vergara", "given": "Alexander", "initials": "A", "orcid": "0000-0001-6535-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/8003432c3c264e78a754fe595297453b.json"}}, {"family": "Aslam", "given": "Rameen", "initials": "R"}, {"family": "Ronne", "given": "Hans", "initials": "H", "orcid": "0000-0002-1645-6091", "researcher": {"href": "https://publications.scilifelab.se/researcher/d700b0be9ea04b588f539186fb92df5d.json"}}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1181-0415", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce.json"}}], "type": "journal article", "published": "2024-04-13", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": null, "issue": null, "pages": null}, "abstract": "Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3'-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3'-ends, overlapping the Lsm3 binding sites \u223c250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.", "doi": "10.1093/nar/gkae266", "pmid": "38613396", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "7645241"}], "notes": [], "created": "2024-04-26T08:51:21.044Z", "modified": "2024-06-28T06:31:12.260Z"}, {"entity": "publication", "iuid": "ce62204de21e4d48a7ac1939f7545c21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce62204de21e4d48a7ac1939f7545c21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce62204de21e4d48a7ac1939f7545c21"}}, "title": "Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.", "authors": [{"family": "Kukanja", "given": "Petra", "initials": "P", "orcid": "0000-0003-1228-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/082ef6e681214c14b8ca36cd0188722b.json"}}, {"family": "Langseth", "given": "Christoffer M", "initials": "CM"}, {"family": "Rubio Rodr\u00edguez-Kirby", "given": "Leslie A", "initials": "LA", "orcid": "0000-0003-4467-2661", "researcher": {"href": "https://publications.scilifelab.se/researcher/9790e215a63d40aa8fac497b537999f9.json"}}, {"family": "Agirre", "given": "Eneritz", "initials": "E", "orcid": "0000-0002-5012-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/a507b19745c64c3bb8ef5dce800c8687.json"}}, {"family": "Zheng", "given": "Chao", "initials": "C"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Tiklov\u00e1", "given": "Katarina", "initials": "K", "orcid": "0000-0002-9529-4552", "researcher": {"href": "https://publications.scilifelab.se/researcher/14bbad41b8ed42268b71014ce111d247.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 O", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2024-04-11", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "187", "issue": "8", "pages": "1990-2009.e19"}, "abstract": "Multiple sclerosis (MS) is a neurological disease characterized by multifocal lesions and smoldering pathology. Although single-cell analyses provided insights into cytopathology, evolving cellular processes underlying MS remain poorly understood. We investigated the cellular dynamics of MS by modeling temporal and regional rates of disease progression in mouse experimental autoimmune encephalomyelitis (EAE). By performing single-cell spatial expression profiling using in situ sequencing (ISS), we annotated disease neighborhoods and found centrifugal evolution of active lesions. We demonstrated that disease-associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course. Single-cell spatial mapping of human archival MS spinal cords confirmed the differential distribution of homeostatic and DA-glia, enabled deconvolution of active and inactive lesions into sub-compartments, and identified new lesion areas. By establishing a spatial resource of mouse and human MS neuropathology at a single-cell resolution, our study unveils the intricate cellular dynamics underlying MS.", "doi": "10.1016/j.cell.2024.02.030", "pmid": "38513664", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "BioImage Informatics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0092-8674(24)00233-2"}], "notes": [], "created": "2024-04-09T12:34:31.275Z", "modified": "2025-10-17T13:02:16.765Z"}, {"entity": "publication", "iuid": "0798e00f4db04115a4fa9921f7c3b57f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0798e00f4db04115a4fa9921f7c3b57f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0798e00f4db04115a4fa9921f7c3b57f"}}, "title": "A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi.", "authors": [{"family": "Roberts", "given": "Kevin T", "initials": "KT", "orcid": "0000-0003-2785-5108", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f74402c368a41f2b5610a946770cbe1.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA"}, {"family": "S\u00fcess", "given": "Philip", "initials": "P"}, {"family": "Lehmann", "given": "Philipp", "initials": "P", "orcid": "0000-0001-8344-6830", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ed560cbb5c84b3e9649daafb72017e0.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}], "type": "journal article", "published": "2024-04-10", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17348", "issn-l": "0962-1083"}, "abstract": "Organisms inhabiting highly seasonal environments must cope with a wide range of environmentally induced challenges. Many seasonal challenges require extensive physiological modification to survive. In winter, to survive extreme cold and limited resources, insects commonly enter diapause, which is an endogenously derived dormant state associated with minimized cellular processes and low energetic expenditure. Due to the high degree of complexity involved in diapause, substantial cellular regulation is required, of which our understanding primarily derives from the transcriptome via messenger RNA expression dynamics. Here we aim to advance our understanding of diapause by investigating microRNA (miRNA) expression in diapausing and direct developing pupae of the butterfly Pieris napi. We identified coordinated patterns of miRNA expression throughout diapause in both head and abdomen tissues of pupae, and via miRNA target identification, found several expression patterns to be enriched for relevant diapause-related physiological processes. We also identified two candidate miRNAs, miR-14-5p and miR-2a-3p, that are likely involved in diapause progression through their activity in the ecdysone pathway, a critical regulator of diapause termination. miR-14-5p targets phantom, a gene in the ecdysone synthesis pathway, and is upregulated early in diapause. miR-2a-3p has been found to be expressed in response to ecdysone, and is upregulated during diapause termination. Together, the expression patterns of these two miRNAs match our current understanding of the timing of hormonal regulation of diapause in P. napi and provide interesting candidates to further explore the mechanistic role of microRNAs in diapause regulation.", "doi": "10.1111/mec.17348", "pmid": "38597329", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-04-26T08:53:10.936Z", "modified": "2025-02-28T14:20:20.940Z"}, {"entity": "publication", "iuid": "e38b3ec0dd384974b869f7aba446939c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e38b3ec0dd384974b869f7aba446939c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e38b3ec0dd384974b869f7aba446939c"}}, "title": "Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model.", "authors": [{"family": "Yaghmaeian Salmani", "given": "Behzad", "initials": "B", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Lahti", "given": "Laura", "initials": "L"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Jacobsen", "given": "Jesper Kjaer", "initials": "JK"}, {"family": "Mantas", "given": "Ioannis", "initials": "I"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Perlmann", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4821-8036", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c8dc93c324455b93aa392fcbb67315.json"}}], "type": "journal article", "published": "2024-04-08", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Midbrain dopamine (mDA) neurons comprise diverse cells with unique innervation targets and functions. This is illustrated by the selective sensitivity of mDA neurons of the substantia nigra compacta (SNc) in patients with Parkinson's disease, while those in the ventral tegmental area (VTA) are relatively spared. Here, we used single nuclei RNA sequencing (snRNA-seq) of approximately 70,000 mouse midbrain cells to build a high-resolution atlas of mouse mDA neuron diversity at the molecular level. The results showed that differences between mDA neuron groups could best be understood as a continuum without sharp differences between subtypes. Thus, we assigned mDA neurons to several 'territories' and 'neighborhoods' within a shifting gene expression landscape where boundaries are gradual rather than discrete. Based on the enriched gene expression patterns of these territories and neighborhoods, we were able to localize them in the adult mouse midbrain. Moreover, because the underlying mechanisms for the variable sensitivities of diverse mDA neurons to pathological insults are not well understood, we analyzed surviving neurons after partial 6-hydroxydopamine (6-OHDA) lesions to unravel gene expression patterns that correlate with mDA neuron vulnerability and resilience. Together, this atlas provides a basis for further studies on the neurophysiological role of mDA neurons in health and disease.", "doi": "10.7554/eLife.89482", "pmid": "38587883", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11001297"}, {"db": "pii", "key": "89482"}, {"db": "GEO", "key": "GSE233866"}, {"db": "GEO", "key": "GSE178265"}], "notes": [], "created": "2024-10-14T11:47:35.603Z", "modified": "2024-11-25T10:34:12.402Z"}, {"entity": "publication", "iuid": "7d3c4336130e450099e81cfa741064ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d3c4336130e450099e81cfa741064ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d3c4336130e450099e81cfa741064ec"}}, "title": "Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.", "authors": [{"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Yang", "given": "Weizhao", "initials": "W"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "While", "given": "Geoffrey M", "initials": "GM", "orcid": "0000-0001-8122-9322", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40ba32f8185473fa3543815e8a539fe.json"}}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications.scilifelab.se/researcher/6346267a5c3e41c6a6825b7b20a53fa5.json"}}], "type": "journal article", "published": "2024-04-05", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "14", "pages": "eadk9315", "issn-l": "2375-2548"}, "abstract": "The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such \"phenotypic syndromes\" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a ~400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.", "doi": "10.1126/sciadv.adk9315", "pmid": "38569035", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10990284"}], "notes": [], "created": "2024-04-09T12:41:11.047Z", "modified": "2024-11-25T10:28:12.121Z"}, {"entity": "publication", "iuid": "72f3aa35636c456e84ca5ceb90728c2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72f3aa35636c456e84ca5ceb90728c2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72f3aa35636c456e84ca5ceb90728c2a"}}, "title": "Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.", "authors": [{"family": "Sommerauer", "given": "Christian", "initials": "C", "orcid": "0000-0001-7132-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/01320952391e4afe9b924dcf85b5d50a.json"}}, {"family": "Gallardo-Dodd", "given": "Carlos J", "initials": "CJ"}, {"family": "Savva", "given": "Christina", "initials": "C"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Indukuri", "given": "Rajitha", "initials": "R"}, {"family": "Shen", "given": "Joanne X", "initials": "JX", "orcid": "0009-0008-0322-5615", "researcher": {"href": "https://publications.scilifelab.se/researcher/519a2d0afb6747c6ad3cf2b12c4d0bf3.json"}}, {"family": "Carravilla", "given": "Pablo", "initials": "P"}, {"family": "Geng", "given": "Keyi", "initials": "K"}, {"family": "N\u00f8rskov S\u00f8ndergaard", "given": "Jonas", "initials": "J", "orcid": "0000-0002-4438-6756", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0125f039a4949d8a22b9048d7f6b7d8.json"}}, {"family": "Ferrer-Aumatell", "given": "Cl\u00e0udia", "initials": "C"}, {"family": "Mercier", "given": "Gr\u00e9goire", "initials": "G"}, {"family": "Sezgin", "given": "Erdinc", "initials": "E", "orcid": "0000-0002-4915-388X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34d3b05d68d64f698ff08dc655d2fe26.json"}}, {"family": "Korach-Andr\u00e9", "given": "Marion", "initials": "M"}, {"family": "Petersson", "given": "Carl", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Hannes", "initials": "H"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM", "orcid": "0000-0002-1140-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c123916fbf4948a911560c1a259496.json"}}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C"}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications.scilifelab.se/researcher/61f2e0e6c9be43ac946b318d080d5cca.json"}}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "volume": "20", "issue": "4", "pages": "374-402", "issn-l": "1744-4292"}, "abstract": "Sex-based differences in obesity-related hepatic malignancies suggest the protective roles of estrogen. Using a preclinical model, we dissected estrogen receptor (ER) isoform-driven molecular responses in high-fat diet (HFD)-induced liver diseases of male and female mice treated with or without an estrogen agonist by integrating liver multi-omics data. We found that selective ER activation recovers HFD-induced molecular and physiological liver phenotypes. HFD and systemic ER activation altered core liver pathways, beyond lipid metabolism, that are consistent between mice and primates. By including patient cohort data, we uncovered that ER-regulated enhancers govern central regulatory and metabolic genes with clinical significance in metabolic dysfunction-associated steatotic liver disease (MASLD) patients, including the transcription factor TEAD1. TEAD1 expression increased in MASLD patients, and its downregulation by short interfering RNA reduced intracellular lipid content. Subsequent TEAD small molecule inhibition improved steatosis in primary human hepatocyte spheroids by suppressing lipogenic pathways. Thus, TEAD1 emerged as a new therapeutic candidate whose inhibition ameliorates hepatic steatosis.", "doi": "10.1038/s44320-024-00024-x", "pmid": "38459198", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Integrated Microscopy Technologies Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10987545"}, {"db": "pii", "key": "10.1038/s44320-024-00024-x"}], "notes": [], "created": "2024-03-14T11:08:10.304Z", "modified": "2025-02-28T14:16:38.102Z"}, {"entity": "publication", "iuid": "038e2711a4f84e74959ab4951cfade3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/038e2711a4f84e74959ab4951cfade3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/038e2711a4f84e74959ab4951cfade3a"}}, "title": "METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma.", "authors": [{"family": "Vaid", "given": "Roshan", "initials": "R", "orcid": "0000-0002-2074-5080", "researcher": {"href": "https://publications.scilifelab.se/researcher/64693febab0b42ee8546e0e7fb3d1763.json"}}, {"family": "Thombare", "given": "Ketan", "initials": "K", "orcid": "0000-0002-0183-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/abe760c0d75247668935c84b3789f9a7.json"}}, {"family": "Mendez", "given": "Akram", "initials": "A", "orcid": "0000-0001-9195-3808", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a35073338c44086b6ccfe9209a0d3a6.json"}}, {"family": "Burgos-Panadero", "given": "Rebeca", "initials": "R", "orcid": "0000-0003-0811-2675", "researcher": {"href": "https://publications.scilifelab.se/researcher/886dabcfd1a84a30b3beeb35fa4241a1.json"}}, {"family": "Djos", "given": "Anna", "initials": "A"}, {"family": "Jachimowicz", "given": "Daniel", "initials": "D"}, {"family": "Lundberg", "given": "Kristina Ihrmark", "initials": "KI"}, {"family": "Bartenhagen", "given": "Christoph", "initials": "C"}, {"family": "Kumar", "given": "Navinder", "initials": "N"}, {"family": "T\u00fcmmler", "given": "Conny", "initials": "C"}, {"family": "Sihlbom", "given": "Carina", "initials": "C"}, {"family": "Fransson", "given": "Susanne", "initials": "S", "orcid": "0000-0002-9713-3074", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f155163dae47478aae39b9c47fdadc.json"}}, {"family": "Johnsen", "given": "John Inge", "initials": "JI"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}, {"family": "Fischer", "given": "Matthias", "initials": "M"}, {"family": "Mondal", "given": "Tanmoy", "initials": "T", "orcid": "0000-0001-6228-8001", "researcher": {"href": "https://publications.scilifelab.se/researcher/60ae61d730214113bea3d17b0d5ada63.json"}}], "type": "journal article", "published": "2024-03-21", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "5", "pages": "2648-2671", "issn-l": "0305-1048"}, "abstract": "Telomerase-negative tumors maintain telomere length by alternative lengthening of telomeres (ALT), but the underlying mechanism behind ALT remains poorly understood. A proportion of aggressive neuroblastoma (NB), particularly relapsed tumors, are positive for ALT (ALT+), suggesting that a better dissection of the ALT mechanism could lead to novel therapeutic opportunities. TERRA, a long non-coding RNA (lncRNA) derived from telomere ends, localizes to telomeres in a R-loop-dependent manner and plays a crucial role in telomere maintenance. Here we present evidence that RNA modification at the N6 position of internal adenosine (m6A) in TERRA by the methyltransferase METTL3 is essential for telomere maintenance in ALT+ cells, and the loss of TERRA m6A/METTL3 results in telomere damage. We observed that m6A modification is abundant in R-loop enriched TERRA, and the m6A-mediated recruitment of hnRNPA2B1 to TERRA is critical for R-loop formation. Our findings suggest that m6A drives telomere targeting of TERRA via R-loops, and this m6A-mediated R-loop formation could be a widespread mechanism employed by other chromatin-interacting lncRNAs. Furthermore, treatment of ALT+ NB cells with a METTL3 inhibitor resulted in compromised telomere targeting of TERRA and accumulation of DNA damage at telomeres, indicating that METTL3 inhibition may represent a therapeutic approach for ALT+ NB.", "doi": "10.1093/nar/gkad1242", "pmid": "38180812", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10954483"}, {"db": "pii", "key": "7511755"}], "notes": [], "created": "2024-03-14T11:27:14.986Z", "modified": "2025-02-28T14:19:05.780Z"}, {"entity": "publication", "iuid": "0885ec9c38e64c2f8cf9d3d8eb45ec51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0885ec9c38e64c2f8cf9d3d8eb45ec51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0885ec9c38e64c2f8cf9d3d8eb45ec51"}}, "title": "Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure.", "authors": [{"family": "Frisk", "given": "Christoffer", "initials": "C"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Walentinsson", "given": "Anna", "initials": "A"}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Hage", "given": "Camilla", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Maret", "given": "Eva", "initials": "E"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Persson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2024-03-09", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "5811", "issn-l": "2045-2322"}, "abstract": "New or mild heart failure (HF) is mainly caused by left ventricular dysfunction. We hypothesised that gene expression differ between the left (LV) and right ventricle (RV) and secondly by type of LV dysfunction. We compared gene expression through myocardial biopsies from LV and RV of patients undergoing elective coronary bypass surgery (CABG). Patients were categorised based on LV ejection fraction (EF), diastolic function and NT-proBNP into pEF (preserved; LVEF \u2265 45%), rEF (reduced; LVEF < 45%) or normal LV function. Principal component analysis of gene expression displayed two clusters corresponding to LV and RV. Up-regulated genes in LV included natriuretic peptides NPPA and NPPB, transcription factors/coactivators STAT4 and VGLL2, ion channel related HCN2 and LRRC38 associated with cardiac muscle contraction, cytoskeleton, and cellular component movement. Patients with pEF phenotype versus normal differed in gene expression predominantly in LV, supporting that diastolic dysfunction and structural changes reflect early LV disease in pEF. DKK2 was overexpressed in LV of HFpEF phenotype, potentially leading to lower expression levels of \u03b2-catenin, \u03b1-SMA (smooth muscle actin), and enhanced apoptosis, and could be a possible factor in the development of HFpEF. CXCL14 was down-regulated in both pEF and rEF, and may play a role to promote development of HF.", "doi": "10.1038/s41598-024-56025-1", "pmid": "38461325", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10924960"}, {"db": "pii", "key": "10.1038/s41598-024-56025-1"}], "notes": [], "created": "2024-03-14T11:07:07.576Z", "modified": "2024-11-25T10:20:58.292Z"}, {"entity": "publication", "iuid": "3450b7c1f75249119cccdb958020c5dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3450b7c1f75249119cccdb958020c5dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3450b7c1f75249119cccdb958020c5dc"}}, "title": "Identification of microbial pathogens in Neolithic Scandinavian humans.", "authors": [{"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Mirabello", "given": "Claudio", "initials": "C"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Jorgensen", "given": "Roger", "initials": "R"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2024-03-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "14", "issue": "1", "pages": "5630"}, "abstract": "With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.", "doi": "10.1038/s41598-024-56096-0", "pmid": "38453993", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10920878"}, {"db": "pii", "key": "10.1038/s41598-024-56096-0"}], "notes": [], "created": "2024-03-14T11:09:30.525Z", "modified": "2024-11-25T10:21:03.650Z"}, {"entity": "publication", "iuid": "cf7ea31e683f4c45835678b143349f84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf7ea31e683f4c45835678b143349f84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf7ea31e683f4c45835678b143349f84"}}, "title": "fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles.", "authors": [{"family": "Dennhag", "given": "Nils", "initials": "N", "orcid": "0000-0003-0885-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf9ac3fa9a504dcb877d144438ed5161.json"}}, {"family": "Kahsay", "given": "Abraha", "initials": "A", "orcid": "0000-0003-1518-9785", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b2b788339fd463fa1a2c777bcf87948.json"}}, {"family": "Nissen", "given": "Itzel", "initials": "I", "orcid": "0000-0002-0741-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4f02fa8059145bc9b17d0c1ef978ee2.json"}}, {"family": "Nord", "given": "Hanna", "initials": "H", "orcid": "0000-0002-6098-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/22d8cc445c6b41b4a8488d620995d8c3.json"}}, {"family": "Chermenina", "given": "Maria", "initials": "M"}, {"family": "Liu", "given": "Jiao", "initials": "J"}, {"family": "Arner", "given": "Anders", "initials": "A"}, {"family": "Liu", "given": "Jing-Xia", "initials": "JX", "orcid": "0000-0003-2508-9921", "researcher": {"href": "https://publications.scilifelab.se/researcher/353db8f1d54e4d0ca55b64ef7b0249d7.json"}}, {"family": "Backman", "given": "Ludvig J", "initials": "LJ"}, {"family": "Remeseiro", "given": "Silvia", "initials": "S", "orcid": "0000-0001-5343-007X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb0bc2da415e4c6aafc3f55fba80a12b.json"}}, {"family": "von Hofsten", "given": "Jonas", "initials": "J", "orcid": "0000-0003-3730-1790", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee9e4dc7b9a44b818e4c10aea633a934.json"}}, {"family": "Pedrosa Domell\u00f6f", "given": "Fatima", "initials": "F", "orcid": "0000-0002-0648-4996", "researcher": {"href": "https://publications.scilifelab.se/researcher/30143e3ec79a4f16b82495ce9e453750.json"}}], "type": "journal article", "published": "2024-03-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1950", "issn-l": "2041-1723"}, "abstract": "In muscular dystrophies, muscle fibers loose integrity and die, causing significant suffering and premature death. Strikingly, the extraocular muscles (EOMs) are spared, functioning well despite the disease progression. Although EOMs have been shown to differ from body musculature, the mechanisms underlying this inherent resistance to muscle dystrophies remain unknown. Here, we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscles in zebrafish via transcriptomic profiling. We show that the LIM-protein Fhl2 is increased in response to the knockout of desmin, plectin and obscurin, cytoskeletal proteins whose knockout causes different muscle dystrophies, and contributes to disease protection of the EOMs. Moreover, we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje, significantly improving their survival. Therefore, Fhl2 is a protective agent and a candidate target gene for therapy of muscular dystrophies.", "doi": "10.1038/s41467-024-46187-x", "pmid": "38431640", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10908798"}, {"db": "pii", "key": "10.1038/s41467-024-46187-x"}], "notes": [], "created": "2024-03-14T11:06:34.815Z", "modified": "2024-11-25T10:16:22.287Z"}, {"entity": "publication", "iuid": "3338a6f2c5b143219504dff0b95a9424", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3338a6f2c5b143219504dff0b95a9424.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3338a6f2c5b143219504dff0b95a9424"}}, "title": "Rare coding variants in NOX4 link high ROS levels to psoriatic arthritis mutilans.", "authors": [{"family": "Wang", "given": "Sailan", "initials": "S", "orcid": "0000-0002-1269-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0dc9eda6e3a4cc2a68abf0e6d47f9f9.json"}}, {"family": "Nikamo", "given": "Pernilla", "initials": "P"}, {"family": "Laasonen", "given": "Leena", "initials": "L"}, {"family": "Gudbjornsson", "given": "Bjorn", "initials": "B", "orcid": "0000-0003-4631-6505", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fb0b2ab4bd24099966d487f6f299303.json"}}, {"family": "Ejstrup", "given": "Leif", "initials": "L"}, {"family": "Iversen", "given": "Lars", "initials": "L", "orcid": "0000-0003-1816-4508", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed66867f11dd4dffb67e3f32e37d1ec8.json"}}, {"family": "Lindqvist", "given": "Ulla", "initials": "U"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ", "orcid": "0000-0002-2066-9073", "researcher": {"href": "https://publications.scilifelab.se/researcher/9800995eec454011a4ec3b682789eca0.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Zheng", "given": "Xiaowei", "initials": "X"}, {"family": "Catrina", "given": "Sergiu-Bogdan", "initials": "SB", "orcid": "0000-0002-6914-3902", "researcher": {"href": "https://publications.scilifelab.se/researcher/efbe5c0830144b63a644c0dcc6864e02.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Vaz", "given": "Raquel", "initials": "R"}, {"family": "St\u00e5hle", "given": "Mona", "initials": "M", "orcid": "0000-0002-3916-9343", "researcher": {"href": "https://publications.scilifelab.se/researcher/4efdec4c51bb4cfa8186086179a73254.json"}}, {"family": "Tapia-Paez", "given": "Isabel", "initials": "I", "orcid": "0000-0002-0535-4233", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ed50bc3a5034bafbff8ee63e129fb10.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "EMBO Mol Med", "issn": "1757-4684", "issn-l": "1757-4676", "volume": "16", "issue": "3", "pages": "596-615"}, "abstract": "Psoriatic arthritis mutilans (PAM) is the rarest and most severe form of psoriatic arthritis, characterized by erosions of the small joints and osteolysis leading to joint disruption. Despite its severity, the underlying mechanisms are unknown, and no susceptibility genes have hitherto been identified. We aimed to investigate the genetic basis of PAM by performing massive parallel sequencing in sixty-one patients from the PAM Nordic cohort. We found rare variants in the NADPH oxidase 4 (NOX4) in four patients. In silico predictions show that the identified variants are potentially damaging. NOXs are the only enzymes producing reactive oxygen species (ROS). NOX4 is specifically involved in the differentiation of osteoclasts, the cells implicated in bone resorption. Functional follow-up studies using cell culture, zebrafish models, and measurement of ROS in patients uncovered that these NOX4 variants increase ROS levels both in vitro and in vivo. We propose NOX4 as the first candidate susceptibility gene for PAM. Our study links high levels of ROS caused by NOX4 variants to the development of PAM, offering a potential therapeutic target.", "doi": "10.1038/s44321-024-00035-z", "pmid": "38379095", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10940640"}, {"db": "pii", "key": "10.1038/s44321-024-00035-z"}], "notes": [], "created": "2024-03-21T12:09:34.802Z", "modified": "2025-02-28T14:16:43.516Z"}, {"entity": "publication", "iuid": "8822f79ce12c4158bd6128531eaf7657", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8822f79ce12c4158bd6128531eaf7657.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8822f79ce12c4158bd6128531eaf7657"}}, "title": "Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult.", "authors": [{"family": "Di Nunzio", "given": "Giada", "initials": "G"}, {"family": "Hellberg", "given": "Sanna", "initials": "S", "orcid": "0000-0003-1791-3693", "researcher": {"href": "https://publications.scilifelab.se/researcher/053fd0cc678f48abb083aaf102f1cec4.json"}}, {"family": "Zhang", "given": "Yuyang", "initials": "Y", "orcid": "0000-0002-3806-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/d469b9b7fccd4f65a66b2cb87939a157.json"}}, {"family": "Ahmed", "given": "Osman", "initials": "O", "orcid": "0000-0002-2854-2552", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb219b9efad046f6badae392587f62b1.json"}}, {"family": "Wang", "given": "Jiawen", "initials": "J"}, {"family": "Zhang", "given": "Xueming", "initials": "X"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM"}, {"family": "Chizh", "given": "Veronika", "initials": "V"}, {"family": "Schipper", "given": "Ruby", "initials": "R"}, {"family": "Aulin", "given": "Hanna", "initials": "H"}, {"family": "Francis", "given": "Roy", "initials": "R"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Gister\u00e5", "given": "Anton", "initials": "A", "orcid": "0000-0002-4614-8030", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e2beec3559745a6ba1859252df4a547.json"}}, {"family": "Metso", "given": "Jari", "initials": "J"}, {"family": "Manf\u00e9", "given": "Valentina", "initials": "V"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Jauhiainen", "given": "Matti", "initials": "M"}, {"family": "Hagberg", "given": "Carolina E", "initials": "CE", "orcid": "0000-0002-5497-2855", "researcher": {"href": "https://publications.scilifelab.se/researcher/66bbd07c59044b279527c75f12cd4c04.json"}}, {"family": "Olofsson", "given": "Peder S", "initials": "PS", "orcid": "0000-0003-3473-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/527d940eee82480bae882e2c8b4af99f.json"}}, {"family": "Malin", "given": "Stephen G", "initials": "SG", "orcid": "0000-0001-7723-9579", "researcher": {"href": "https://publications.scilifelab.se/researcher/86c05018e1e9477181eb7aa86faef7d1.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Nat Cardiovasc Res", "issn": "2731-0590", "volume": "3", "issue": "3", "pages": "356-371", "issn-l": null}, "abstract": "Apolipoprotein-B (APOB)-containing lipoproteins cause atherosclerosis. Whether the vasculature is the initially responding site or if atherogenic dyslipidemia affects other organs simultaneously is unknown. Here we show that the liver responds to a dyslipidemic insult based on inducible models of familial hypercholesterolemia and APOB tracing. An acute transition to atherogenic APOB lipoprotein levels resulted in uptake by Kupffer cells and rapid accumulation of triglycerides and cholesterol in the liver. Bulk and single-cell RNA sequencing revealed a Kupffer-cell-specific transcriptional program that was not activated by a high-fat diet alone or detected in standard liver function or pathological assays, even in the presence of fulminant atherosclerosis. Depletion of Kupffer cells altered the dynamic of plasma and liver lipid concentrations, indicating that these liver macrophages help restrain and buffer atherogenic lipoproteins while simultaneously secreting atherosclerosis-modulating factors into plasma. Our results place Kupffer cells as key sentinels in organizing systemic responses to lipoproteins at the initiation of atherosclerosis.", "doi": "10.1038/s44161-024-00448-6", "pmid": "39196121", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11358021"}, {"db": "pii", "key": "10.1038/s44161-024-00448-6"}], "notes": [], "created": "2024-10-14T13:20:41.587Z", "modified": "2025-02-28T14:16:26.867Z"}, {"entity": "publication", "iuid": "2930d1923c4f4a50a0b8f52e9b9820db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2930d1923c4f4a50a0b8f52e9b9820db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2930d1923c4f4a50a0b8f52e9b9820db"}}, "title": "Genetic constraints in genes exhibiting splicing plasticity in facultative diapause.", "authors": [{"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Roberts", "given": "Kevin T", "initials": "KT", "orcid": "0000-0003-2785-5108", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f74402c368a41f2b5610a946770cbe1.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "132", "issue": "3", "pages": "142-155", "issn-l": "0018-067X"}, "abstract": "Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.", "doi": "10.1038/s41437-024-00669-2", "pmid": "38291272", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10923799"}, {"db": "pii", "key": "10.1038/s41437-024-00669-2"}], "notes": [], "created": "2024-03-14T11:16:17.218Z", "modified": "2025-02-28T14:14:07.422Z"}, {"entity": "publication", "iuid": "b65e656b7fd14984a6c8a44d2edb0795", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b65e656b7fd14984a6c8a44d2edb0795.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b65e656b7fd14984a6c8a44d2edb0795"}}, "title": "Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Norberg", "given": "Zandra", "initials": "Z"}, {"family": "Cordier", "given": "Julie", "initials": "J"}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Bassereh", "given": "Hassan", "initials": "H", "orcid": "0000-0002-9202-3765", "researcher": {"href": "https://publications.scilifelab.se/researcher/83cc119164de497f95b65f8ad11cac79.json"}}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N"}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S", "orcid": "0000-0002-0834-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1917cb059924a779ac38e3023778461.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "7", "issue": "3", "issn-l": "2575-1077"}, "abstract": "Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of three blood stem-like cell lines treated with carboplatin or gemcitabine. Taking advantage of publicly available enhancer datasets, we validated HiCap results in silico and in living cells using epigenetic CRISPR technology. We also developed a network approach for interactome analysis and detection of differentially interacting genes. Differential interaction analysis provided additional information on relevant genes and pathways for myelosuppression compared with differential gene expression analysis at the bulk level. Moreover, we showed that enhancers of differentially interacting genes are highly enriched for variants associated with differing levels of myelosuppression. Altogether, our work represents a prominent example of integrative transcriptome and gene regulatory datasets analysis for the functional annotation of noncoding mutations.", "doi": "10.26508/lsa.202302244", "pmid": "38228368", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796589"}, {"db": "pii", "key": "7/3/e202302244"}], "notes": [], "created": "2024-03-18T09:44:22.332Z", "modified": "2025-02-28T14:23:45.768Z"}, {"entity": "publication", "iuid": "80c75635458e45f883e80acd6b1c4fc1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80c75635458e45f883e80acd6b1c4fc1"}}, "title": "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.", "authors": [{"family": "Chen", "given": "Jinxin Phaedo", "initials": "JP", "orcid": "0000-0002-0729-5214", "researcher": {"href": "https://publications.scilifelab.se/researcher/25fca568763f4476b53bdf7297689a2e.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wu", "given": "Honggui", "initials": "H", "orcid": "0000-0001-7880-0591", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9697e391fe493ab4b26d2c40e7565f.json"}}, {"family": "Chen", "given": "Chong", "initials": "C", "orcid": "0000-0002-6787-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8a6778068124d7cb3dd1aca6e7cc0ec.json"}}, {"family": "Della Chiara", "given": "Giulia", "initials": "G", "orcid": "0000-0001-5211-3814", "researcher": {"href": "https://publications.scilifelab.se/researcher/3410a95b5b674fa69d2c83b479d345a8.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6728-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/d254d4e308064696b50b17806dec1a60.json"}}, {"family": "Georgiadis", "given": "Konstantinos L", "initials": "KL"}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM"}, {"family": "Virdi", "given": "Mohit", "initials": "M"}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Bellomo", "given": "Sara Erika", "initials": "SE"}, {"family": "Marchi\u00f2", "given": "Caterina", "initials": "C"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1768", "issn-l": "2041-1723"}, "abstract": "Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.", "doi": "10.1038/s41467-024-45972-y", "pmid": "38409079", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10897160"}, {"db": "pii", "key": "10.1038/s41467-024-45972-y"}], "notes": [], "created": "2024-03-14T11:05:03.191Z", "modified": "2024-04-26T09:08:57.780Z"}, {"entity": "publication", "iuid": "d4835bd8e2744419b81fc0ab88ed052a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4835bd8e2744419b81fc0ab88ed052a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4835bd8e2744419b81fc0ab88ed052a"}}, "title": "Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).", "authors": [{"family": "Jiang", "given": "Zhiyong", "initials": "Z"}, {"family": "Zang", "given": "Wenqing", "initials": "W"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Song", "given": "Gang", "initials": "G"}, {"family": "Wu", "given": "Shaoyuan", "initials": "S"}, {"family": "Feng", "given": "Shaohong", "initials": "S"}, {"family": "Drovetski", "given": "Sergei V", "initials": "SV"}, {"family": "Liu", "given": "Gang", "initials": "G"}, {"family": "Zhang", "given": "Dezhi", "initials": "D"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Edwards", "given": "Scott V", "initials": "SV"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "22", "issue": "1", "pages": "49", "issn-l": "1741-7007"}, "abstract": "Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.\n\nHere we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.\n\nCollectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.", "doi": "10.1186/s12915-024-01848-7", "pmid": "38413944", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10900574"}, {"db": "pii", "key": "10.1186/s12915-024-01848-7"}], "notes": [], "created": "2024-03-14T11:10:52.935Z", "modified": "2024-11-25T10:30:32.973Z"}, {"entity": "publication", "iuid": "72c0bcbc6ed645e4a14dd4aa365fac7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72c0bcbc6ed645e4a14dd4aa365fac7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72c0bcbc6ed645e4a14dd4aa365fac7e"}}, "title": "Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.", "authors": [{"family": "Kvedaraite", "given": "Egle", "initials": "E", "orcid": "0000-0001-5308-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/78502177bad3453a8d3ed96d4ad334ac.json"}}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Mouratidou", "given": "Natalia", "initials": "N"}, {"family": "D\u00fcking", "given": "Tim", "initials": "T", "orcid": "0000-0002-4347-7648", "researcher": {"href": "https://publications.scilifelab.se/researcher/6acbe8ae50d94479a37dda5f37336422.json"}}, {"family": "Padhi", "given": "Avinash", "initials": "A"}, {"family": "Moll", "given": "Kirsten", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Sinha", "given": "Indranil", "initials": "I", "orcid": "0000-0002-2513-5927", "researcher": {"href": "https://publications.scilifelab.se/researcher/970cda1bb71d4ae1b36cc5628023f7d4.json"}}, {"family": "Xagoraris", "given": "Ioanna", "initials": "I"}, {"family": "Kokkinou", "given": "Efthymia", "initials": "E"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Weigel", "given": "Whitney", "initials": "W"}, {"family": "Hartwig", "given": "Olga", "initials": "O", "orcid": "0000-0001-5016-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a50cebd9533432e80d2fd284c9137eb.json"}}, {"family": "Santos", "given": "Telma E", "initials": "TE"}, {"family": "Soini", "given": "Tea", "initials": "T"}, {"family": "Van Acker", "given": "Aline", "initials": "A"}, {"family": "Rahkonen", "given": "Nelly", "initials": "N"}, {"family": "Flodstr\u00f6m Tullberg", "given": "Malin", "initials": "M", "orcid": "0000-0003-2685-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6d04afbe8141c2b9297854de64dab8.json"}}, {"family": "Ringqvist", "given": "Emma", "initials": "E"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Jorns", "given": "Carl", "initials": "C", "orcid": "0000-0001-7727-8113", "researcher": {"href": "https://publications.scilifelab.se/researcher/59d387bd893f45bdb3663a0ef3aae88a.json"}}, {"family": "Lindforss", "given": "Ulrik", "initials": "U"}, {"family": "Nordenvall", "given": "Caroline", "initials": "C"}, {"family": "Stamper", "given": "Christopher T", "initials": "CT"}, {"family": "Unnersj\u00f6-Jess", "given": "David", "initials": "D", "orcid": "0000-0002-4162-0973", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d475fc7a52a46e4abe984191c5b5b5f.json"}}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Nadisauskaite", "given": "Ruta", "initials": "R"}, {"family": "Jansson", "given": "Jessica", "initials": "J"}, {"family": "Vandamme", "given": "Niels", "initials": "N"}, {"family": "Sorini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-6803-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/975173f37f144f06b236817e224de7f0.json"}}, {"family": "Grundeken", "given": "Marijke Elise", "initials": "ME", "orcid": "0000-0001-6915-0339", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64d9493eccd419d8c8908dea19602df.json"}}, {"family": "Rolandsdotter", "given": "Helena", "initials": "H"}, {"family": "Rassidakis", "given": "George", "initials": "G"}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}, {"family": "Idestr\u00f6m", "given": "Maja", "initials": "M"}, {"family": "Eulitz", "given": "Stefan", "initials": "S"}, {"family": "Arnell", "given": "Henrik", "initials": "H"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J", "orcid": "0000-0002-1119-0976", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcca878a7f314944bf1a4290cfd5d71d.json"}}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI", "orcid": "0000-0002-0629-2126", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1a0d663491c4665a32a612e423dff1b.json"}}, {"family": "Svensson", "given": "Mattias", "initials": "M", "orcid": "0000-0003-1695-7934", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3185cf86534a96983b39dd93df454a.json"}}], "type": "journal article", "published": "2024-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "1752", "issn-l": "2041-1723"}, "abstract": "Stromal cells support epithelial cell and immune cell homeostasis and play an important role in inflammatory bowel disease (IBD) pathogenesis. Here, we quantify the stromal response to inflammation in pediatric IBD and reveal subset-specific inflammatory responses across colon segments and intestinal layers. Using data from a murine dynamic gut injury model and human ex vivo transcriptomic, protein and spatial analyses, we report that PDGFRA+CD142-/low fibroblasts and monocytes/macrophages co-localize in the intestine. In primary human fibroblast-monocyte co-cultures, intestinal PDGFRA+CD142-/low fibroblasts foster monocyte transition to CCR2+CD206+ macrophages through granulocyte-macrophage colony-stimulating factor (GM-CSF). Monocyte-derived CCR2+CD206+ cells from co-cultures have a phenotype similar to intestinal CCR2+CD206+ macrophages from newly diagnosed pediatric IBD patients, with high levels of PD-L1 and low levels of GM-CSF receptor. The study describes subset-specific changes in stromal responses to inflammation and suggests that the intestinal stroma guides intestinal macrophage differentiation.", "doi": "10.1038/s41467-024-46076-3", "pmid": "38409190", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10897309"}, {"db": "pii", "key": "10.1038/s41467-024-46076-3"}], "notes": [], "created": "2024-03-14T11:08:33.238Z", "modified": "2024-10-31T10:36:41.256Z"}, {"entity": "publication", "iuid": "11b11b15651b41dfbb423bc265d224ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b11b15651b41dfbb423bc265d224ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b11b15651b41dfbb423bc265d224ba"}}, "title": "Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea.", "authors": [{"family": "Xu", "given": "Tianshuo", "initials": "T", "orcid": "0000-0002-6392-728X", "researcher": {"href": "https://publications.scilifelab.se/researcher/87eef0aa1f0444f59d6412df0c7efba4.json"}}, {"family": "Novotny", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8910-6183", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c63db5be95c40e49940affadc958928.json"}}, {"family": "Zamora-Terol", "given": "Sara", "initials": "S", "orcid": "0000-0002-7822-3197", "researcher": {"href": "https://publications.scilifelab.se/researcher/25e1b401fc9a49c5b6f89eaa18f89a57.json"}}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}, {"family": "Winder", "given": "Monika", "initials": "M", "orcid": "0000-0001-9467-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b09dfb6b68445249b8a93c655433189.json"}}], "type": "journal article", "published": "2024-02-26", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "87", "issue": "1", "pages": "48", "issn-l": "0095-3628"}, "abstract": "In aquatic ecosystems, zooplankton-associated bacteria potentially have a great impact on the structure of ecosystems and trophic networks by providing various metabolic pathways and altering the ecological niche of host species. To understand the composition and drivers of zooplankton gut microbiota, we investigated the associated microbial communities of four zooplankton genera from different seasons in the Baltic Sea using the 16S rRNA gene. Among the 143 ASVs (amplified sequence variants) observed belonging to heterotrophic bacteria, 28 ASVs were shared across all zooplankton hosts over the season, and these shared core ASVs represented more than 25% and up to 60% of relative abundance in zooplankton hosts but were present at low relative abundance in the filtered water. Zooplankton host identity had stronger effects on bacterial composition than seasonal variation, with the composition of gut bacterial communities showing host-specific clustering patterns. Although bacterial compositions and dominating core bacteria were different between zooplankton hosts, higher gut bacteria diversity and more bacteria contributing to the temporal variation were found in Temora and Pseudocalanus, compared to Acartia and Synchaeta. Diet diatom and filamentous cyanobacteria negatively correlated with gut bacteria diversity, but the difference in diet composition did not explain the dissimilarity of gut bacteria composition, suggesting a general effect of diet on the inner conditions in the zooplankton gut. Synchaeta maintained high stability of gut bacterial communities with unexpectedly low bacteria-bacteria interactions as compared to the copepods, indicating host-specific regulation traits. Our results suggest that the patterns of gut bacteria dynamics are host-specific and the variability of gut bacteria is not only related to host taxonomy but also related to host behavior and life history traits.", "doi": "10.1007/s00248-024-02362-7", "pmid": "38409540", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10896951"}, {"db": "pii", "key": "10.1007/s00248-024-02362-7"}], "notes": [], "created": "2024-03-14T11:09:50.360Z", "modified": "2024-11-25T10:10:49.264Z"}, {"entity": "publication", "iuid": "90c6743864c749ea88a615065315621f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90c6743864c749ea88a615065315621f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90c6743864c749ea88a615065315621f"}}, "title": "The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.", "authors": [{"family": "Renstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0009-0004-8104-3228", "researcher": {"href": "https://publications.scilifelab.se/researcher/b63f6ee710ba4b0a980e29a1689d24cf.json"}}, {"family": "Choudhary", "given": "Shruti", "initials": "S"}, {"family": "Gandla", "given": "Madhavi Latha", "initials": "ML"}, {"family": "J\u00f6nsson", "given": "Leif J", "initials": "LJ"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "J\u00e4mtg\u00e5rd", "given": "Sandra", "initials": "S"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2024-02-21", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "issn-l": "0031-9317", "volume": "176", "issue": "1", "pages": "e14219"}, "abstract": "Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR <0.01) respond to added NO3 - , the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.", "doi": "10.1111/ppl.14219", "pmid": "38380723", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-03-12T15:49:46.223Z", "modified": "2025-10-17T13:03:53.118Z"}, {"entity": "publication", "iuid": "3957b5edaf374769bdfb35b70d40200b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3957b5edaf374769bdfb35b70d40200b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3957b5edaf374769bdfb35b70d40200b"}}, "title": "Clonally heritable gene expression imparts a layer of diversity within cell types.", "authors": [{"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Weissman", "given": "Martin H", "initials": "MH"}, {"family": "Ratz", "given": "Michael", "initials": "M"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Eriksson", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Berghenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C"}, {"family": "von Berlin", "given": "Leonie", "initials": "L"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2024-02-21", "journal": {"title": "Cell Syst", "issn": "2639-5460", "volume": "15", "issue": "2", "pages": "149-165.e10", "issn-l": "2405-4712"}, "abstract": "Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-coverage single-cell RNA profiling, we asked whether long-term, heritable differences in gene expression can impart diversity within cells of the same type. Studying clonal human lymphocytes and mouse brain cells, we uncovered a vast diversity of heritable gene expression patterns among different clones of cells of the same type in vivo. We combined chromatin accessibility and RNA profiling on different lymphocyte clones to reveal thousands of regulatory regions exhibiting interclonal variation, which could be directly linked to interclonal variation in gene expression. Our findings identify a source of cellular diversity, which may have important implications for how cellular populations are shaped by selective processes in development, aging, and disease. A record of this paper's transparent peer review process is included in the supplemental information.", "doi": "10.1016/j.cels.2024.01.004", "pmid": "38340731", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2405-4712(24)00025-5"}], "notes": [], "created": "2024-03-14T11:18:49.826Z", "modified": "2025-02-28T14:12:01.188Z"}, {"entity": "publication", "iuid": "d53efd169d754ccca5fd70684c689438", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d53efd169d754ccca5fd70684c689438.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d53efd169d754ccca5fd70684c689438"}}, "title": "Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.", "authors": [{"family": "Hold", "given": "Katharina", "initials": "K"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC"}, {"family": "Le Moullec", "given": "Mathilde", "initials": "M"}, {"family": "Bieker", "given": "Vanessa C", "initials": "VC"}, {"family": "Ellegaard", "given": "Martin R", "initials": "MR"}, {"family": "Rasmussen", "given": "Jacob A", "initials": "JA"}, {"family": "Kellner", "given": "Fabian L", "initials": "FL"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}, {"family": "Yannic", "given": "Glenn", "initials": "G"}, {"family": "R\u00f8ed", "given": "Knut H", "initials": "KH"}, {"family": "Hansen", "given": "Brage B", "initials": "BB"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2024-02-20", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "14", "issue": "1", "pages": "4143"}, "abstract": "Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.", "doi": "10.1038/s41598-024-54296-2", "pmid": "38374421", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10876933"}, {"db": "pii", "key": "10.1038/s41598-024-54296-2"}], "notes": [], "created": "2024-03-14T11:11:17.523Z", "modified": "2024-11-25T10:20:42.576Z"}, {"entity": "publication", "iuid": "15163fc735054cc69dc35256cde09787", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15163fc735054cc69dc35256cde09787.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15163fc735054cc69dc35256cde09787"}}, "title": "Lymphocytic colitis can be transcriptionally divided into channelopathic and inflammatory lymphocytic colitis.", "authors": [{"family": "Bhardwaj", "given": "Archana", "initials": "A"}, {"family": "M\u00fcnch", "given": "Andreas", "initials": "A", "orcid": "0000-0003-4703-581X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb2eeb24de2f4750927be4460e13b199.json"}}, {"family": "Montague", "given": "Julia", "initials": "J"}, {"family": "Koch", "given": "Stefan", "initials": "S", "orcid": "0000-0003-3579-4229", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c70c1aa5624edfb9d9b36ce7bef947.json"}}, {"family": "Rosenstiel", "given": "Philip", "initials": "P", "orcid": "0000-0002-9692-8828", "researcher": {"href": "https://publications.scilifelab.se/researcher/69ae14d39b21434392b8ad26cca9645a.json"}}, {"family": "Escudero-Hern\u00e1ndez", "given": "Celia", "initials": "C", "orcid": "0000-0001-8906-3101", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffc0645f035e42c59bfdf819621e1394.json"}}], "type": "journal article", "published": "2024-02-17", "journal": {"title": "United European Gastroenterol J", "issn": "2050-6414", "issn-l": null}, "abstract": "The pathobiology of the non-destructive inflammatory bowel disease (IBD) lymphocytic colitis (LC) is poorly understood. We aimed to define an LC-specific mucosal transcriptome to gain insight into LC pathology, identify unique genomic signatures, and uncover potentially druggable disease pathways.\n\nWe performed bulk RNA-sequencing of LC and collagenous colitis (CC) colonic mucosa from patients with active disease, and healthy controls (n = 4-10 per cohort). Differential gene expression was analyzed by gene-set enrichment and deconvolution analyses to identify pathologically relevant pathways and cells, respectively, altered in LC. Key findings were validated using reverse transcription quantitative PCR and/or immunohistochemistry. Finally, we compared our data with a previous cohort of ulcerative colitis and Crohn's disease patients (n = 4 per group) to distinguish non-destructive from classic IBD.\n\nLC can be subdivided into channelopathic LC, which is governed by organic acid and ion transport dysregulation, and inflammatory LC, which is driven by microbial immune responses. Inflammatory LC displays an innate and adaptive immunity that is limited compared to CC and classic IBD. Conversely, we noted a distinct induction of regulatory non-coding RNA species in inflammatory LC samples. Moreover, compared with CC, water channel and cell adhesion molecule gene expression decreased in channelopathic LC, whereas it was accentuated in inflammatory LC and associated with reduced intestinal epithelial cell proliferation.\n\nWe conclude that LC can be subdivided into channelopathic LC and inflammatory LC that could be pathomechanistically distinct subtypes despite their shared clinical presentation. Inflammatory LC exhibits a dampened immune response compared to CC and classic IBDs. Our results point to regulatory micro-RNAs as a potential disease-specific feature that may be amenable to therapeutic intervention.", "doi": "10.1002/ueg2.12531", "pmid": "38366868", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-14T11:03:44.417Z", "modified": "2024-04-26T09:05:57.553Z"}, {"entity": "publication", "iuid": "32a17c9018c043279b6599771e1991ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32a17c9018c043279b6599771e1991ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32a17c9018c043279b6599771e1991ba"}}, "title": "Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.", "authors": [{"family": "Dube", "given": "Faruk", "initials": "F", "orcid": "0000-0003-1340-9123", "researcher": {"href": "https://publications.scilifelab.se/researcher/efd709b6ebf04946bf70f1ab4c8c5cbf.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Martin", "given": "Frida", "initials": "F"}, {"family": "Hinas", "given": "Andrea", "initials": "A", "orcid": "0000-0002-9353-0742", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d94108597af4151876bcb67a3ce857e.json"}}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2024-02-15", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "2", "pages": "e0298039", "issn-l": "1932-6203"}, "abstract": "Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10-11 M and 10-9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10-11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10-11 M to upregulation at 10-9 M IVM. The 10-9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10-11 M IVM. However, after 10-9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.", "doi": "10.1371/journal.pone.0298039", "pmid": "38359071", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10868809"}, {"db": "pii", "key": "PONE-D-23-41473"}], "notes": [], "created": "2024-03-14T11:08:49.813Z", "modified": "2024-11-25T10:32:12.300Z"}, {"entity": "publication", "iuid": "fa3ec7c6d57645dca27002bd711dd76c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa3ec7c6d57645dca27002bd711dd76c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa3ec7c6d57645dca27002bd711dd76c"}}, "title": "A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.", "authors": [{"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Dias", "given": "Guilherme", "initials": "G"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Soares", "given": "Andr\u00e9", "initials": "A"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2024-02-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "2", "issn-l": "1759-6653"}, "abstract": "The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. The development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity, chromosome-level genome assembly of a female clouded apollo butterfly and provide detailed annotations of genes and transposable elements. We find that the large genome (1.5 Gb) of the clouded apollo is extraordinarily repeat rich (73%). Despite that, the combination of sequencing techniques allowed us to assemble all chromosomes (nc = 29) to a high degree of completeness. The annotation resulted in a relatively high number of protein-coding genes (22,854) compared with other Lepidoptera, of which a large proportion (21,635) could be assigned functions based on homology with other species. A comparative analysis indicates that overall genome structure has been largely conserved, both within the genus and compared with the ancestral lepidopteran karyotype. The high-quality genome assembly and detailed annotation presented here will constitute an important tool for forthcoming efforts aimed at understanding the genetic consequences of fragmentation and decline, as well as for assessments of genetic diversity, population structure, inbreeding, and genetic load in the clouded apollo butterfly.", "doi": "10.1093/gbe/evae031", "pmid": "38368625", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10901555"}, {"db": "pii", "key": "7610114"}], "notes": [], "created": "2024-02-29T15:15:06.133Z", "modified": "2025-02-28T14:18:02.771Z"}, {"entity": "publication", "iuid": "5e2a1137c7eb466ebdc8c5b6cbd08f24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e2a1137c7eb466ebdc8c5b6cbd08f24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e2a1137c7eb466ebdc8c5b6cbd08f24"}}, "title": "Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx.", "authors": [{"family": "Lucena-Perez", "given": "Maria", "initials": "M", "orcid": "0000-0002-9676-7155", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f6ded3bc48241caa3174678cf659a46.json"}}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Nocete", "given": "Francisco", "initials": "F", "orcid": "0000-0001-5948-0748", "researcher": {"href": "https://publications.scilifelab.se/researcher/306d6d16740e4549aad6201a89542519.json"}}, {"family": "Nadal", "given": "Jordi", "initials": "J"}, {"family": "Detry", "given": "Cleia", "initials": "C", "orcid": "0000-0002-5359-2500", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b8409a47d734eec80c6bc299bbebad1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Godoy", "given": "Jos\u00e9 A", "initials": "JA", "orcid": "0000-0001-7502-9471", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a92c5bd89c4f19b5f3d829d5cdba3c.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "8", "issue": "2", "pages": "282-292", "issn-l": "2397-334X"}, "abstract": "Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species' gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data from three ancient Iberian lynx (Lynx pardinus) approximately 2,000-4,000 years old and show a continuous or recurrent process of interspecies admixture with the Eurasian lynx (Lynx lynx) that increased modern Iberian lynx genetic diversity above that occurring millennia ago despite its recent demographic decline. Our results add to the accumulating evidence for natural admixture and introgression among closely related species and show that this can result in an increase of species-wide genetic diversity in highly genetically eroded species. The strict avoidance of interspecific sources in current genetic restoration measures needs to be carefully reconsidered, particularly in cases where no conspecific source population exists.", "doi": "10.1038/s41559-023-02267-7", "pmid": "38225424", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-023-02267-7"}], "notes": [], "created": "2024-03-14T11:24:56.694Z", "modified": "2025-02-28T14:15:19.326Z"}, {"entity": "publication", "iuid": "652ef4bf70e84b36b7d9aa8a86e01efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/652ef4bf70e84b36b7d9aa8a86e01efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/652ef4bf70e84b36b7d9aa8a86e01efa"}}, "title": "Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).", "authors": [{"family": "Chondrelli", "given": "Niki", "initials": "N"}, {"family": "Kuehn", "given": "Emily", "initials": "E"}, {"family": "Meurling", "given": "Sara", "initials": "S"}, {"family": "Cort\u00e1zar-Chinarro", "given": "Maria", "initials": "M"}, {"family": "Laurila", "given": "Anssi", "initials": "A"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2024-01-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "2495", "issn-l": "2045-2322"}, "abstract": "Batrachochytrium dendrobatidis (Bd) is a fungal pathogen that has decimated amphibian populations worldwide for several decades. We examined the changes in gene expression in response to Bd infection in two populations of the common toad, Bufo bufo, in a laboratory experiment. We collected B. bufo eggs in southern and northern Sweden, and infected the laboratory-raised metamorphs with two strains of the global panzoonotic lineage Bd-GPL. Differential expression analysis showed significant differences between infected and control individuals in both liver and skin. The skin samples showed no discernible differences in gene expression between the two strains used, while liver samples were differentiated by strain, with one of the strains eliciting no immune response from infected toads. Immune system genes were overexpressed in skin samples from surviving infected individuals, while in liver samples the pattern was more diffuse. Splitting samples by population revealed a stronger immune response in northern individuals. Differences in transcriptional regulation between populations are particularly relevant to study in Swedish amphibians, which may have experienced varying exposure to Bd. Earlier exposure to this pathogen and subsequent adaptation or selection pressure may contribute to the survival of some populations over others, while standing genetic diversity in different populations may also affect the infection outcome.", "doi": "10.1038/s41598-024-52975-8", "pmid": "38291226", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828426"}, {"db": "pii", "key": "10.1038/s41598-024-52975-8"}], "notes": [], "created": "2024-03-21T09:01:24.203Z", "modified": "2025-01-02T10:35:06.385Z"}, {"entity": "publication", "iuid": "817dec7f87cf404fa56707e1b13be7e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/817dec7f87cf404fa56707e1b13be7e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/817dec7f87cf404fa56707e1b13be7e1"}}, "title": "Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.", "authors": [{"family": "Gruj\u010di\u0107", "given": "Vesna", "initials": "V", "orcid": "0000-0002-3322-599X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd1ed7a2d7e477d8f8c5a340152b36c.json"}}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Sennblad", "given": "Bengt", "initials": "B", "orcid": "0000-0002-4360-8003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c991150beec46ba8886379193d6037b.json"}}, {"family": "Norgren", "given": "Benjamin", "initials": "B"}, {"family": "Latz", "given": "Meike", "initials": "M"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Foster", "given": "Rachel A", "initials": "RA"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2024-01-19", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "19", "issue": "1", "pages": "e0296672"}, "abstract": "Single-cell transcriptomics has the potential to provide novel insights into poorly studied microbial eukaryotes. Although several such technologies are available and benchmarked on mammalian cells, few have been tested on protists. Here, we applied a microarray single-cell sequencing (MASC-seq) technology, that generates microscope images of cells in parallel with capturing their transcriptomes, on three species representing important plankton groups with different cell structures; the ciliate Tetrahymena thermophila, the diatom Phaeodactylum tricornutum, and the dinoflagellate Heterocapsa sp. Both the cell fixation and permeabilization steps were adjusted. For the ciliate and dinoflagellate, the number of transcripts of microarray spots with single cells were significantly higher than for background spots, and the overall expression patterns were correlated with that of bulk RNA, while for the much smaller diatom cells, it was not possible to separate single-cell transcripts from background. The MASC-seq method holds promise for investigating \"microbial dark matter\", although further optimizations are necessary to increase the signal-to-noise ratio.", "doi": "10.1371/journal.pone.0296672", "pmid": "38241213", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10798536"}, {"db": "pii", "key": "PONE-D-23-10489"}], "notes": [], "created": "2024-03-14T11:18:03.349Z", "modified": "2024-11-25T10:32:07.185Z"}, {"entity": "publication", "iuid": "50f17519fbe44f2eb49fdc91933ee0ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50f17519fbe44f2eb49fdc91933ee0ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50f17519fbe44f2eb49fdc91933ee0ee"}}, "title": "Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.", "authors": [{"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Damlien", "given": "Hege", "initials": "H"}, {"family": "Manninen", "given": "Mikael A", "initials": "MA"}, {"family": "Nordqvist", "given": "Bengt", "initials": "B"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Lindberg", "given": "A Michael", "initials": "AM"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Aravena", "given": "Andr\u00e9s", "initials": "A"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "case reports", "published": "2024-01-18", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "22125"}, "abstract": "Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.", "doi": "10.1038/s41598-023-48762-6", "pmid": "38238372", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796427"}, {"db": "pii", "key": "10.1038/s41598-023-48762-6"}], "notes": [], "created": "2024-01-19T06:32:34.876Z", "modified": "2024-11-25T10:20:27.063Z"}, {"entity": "publication", "iuid": "b4ff3ca17be540cbb545c1a64ee4e126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4ff3ca17be540cbb545c1a64ee4e126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4ff3ca17be540cbb545c1a64ee4e126"}}, "title": "Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts.", "authors": [{"family": "Moura", "given": "Pedro L", "initials": "PL", "orcid": "0000-0002-0493-5394", "researcher": {"href": "https://publications.scilifelab.se/researcher/12216bfd20fa4056b844842908efc829.json"}}, {"family": "Mortera-Blanco", "given": "Teresa", "initials": "T", "orcid": "0000-0002-8399-1430", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a4cccc1f92842b78d19b5c232a655fe.json"}}, {"family": "Hofman", "given": "Isabel J", "initials": "IJ", "orcid": "0000-0001-7825-843X", "researcher": {"href": "https://publications.scilifelab.se/researcher/28b2678b6e1d45299c3a446b4f305762.json"}}, {"family": "Todisco", "given": "Gabriele", "initials": "G", "orcid": "0000-0001-6583-3829", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bdb2b7dcd8a4fa497748ee5e165f11e.json"}}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW", "orcid": "0000-0002-2575-0807", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67389ef276a47cfacec7cbe50da37a7.json"}}, {"family": "Bj\u00f6rklund", "given": "Ann-Charlotte", "initials": "AC", "orcid": "0009-0008-3745-503X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a03cc050a5d446ca3872007f15db3d3.json"}}, {"family": "Creignou", "given": "Maria", "initials": "M", "orcid": "0000-0002-7629-0871", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7d3e87602e943a296e10038400ff2dc.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/3297f21f1a174cd388ac586eda2b5177.json"}}, {"family": "Cabrerizo Granados", "given": "David", "initials": "D", "orcid": "0000-0001-5719-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/610eac412b5a4527b11776794607930f.json"}}, {"family": "Barbosa", "given": "Indira", "initials": "I", "orcid": "0009-0004-1171-2932", "researcher": {"href": "https://publications.scilifelab.se/researcher/20efd8770db84811a240a8bb70c43939.json"}}, {"family": "Walldin", "given": "Gunilla", "initials": "G", "orcid": "0009-0005-6663-6540", "researcher": {"href": "https://publications.scilifelab.se/researcher/24fb888d0212421eaa2353ed6cc31ac7.json"}}, {"family": "Jansson", "given": "Monika", "initials": "M", "orcid": "0000-0002-9257-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccbf1b2b281742feba0dbd215b6f3228.json"}}, {"family": "Ashley", "given": "Neil", "initials": "N", "orcid": "0000-0002-1655-5137", "researcher": {"href": "https://publications.scilifelab.se/researcher/db3c5c75f5684026a6e267a664c8da99.json"}}, {"family": "Mead", "given": "Adam J", "initials": "AJ", "orcid": "0000-0001-8522-1002", "researcher": {"href": "https://publications.scilifelab.se/researcher/8409c8c7eb604ece9e2ea80ee419336a.json"}}, {"family": "Lundin", "given": "Vanessa", "initials": "V", "orcid": "0000-0003-2335-3370", "researcher": {"href": "https://publications.scilifelab.se/researcher/4648601ee2b74061aadb746516203707.json"}}, {"family": "Dimitriou", "given": "Marios", "initials": "M", "orcid": "0000-0001-8362-2099", "researcher": {"href": "https://publications.scilifelab.se/researcher/531c153359bb400fb48c7324a3bd69ad.json"}}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T", "orcid": "0000-0003-4283-2983", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6f499e339d2444b817a81ab2712b9e5.json"}}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ae0c1d2cf5461894c6d0d80ed42f68.json"}}, {"family": "Ogawa", "given": "Seishi", "initials": "S", "orcid": "0000-0002-7778-5374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcc3b1b5f3045a7acd123222445449d.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fc5e4f49e4330b095c26cd965cc98.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}], "type": "journal article", "published": "2024-01-16", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "84", "issue": "2", "pages": "211-225", "issn-l": "0008-5472"}, "abstract": "Myelodysplastic syndromes with ring sideroblasts (MDS-RS) commonly develop from hematopoietic stem cells (HSC) bearing mutations in the splicing factor SF3B1 (SF3B1mt). Direct studies into MDS-RS pathobiology have been limited by a lack of model systems that fully recapitulate erythroid biology and RS development and the inability to isolate viable human RS. Here, we combined successful direct RS isolation from patient samples, high-throughput multiomics analysis of cells encompassing the SF3B1mt stem-erythroid continuum, and functional assays to investigate the impact of SF3B1mt on erythropoiesis and RS accumulation. The isolated RS differentiated, egressed into the blood, escaped traditional nonsense-mediated decay (NMD) mechanisms, and leveraged stress-survival pathways that hinder wild-type hematopoiesis through pathogenic GDF15 overexpression. Importantly, RS constituted a contaminant of magnetically enriched CD34+ cells, skewing bulk transcriptomic data. Mis-splicing in SF3B1mt cells was intensified by erythroid differentiation through accelerated RNA splicing and decreased NMD activity, and SF3B1mt led to truncations in several MDS-implicated genes. Finally, RNA mis-splicing induced an uncoupling of RNA and protein expression, leading to critical abnormalities in proapoptotic p53 pathway genes. Overall, this characterization of erythropoiesis in SF3B1mt RS provides a resource for studying MDS-RS and uncovers insights into the unexpectedly active biology of the \"dead-end\" RS.\n\nRing sideroblast isolation combined with state-of-the-art multiomics identifies survival mechanisms underlying SF3B1-mutant erythropoiesis and establishes an active role for erythroid differentiation and ring sideroblasts themselves in SF3B1-mutant myelodysplastic syndrome pathogenesis.", "doi": "10.1158/0008-5472.CAN-23-3038", "pmid": "37921711", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10790130"}, {"db": "pii", "key": "730004"}], "notes": [], "created": "2024-03-14T11:43:21.354Z", "modified": "2025-02-28T14:21:18.908Z"}, {"entity": "publication", "iuid": "9b5552f6ed314a64a3613c88047c30d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b5552f6ed314a64a3613c88047c30d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b5552f6ed314a64a3613c88047c30d0"}}, "title": "Identification of a Notch transcriptomic signature for breast cancer.", "authors": [{"family": "Braune", "given": "Eike-Benjamin", "initials": "EB"}, {"family": "Geist", "given": "Felix", "initials": "F"}, {"family": "Tang", "given": "Xiaojia", "initials": "X"}, {"family": "Kalari", "given": "Krishna", "initials": "K"}, {"family": "Boughey", "given": "Judy", "initials": "J"}, {"family": "Wang", "given": "Liewei", "initials": "L"}, {"family": "Leon-Ferre", "given": "Roberto A", "initials": "RA"}, {"family": "D'Assoro", "given": "Antonino B", "initials": "AB"}, {"family": "Ingle", "given": "James N", "initials": "JN"}, {"family": "Goetz", "given": "Matthew P", "initials": "MP"}, {"family": "Kreis", "given": "Julian", "initials": "J"}, {"family": "Wang", "given": "Kang", "initials": "K"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T"}, {"family": "Seshire", "given": "Anita", "initials": "A"}, {"family": "Wienke", "given": "Dirk", "initials": "D"}, {"family": "Lendahl", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2024-01-03", "journal": {"title": "Breast Cancer Res.", "issn": "1465-542X", "volume": "26", "issue": "1", "pages": "4", "issn-l": "1465-5411"}, "abstract": "Dysregulated Notch signalling contributes to breast cancer development and progression, but validated tools to measure the level of Notch signalling in breast cancer subtypes and in response to systemic therapy are largely lacking. A transcriptomic signature of Notch signalling would be warranted, for example to monitor the effects of future Notch-targeting therapies and to learn whether altered Notch signalling is an off-target effect of current breast cancer therapies. In this report, we have established such a classifier.\n\nTo generate the signature, we first identified Notch-regulated genes from six basal-like breast cancer cell lines subjected to elevated or reduced Notch signalling by culturing on immobilized Notch ligand Jagged1 or blockade of Notch by \u03b3-secretase inhibitors, respectively. From this cadre of Notch-regulated genes, we developed candidate transcriptomic signatures that were trained on a breast cancer patient dataset (the TCGA-BRCA cohort) and a broader breast cancer cell line cohort and sought to validate in independent datasets.\n\nAn optimal 20-gene transcriptomic signature was selected. We validated the signature on two independent patient datasets (METABRIC and Oslo2), and it showed an improved coherence score and tumour specificity compared with previously published signatures. Furthermore, the signature score was particularly high for basal-like breast cancer, indicating an enhanced level of Notch signalling in this subtype. The signature score was increased after neoadjuvant treatment in the PROMIX and BEAUTY patient cohorts, and a lower signature score generally correlated with better clinical outcome.\n\nThe 20-gene transcriptional signature will be a valuable tool to evaluate the response of future Notch-targeting therapies for breast cancer, to learn about potential effects on Notch signalling from conventional breast cancer therapies and to better stratify patients for therapy considerations.", "doi": "10.1186/s13058-023-01757-7", "pmid": "38172915", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10765899"}, {"db": "pii", "key": "10.1186/s13058-023-01757-7"}], "notes": [], "created": "2024-03-14T11:19:34.094Z", "modified": "2024-03-14T11:20:32.303Z"}, {"entity": "publication", "iuid": "a084cdaa37c24b40adf21ef8cec47e14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a084cdaa37c24b40adf21ef8cec47e14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a084cdaa37c24b40adf21ef8cec47e14"}}, "title": "Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.", "authors": [{"family": "Hunt", "given": "George", "initials": "G"}, {"family": "Vaid", "given": "Roshan", "initials": "R"}, {"family": "Pirogov", "given": "Sergei", "initials": "S"}, {"family": "Pfab", "given": "Alexander", "initials": "A"}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Mannervik", "given": "Mattias", "initials": "M", "orcid": "0000-0003-4999-9655", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0f0a726c543479d9da775e31d24630a.json"}}], "type": "journal article", "published": "2024-01-02", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "25", "issue": "1", "pages": "2"}, "abstract": "Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood.\r\n\r\nHere we comprehensively resolve differential transcriptional and chromatin states during Drosophila DV patterning. We find that RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues.\r\n\r\nThe data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. Our results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues.", "doi": "10.1186/s13059-023-03135-0", "pmid": "38166964", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10763363"}, {"db": "pii", "key": "10.1186/s13059-023-03135-0"}], "notes": [], "created": "2024-03-14T11:22:29.164Z", "modified": "2024-12-16T08:32:37.972Z"}, {"entity": "publication", "iuid": "9362d0a9e2424b878878c0da9a3d7c67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9362d0a9e2424b878878c0da9a3d7c67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9362d0a9e2424b878878c0da9a3d7c67"}}, "title": "A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.", "authors": [{"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Brugel", "given": "Sonia", "initials": "S"}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B"}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "dataset", "published": "2024-01-02", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "18", "issn-l": "2052-4463"}, "abstract": "The Baltic Sea is one of the largest brackish water environments on earth and is characterised by pronounced physicochemical gradients and seasonal dynamics. Although the Baltic Sea has a long history of microscopy-based plankton monitoring, DNA-based metabarcoding has so far mainly been limited to individual transect cruises or time-series of single stations. Here we report a dataset covering spatiotemporal variation in prokaryotic and eukaryotic microbial communities and physicochemical parameters. Within 13-months between January 2019 and February 2020, 341 water samples were collected at 22 stations during monthly cruises along the salinity gradient. Both salinity and seasonality are strongly reflected in the data. Since the dataset was generated with both metabarcoding and microscopy-based methods, it provides unique opportunities for both technical and ecological analyses, and is a valuable biodiversity reference for future studies, in the prospect of climate change.", "doi": "10.1038/s41597-023-02825-5", "pmid": "38168085", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10761891"}, {"db": "pii", "key": "10.1038/s41597-023-02825-5"}], "notes": [], "created": "2024-01-10T09:46:47.061Z", "modified": "2024-11-25T10:20:00.758Z"}, {"entity": "publication", "iuid": "e01f2e61d2c84f2c9ecbee35a68a5d2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e01f2e61d2c84f2c9ecbee35a68a5d2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e01f2e61d2c84f2c9ecbee35a68a5d2c"}}, "title": "Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF.", "authors": [{"family": "Struck", "given": "Eike C", "initials": "EC"}, {"family": "Belova", "given": "Tatiana", "initials": "T"}, {"family": "Hsieh", "given": "Ping-Han", "initials": "PH"}, {"family": "Odeberg", "given": "Jacob O", "initials": "JO"}, {"family": "Kuijjer", "given": "Marieke L", "initials": "ML", "orcid": "0000-0001-6280-3130", "researcher": {"href": "https://publications.scilifelab.se/researcher/e706d501bdb54dc2b7c655e2d8e972b6.json"}}, {"family": "Dusart", "given": "Philip J", "initials": "PJ", "orcid": "0000-0003-2747-3214", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dffee863552446eb498f96e04a0fe4d.json"}}, {"family": "Butler", "given": "Lynn M", "initials": "LM", "orcid": "0000-0002-2352-8217", "researcher": {"href": "https://publications.scilifelab.se/researcher/069263856386498c8262acf10587177c.json"}}], "type": "journal article", "published": "2024-01-01", "journal": {"title": "J. Immunol.", "issn": "1550-6606", "volume": "212", "issue": "1", "pages": "117-129", "issn-l": "0022-1767"}, "abstract": "The vascular endothelium acts as a dynamic interface between blood and tissue. TNF-\u03b1, a major regulator of inflammation, induces endothelial cell (EC) transcriptional changes, the overall response dynamics of which have not been fully elucidated. In the present study, we conducted an extended time-course analysis of the human EC response to TNF, from 30 min to 72 h. We identified regulated genes and used weighted gene network correlation analysis to decipher coexpression profiles, uncovering two distinct temporal phases: an acute response (between 1 and 4 h) and a later phase (between 12 and 24 h). Sex-based subset analysis revealed that the response was comparable between female and male cells. Several previously uncharacterized genes were strongly regulated during the acute phase, whereas the majority in the later phase were IFN-stimulated genes. A lack of IFN transcription indicated that this IFN-stimulated gene expression was independent of de novo IFN production. We also observed two groups of genes whose transcription was inhibited by TNF: those that resolved toward baseline levels and those that did not. Our study provides insights into the global dynamics of the EC transcriptional response to TNF, highlighting distinct gene expression patterns during the acute and later phases. Data for all coding and noncoding genes is provided on the Web site (http://www.endothelial-response.org/). These findings may be useful in understanding the role of ECs in inflammation and in developing TNF signaling-targeted therapies.", "doi": "10.4049/jimmunol.2300419", "pmid": "38019121", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10733583"}, {"db": "pii", "key": "266486"}], "notes": [], "created": "2024-01-02T13:38:32.060Z", "modified": "2024-01-02T13:38:32.158Z"}, {"entity": "publication", "iuid": "8fa9365b538b47bcaf8b1fc0e6299f18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fa9365b538b47bcaf8b1fc0e6299f18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fa9365b538b47bcaf8b1fc0e6299f18"}}, "title": "Substance P, NPY, CCK and their receptors in five brain regions in major depressive disorder with transcriptomic analysis of locus coeruleus neurons.", "authors": [{"family": "Barde", "given": "Swapnali", "initials": "S"}, {"family": "Aguila", "given": "Julio", "initials": "J"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Solarz", "given": "Anna", "initials": "A"}, {"family": "Mei", "given": "Irene", "initials": "I"}, {"family": "Prud'homme", "given": "Josee", "initials": "J"}, {"family": "Palkovits", "given": "Miklos", "initials": "M"}, {"family": "Turecki", "given": "Gustavo", "initials": "G"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Nagy", "given": "Corina", "initials": "C"}, {"family": "Mechawar", "given": "Naguib", "initials": "N"}, {"family": "Hedlund", "given": "Eva", "initials": "E"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Eur Neuropsychopharmacol", "issn": "1873-7862", "volume": "78", "pages": "54-63", "issn-l": "0924-977X"}, "abstract": "Major depressive disorder (MDD) is a serious disease and a burden to patients, families and society. Rodent experiments and human studies suggest that several neuropeptide systems are involved in mood regulation. The aim of this study is two-fold: (i) to monitor, with qPCR, transcript levels of the substance P/tachykinin (TAC), NPY and CCK systems in bulk samples from control and suicide subjects, targeting five postmortem brain regions including locus coeruleus (LC); and (ii) to analyse expression of neuropeptide family transcripts in LC neurons of 'normal' postmortem brains by using laser capture microdissection with Smart-Seq2 RNA sequencing. qPCR revealed distinct regional expression patterns in male and female controls with higher levels for the TAC system in the dorsal raphe nucleus and LC, versus higher transcripts levels of the NPY and CCK systems in prefrontal cortex. In suicide patients, TAC, TAC receptors and a few NPY family transcript levels were increased mainly in prefrontal cortex and LC. The second study on 'normal' noradrenergic LC neurons revealed expression of transcripts for GAL, NPY, TAC1, CCK, and TACR1 and many other peptides (e.g. Cerebellin4 and CARTPT) and receptors (e.g. Adcyap1R1 and GPR173). These data and our previous results on suicide brains indicates that the tachykinin and galanin systems may be valid targets for developing antidepressant medicines. Moreover, the perturbation of neuropeptide systems in MDD patients, and the detection of further neuropeptide and receptor transcripts in LC, shed new light on signalling in noradrenergic LC neurons and on mechanisms possibly associated with mood disorders.", "doi": "10.1016/j.euroneuro.2023.09.004", "pmid": "37931511", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0924-977X(23)00682-X"}], "notes": [], "created": "2024-10-16T07:07:40.740Z", "modified": "2024-10-16T07:07:40.748Z"}, {"entity": "publication", "iuid": "dcbd5db61afd44e1a12825cbf9aa3ab7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcbd5db61afd44e1a12825cbf9aa3ab7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcbd5db61afd44e1a12825cbf9aa3ab7"}}, "title": "Population genomics of the muskox' resilience in the near absence of genetic variation.", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Garcia-Erill", "given": "Gen\u00eds", "initials": "G", "orcid": "0000-0003-3150-1708", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f24c82ea67a4df19363eb616a422eb4.json"}}, {"family": "Hangh\u00f8j", "given": "Kristian", "initials": "K", "orcid": "0000-0003-1941-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/b992ca7293ea408185d741d2af179ab4.json"}}, {"family": "Rasmussen", "given": "Malthe Sebro", "initials": "MS", "orcid": "0000-0002-2982-6258", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f925cfd53d46e3a20889d86bb75361.json"}}, {"family": "Meisner", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9540-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/b04643f766854c2ebd98d74592fe2f03.json"}}, {"family": "Liu", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-8839-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/fabce70bd90a4bfe8923d6167e236cff.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Santander", "given": "Cindy G", "initials": "CG", "orcid": "0000-0003-3021-6809", "researcher": {"href": "https://publications.scilifelab.se/researcher/da5878fe3c394895ad89147310debb7e.json"}}, {"family": "Quinn", "given": "Liam", "initials": "L", "orcid": "0000-0002-3597-2948", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8670190c2054747876bf67f9509284b.json"}}, {"family": "Lin", "given": "Long", "initials": "L", "orcid": "0000-0002-1075-6800", "researcher": {"href": "https://publications.scilifelab.se/researcher/b26a9f7b72764d298b2f1fbd618ce7a5.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S", "orcid": "0000-0001-8118-8313", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8eebb29461c4496a1b4e1b033f1afec.json"}}, {"family": "Car\u00f8e", "given": "Christian", "initials": "C", "orcid": "0000-0001-9601-6768", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb28fc94b3ad42139d7e739566f8dd90.json"}}, {"family": "Dalerum", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9737-8242", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bec76c703ab493cb883105e2ec6b2e9.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "M\u00e5sviken", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2660-7081", "researcher": {"href": "https://publications.scilifelab.se/researcher/b060865f580a44f29d46bf1bb6030f1f.json"}}, {"family": "Vartanyan", "given": "Sergey", "initials": "S", "orcid": "0000-0001-7806-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c472e06d8fa43a0b8a5575d5aec48e8.json"}}, {"family": "Raundrup", "given": "Katrine", "initials": "K", "orcid": "0000-0002-2110-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/0076f2642729447c887937c94b6b6df8.json"}}, {"family": "Al-Chaer", "given": "Amal", "initials": "A"}, {"family": "Rasmussen", "given": "Linett", "initials": "L", "orcid": "0000-0002-8050-5732", "researcher": {"href": "https://publications.scilifelab.se/researcher/d011adfb3d1d4074b3a404967b36a415.json"}}, {"family": "Hvilsom", "given": "Christina", "initials": "C", "orcid": "0000-0001-7870-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e68386a9414dad9162026abafad7ce.json"}}, {"family": "Heide-J\u00f8rgensen", "given": "Mads Peter", "initials": "MP", "orcid": "0000-0003-4846-7622", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9e5faf23cc44a0cb5d1c122a4e30ce1.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Aastrup", "given": "Peter", "initials": "P", "orcid": "0000-0003-4258-3358", "researcher": {"href": "https://publications.scilifelab.se/researcher/27511a58dd334aebbe0947cac97cb1bb.json"}}, {"family": "Van Coeverden de Groot", "given": "Peter J", "initials": "PJ"}, {"family": "Schmidt", "given": "Niels Martin", "initials": "NM", "orcid": "0000-0002-4166-6218", "researcher": {"href": "https://publications.scilifelab.se/researcher/0248915d131f49869c9c34312664b57a.json"}}, {"family": "Albrechtsen", "given": "Anders", "initials": "A", "orcid": "0000-0001-7306-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/876472bb22b141bf8d20ac3f8d04077b.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Heller", "given": "Rasmus", "initials": "R", "orcid": "0000-0001-6583-6923", "researcher": {"href": "https://publications.scilifelab.se/researcher/0289add03723441ab92592b4e3702a2c.json"}}, {"family": "Moltke", "given": "Ida", "initials": "I", "orcid": "0000-0001-7052-8554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9529133a359142b89858b1fad77ac265.json"}}, {"family": "Siegismund", "given": "Hans Redlef", "initials": "HR", "orcid": "0000-0001-5757-3131", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6451365bb8d4e86933d6c1c44e77de2.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "2", "pages": "e17205", "issn-l": "0962-1083"}, "abstract": "Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.", "doi": "10.1111/mec.17205", "pmid": "37971141", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-02T13:39:50.306Z", "modified": "2024-11-25T10:27:04.091Z"}, {"entity": "publication", "iuid": "24d4fbfa02774c67bc52b35054cf8840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24d4fbfa02774c67bc52b35054cf8840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24d4fbfa02774c67bc52b35054cf8840"}}, "title": "Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).", "authors": [{"family": "Thureborn", "given": "Olle", "initials": "O", "orcid": "0000-0002-9609-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e3d14e6d70a454babea2bbc6e0f9fc2.json"}}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N", "orcid": "0000-0002-4276-9366", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4b4d15d30e64e2c8a1a5fc0a96b9671.json"}}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG", "orcid": "0000-0003-3618-4676", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ebbe5772ea242cab27785ab8cddcdf8.json"}}, {"family": "Rydin", "given": "Catarina", "initials": "C", "orcid": "0000-0002-3347-7820", "researcher": {"href": "https://publications.scilifelab.se/researcher/70fff179e5b549c182dd7929b20f2e22.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "14", "issue": "1", "pages": "e10868", "issn-l": "2045-7758"}, "abstract": "Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.", "doi": "10.1002/ece3.10868", "pmid": "38274863", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10809029"}, {"db": "pii", "key": "ECE310868"}, {"db": "Dryad", "key": "10.5061/dryad.80gb5mkx4"}], "notes": [], "created": "2024-03-14T11:14:28.589Z", "modified": "2025-02-28T14:09:54.820Z"}, {"entity": "publication", "iuid": "3414b7217f41498abe013aa4b1b94884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3414b7217f41498abe013aa4b1b94884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3414b7217f41498abe013aa4b1b94884"}}, "title": "Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.", "authors": [{"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Rezaei Somee", "given": "Maryam", "initials": "M"}, {"family": "Gonz\u00e1lez-Rosales", "given": "Carolina", "initials": "C"}, {"family": "Lui", "given": "Lauren M", "initials": "LM"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "Westmeijer", "given": "George", "initials": "G"}, {"family": "Ashoor", "given": "Kamal", "initials": "K"}, {"family": "Nielsen", "given": "Torben N", "initials": "TN"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "4", "issue": "1", "pages": "ycae113", "issn-l": null}, "abstract": "The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.", "doi": "10.1093/ismeco/ycae113", "pmid": "39421601", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Other": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11484514"}, {"db": "pii", "key": "ycae113"}, {"db": "figshare", "key": "10.6084/m9.figshare.12170313"}], "notes": [], "created": "2024-10-31T12:39:00.306Z", "modified": "2024-11-25T10:24:49.453Z"}, {"entity": "publication", "iuid": "d63a8f09078149d8bf45ad1611ae68e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d63a8f09078149d8bf45ad1611ae68e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d63a8f09078149d8bf45ad1611ae68e1"}}, "title": "New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Keehnen", "given": "Naomi", "initials": "N"}, {"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "2", "pages": "e17213", "issn-l": "0962-1083"}, "abstract": "International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's \u03f4 and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.", "doi": "10.1111/mec.17213", "pmid": "38014725", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-02T13:26:58.174Z", "modified": "2024-11-25T10:27:09.260Z"}, {"entity": "publication", "iuid": "c7dc193c604c4e5fa865e49344129528", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528"}}, "title": "New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.", "authors": [{"family": "Bittner", "given": "Meriel J", "initials": "MJ", "orcid": "0000-0002-3798-6315", "researcher": {"href": "https://publications.scilifelab.se/researcher/5abcc332fec3408f996fff6e2470f304.json"}}, {"family": "Bannon", "given": "Catherine C", "initials": "CC", "orcid": "0000-0002-8581-1069", "researcher": {"href": "https://publications.scilifelab.se/researcher/176684868401463e8e36980a8f297ab8.json"}}, {"family": "Rowland", "given": "Elden", "initials": "E", "orcid": "0000-0003-4756-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1d771d5585492681b9c2a296a78914.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bertrand", "given": "Erin M", "initials": "EM", "orcid": "0000-0002-5950-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc79515185fc4304bb690324be48adf2.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Paerl", "given": "Ryan W", "initials": "RW", "orcid": "0000-0003-3980-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/1267dafcedd84e77aa550169e4340998.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "4", "issue": "1", "pages": "ycad016"}, "abstract": "Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.", "doi": "10.1093/ismeco/ycad016", "pmid": "38390520", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10881298"}, {"db": "pii", "key": "ycad016"}, {"db": "figshare", "key": "10.6084/m9.figshare.23634429"}], "notes": [], "created": "2024-03-14T11:11:47.095Z", "modified": "2025-02-28T14:18:29.377Z"}, {"entity": "publication", "iuid": "5e473ab0cf4f4a4e87c0fec8d4bc5aa1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e473ab0cf4f4a4e87c0fec8d4bc5aa1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e473ab0cf4f4a4e87c0fec8d4bc5aa1"}}, "title": "Molecular profiling of high-level athlete skeletal muscle after acute endurance or resistance exercise \u2013 A systems biology approach", "authors": [{"family": "Reitzner", "given": "Stefan M", "initials": "SM", "orcid": "0000-0003-0151-2780", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ca59c30b2e45459eb3638c65b452b3.json"}}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Kaczkowski", "given": "Bogumil", "initials": "B"}, {"family": "Kwon", "given": "Andrew TJ", "initials": "AT"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Chapman", "given": "Mark A", "initials": "MA"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}], "type": "journal-article", "published": "2024-01-00", "journal": {"title": "Mol Metab", "issn": "2212-8778", "pages": "101857", "volume": "79", "issn-l": "2212-8778"}, "abstract": "Long-term high-level exercise training leads to improvements in physical performance and multi-tissue adaptation following changes in molecular pathways. While skeletal muscle baseline differences between exercise-trained and untrained individuals have been previously investigated, it remains unclear how training history influences human multi-omics responses to acute exercise.\n\nWe recruited and extensively characterized 24 individuals categorized as endurance athletes with >15 years of training history, strength athletes or control subjects. Timeseries skeletal muscle biopsies were taken from M. vastus lateralis at three time-points after endurance or resistance exercise was performed and multi-omics molecular analysis performed.\n\nOur analyses revealed distinct activation differences of molecular processes such as fatty- and amino acid metabolism and transcription factors such as HIF1A and the MYF-family. We show that endurance athletes have an increased abundance of carnitine-derivates while strength athletes increase specific phospholipid metabolites compared to control subjects. Additionally, for the first time, we show the metabolite sorbitol to be substantially increased with acute exercise. On transcriptional level, we show that acute resistance exercise stimulates more gene expression than acute endurance exercise. This follows a specific pattern, with endurance athletes uniquely down-regulating pathways related to mitochondria, translation and ribosomes. Finally, both forms of exercise training specialize in diverging transcriptional directions, differentiating themselves from the transcriptome of the untrained control group.\n\nWe identify a \"transcriptional specialization effect\" by transcriptional narrowing and intensification, and molecular specialization effects on metabolomic level Additionally, we performed multi-omics network and cluster analysis, providing a novel resource of skeletal muscle transcriptomic and metabolomic profiling in highly trained and untrained individuals.", "doi": "10.1016/j.molmet.2023.101857", "pmid": "38141850", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S2212-8778(23)00191-6"}], "notes": [], "created": "2024-01-02T13:40:30.736Z", "modified": "2025-10-17T13:03:13.246Z"}, {"entity": "publication", "iuid": "e23ef99085934c69bd88198fd5fcca59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e23ef99085934c69bd88198fd5fcca59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e23ef99085934c69bd88198fd5fcca59"}}, "title": "Molecular blueprints for spinal circuit modules controlling locomotor speed in zebrafish.", "authors": [{"family": "Pallucchi", "given": "Irene", "initials": "I", "orcid": "0000-0001-6937-7306", "researcher": {"href": "https://publications.scilifelab.se/researcher/79da75b0ff6f42b996503a8b4aef7574.json"}}, {"family": "Bertuzzi", "given": "Maria", "initials": "M"}, {"family": "Madrid", "given": "David", "initials": "D"}, {"family": "Fontanel", "given": "Pierre", "initials": "P", "orcid": "0000-0002-6017-2547", "researcher": {"href": "https://publications.scilifelab.se/researcher/811aba1a7e304cbeabcdc535699f2ada.json"}}, {"family": "Higashijima", "given": "Shin-Ichi", "initials": "SI", "orcid": "0000-0001-6350-4992", "researcher": {"href": "https://publications.scilifelab.se/researcher/143e53ea3af94614b9634ad2b6a5319b.json"}}, {"family": "El Manira", "given": "Abdeljabbar", "initials": "A", "orcid": "0000-0001-5920-9384", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c6e1ed8fbb547b1844b979220d8514a.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "27", "issue": "1", "pages": "78-89", "issn-l": "1097-6256"}, "abstract": "The flexibility of motor actions is ingrained in the diversity of neurons and how they are organized into functional circuit modules, yet our knowledge of the molecular underpinning of motor circuit modularity remains limited. Here we use adult zebrafish to link the molecular diversity of motoneurons (MNs) and the rhythm-generating V2a interneurons (INs) with the modular circuit organization that is responsible for changes in locomotor speed. We show that the molecular diversity of MNs and V2a INs reflects their functional segregation into slow, intermediate or fast subtypes. Furthermore, we reveal shared molecular signatures between V2a INs and MNs of the three speed circuit modules. Overall, by characterizing how the molecular diversity of MNs and V2a INs relates to their function, connectivity and behavior, our study provides important insights not only into the molecular mechanisms for neuronal and circuit diversity for locomotor flexibility but also for charting circuits for motor actions in general.", "doi": "10.1038/s41593-023-01479-1", "pmid": "37919423", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10774144"}, {"db": "pii", "key": "10.1038/s41593-023-01479-1"}], "notes": [], "created": "2024-10-16T13:46:02.664Z", "modified": "2024-10-16T13:46:03.244Z"}, {"entity": "publication", "iuid": "2f5db4300ce24ef6a1dbbf1fc20fbda7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f5db4300ce24ef6a1dbbf1fc20fbda7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f5db4300ce24ef6a1dbbf1fc20fbda7"}}, "title": "DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems.", "authors": [{"family": "Diaz-Suarez", "given": "Alfonso", "initials": "A"}, {"family": "Noreikiene", "given": "Kristina", "initials": "K"}, {"family": "Kahar", "given": "Siim", "initials": "S"}, {"family": "Ozerov", "given": "Mikhail Y", "initials": "MY"}, {"family": "Gross", "given": "Riho", "initials": "R"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Vasem\u00e4gi", "given": "Anti", "initials": "A"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Int J Parasitol", "issn": "1879-0135", "volume": "54", "issue": "1", "pages": "33-46", "issn-l": null}, "abstract": "Eye flukes (Diplostomidae) are diverse and abundant trematode parasites that form multi-species communities in fish with negative effects on host fitness and survival. However, the environmental factors and host-related characteristics that determine species diversity, composition, and coexistence in such communities remain poorly understood. Here, we developed a cost-effective cox1 region-specific DNA metabarcoding approach to characterize parasitic diplostomid communities in two common fish species (Eurasian perch and common roach) collected from seven temperate lakes in Estonia. We found considerable inter- and intra-lake, as well as inter-host species, variation in diplostomid communities. Sympatric host species characterization revealed that parasite communities were typically more diverse in roach than perch. Additionally, we detected five positive and two negative diplostomid species associations in roach, whereas only a single negative association was observed in perch. These results indicate that diplostomid communities in temperate lakes are complex and dynamic systems exhibiting both spatial and temporal heterogeneity. They are influenced by various environmental factors and by host-parasite and inter-parasite interactions. We expect that the described methodology facilitates ecological and biodiversity research of diplostomid parasites. It is also adaptable to other parasite groups where it could serve to improve current understanding of diversity, distribution, and interspecies interactions of other understudied taxa.", "doi": "10.1016/j.ijpara.2023.07.005", "pmid": "37633409", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0020-7519(23)00173-X"}], "notes": [], "created": "2023-11-25T05:39:20.836Z", "modified": "2024-08-15T12:06:29.900Z"}, {"entity": "publication", "iuid": "437e080835214ee29720700ba7ce89d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/437e080835214ee29720700ba7ce89d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/437e080835214ee29720700ba7ce89d8"}}, "title": "Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV.", "authors": [{"family": "Ray", "given": "Shilpa", "initials": "S", "orcid": "0000-0002-9940-7366", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7aa8a3e3b554695989dfe15ee1e9239.json"}}, {"family": "Narayanan", "given": "Aswathy", "initials": "A"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Blennow", "given": "Ola", "initials": "O"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Gabarrini", "given": "Giorgio", "initials": "G", "orcid": "0000-0001-6936-4919", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbb92481579b4a23afefbbed5ad59a9a.json"}}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "H"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Chen", "given": "Margaret S\u00e4llberg", "initials": "MS", "orcid": "0000-0002-3793-4064", "researcher": {"href": "https://publications.scilifelab.se/researcher/af31e38e29a24d208df80184c563357f.json"}}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}], "type": "journal article", "published": "2023-12-20", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "issn-l": "2055-5008", "volume": "9", "issue": "1", "pages": "104"}, "abstract": "Although mRNA SARS-CoV-2 vaccines are generally safe and effective, in certain immunocompromised individuals they can elicit poor immunogenic responses. Among these individuals, people living with HIV (PLWH) have poor immunogenicity to several oral and parenteral vaccines. As the gut microbiome is known to affect vaccine immunogenicity, we investigated whether baseline gut microbiota predicts immune responses to the BNT162b2 mRNA SARS-CoV-2 vaccine in healthy controls and PLWH after two doses of BNT162b2. Individuals with high spike IgG titers and high spike-specific CD4+ T-cell responses against SARS-CoV-2 showed low \u03b1-diversity in the gut. Here, we investigated and presented initial evidence that the gut microbial composition influences the response to BNT162b2 in PLWH. From our predictive models, Bifidobacterium and Faecalibacterium appeared to be microbial markers of individuals with higher spike IgG titers, while Cloacibacillus was associated with low spike IgG titers. We therefore propose that microbiome modulation could optimize immunogenicity of SARS-CoV-2 mRNA vaccines.", "doi": "10.1038/s41522-023-00461-w", "pmid": "38123600", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10733305"}, {"db": "pii", "key": "10.1038/s41522-023-00461-w"}], "notes": [], "created": "2024-01-02T13:29:41.728Z", "modified": "2025-11-21T12:35:21.101Z"}, {"entity": "publication", "iuid": "fc17e24f28364d3bbe5ea2d8805ae454", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc17e24f28364d3bbe5ea2d8805ae454.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc17e24f28364d3bbe5ea2d8805ae454"}}, "title": "Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish.", "authors": [{"family": "Berggren", "given": "Hanna", "initials": "H", "orcid": "0000-0002-0433-6295", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bad0ab76173410a9f73ad88c2893474.json"}}, {"family": "Nordahl", "given": "Oscar", "initials": "O"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Ye\u015ferin", "initials": "Y"}, {"family": "Larsson", "given": "Per", "initials": "P"}, {"family": "Tibblin", "given": "Petter", "initials": "P", "orcid": "0000-0001-6804-5342", "researcher": {"href": "https://publications.scilifelab.se/researcher/edb13a2aad9b4fc6a02d2ca0fb24bcb8.json"}}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}], "type": "journal article", "published": "2023-12-20", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "290", "issue": "2013", "pages": "20231608", "issn-l": "0962-8452"}, "abstract": "Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).", "doi": "10.1098/rspb.2023.1608", "pmid": "38113936", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10730295"}], "notes": [], "created": "2024-01-02T13:28:10.019Z", "modified": "2024-11-25T10:26:07.218Z"}, {"entity": "publication", "iuid": "79c72c42ec3a4ac5a5ca948ca0fdc2ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79c72c42ec3a4ac5a5ca948ca0fdc2ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79c72c42ec3a4ac5a5ca948ca0fdc2ef"}}, "title": "Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans.", "authors": [{"family": "Pu", "given": "Longjun", "initials": "L"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Lu", "given": "Qiongxuan", "initials": "Q"}, {"family": "Nilsson", "given": "Lars", "initials": "L"}, {"family": "Philbrook", "given": "Alison", "initials": "A"}, {"family": "Pandey", "given": "Anjali", "initials": "A"}, {"family": "Zhao", "given": "Lina", "initials": "L"}, {"family": "Schendel", "given": "Robin van", "initials": "RV", "orcid": "0000-0001-7068-0679", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aa5a36e5b534bab8a04b4c8f040abb4.json"}}, {"family": "Koh", "given": "Alan", "initials": "A", "orcid": "0000-0002-9267-455X", "researcher": {"href": "https://publications.scilifelab.se/researcher/af8b3e661b9247bd866018357cef9436.json"}}, {"family": "Peres", "given": "Tanara V", "initials": "TV", "orcid": "0000-0003-0199-8653", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb3594666cf4c298ca22e457ec20e28.json"}}, {"family": "Hashi", "given": "Weheliye H", "initials": "WH"}, {"family": "Myint", "given": "Si Lhyam", "initials": "SL"}, {"family": "Williams", "given": "Chloe", "initials": "C"}, {"family": "Gilthorpe", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-6884-4774", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb2a4f38fdc4e0db2516a17d9abdf06.json"}}, {"family": "Wai", "given": "Sun Nyunt", "initials": "SN", "orcid": "0000-0003-4793-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/261986c5cf8f48878b74c4f60cc7af69.json"}}, {"family": "Brown", "given": "Andre", "initials": "A"}, {"family": "Tijsterman", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8465-9002", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1e816845f6048e2a2c7dc29e9a13cdf.json"}}, {"family": "Sengupta", "given": "Piali", "initials": "P", "orcid": "0000-0001-7468-0035", "researcher": {"href": "https://publications.scilifelab.se/researcher/244628c8890d4399a0a98fb0f8bc5ae7.json"}}, {"family": "Henriksson", "given": "Johan", "initials": "J", "orcid": "0000-0002-7745-2844", "researcher": {"href": "https://publications.scilifelab.se/researcher/44339821900646b3881d4b4dfd09e8d5.json"}}, {"family": "Chen", "given": "Changchun", "initials": "C", "orcid": "0000-0003-2233-8996", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cfa009cd5bc4951bcf6d5f4265b2c68.json"}}], "type": "journal article", "published": "2023-12-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8410", "issn-l": "2041-1723"}, "abstract": "G protein-coupled receptors (GPCRs) mediate responses to various extracellular and intracellular cues. However, the large number of GPCR genes and their substantial functional redundancy make it challenging to systematically dissect GPCR functions in vivo. Here, we employ a CRISPR/Cas9-based approach, disrupting 1654 GPCR-encoding genes in 284 strains and mutating 152 neuropeptide-encoding genes in 38 strains in C. elegans. These two mutant libraries enable effective deorphanization of chemoreceptors, and characterization of receptors for neuropeptides in various cellular processes. Mutating a set of closely related GPCRs in a single strain permits the assignment of functions to GPCRs with functional redundancy. Our analyses identify a neuropeptide that interacts with three receptors in hypoxia-evoked locomotory responses, unveil a collection of regulators in pathogen-induced immune responses, and define receptors for the volatile food-related odorants. These results establish our GPCR and neuropeptide mutant libraries as valuable resources for the C. elegans community to expedite studies of GPCR signaling in multiple contexts.", "doi": "10.1038/s41467-023-44177-z", "pmid": "38110404", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10728192"}, {"db": "pii", "key": "10.1038/s41467-023-44177-z"}], "notes": [], "created": "2024-01-02T13:26:28.816Z", "modified": "2024-11-25T10:16:17.175Z"}, {"entity": "publication", "iuid": "a74a0b23a37645c6b5280129bdc64da8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a74a0b23a37645c6b5280129bdc64da8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a74a0b23a37645c6b5280129bdc64da8"}}, "title": "Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts.", "authors": [{"family": "Akuwudike", "given": "Pamela", "initials": "P"}, {"family": "L\u00f3pez-Riego", "given": "Milagrosa", "initials": "M"}, {"family": "Marczyk", "given": "Michal", "initials": "M"}, {"family": "Kocibalova", "given": "Zuzana", "initials": "Z"}, {"family": "Br\u00fcckner", "given": "Fabian", "initials": "F"}, {"family": "Pola\u0144ska", "given": "Joanna", "initials": "J"}, {"family": "Wojcik", "given": "Andrzej", "initials": "A"}, {"family": "Lundholm", "given": "Lovisa", "initials": "L"}], "type": "journal article", "published": "2023-12-15", "journal": {"title": "Front Public Health", "issn": "2296-2565", "volume": "11", "pages": "1297942", "issn-l": null}, "abstract": "Experimental studies complement epidemiological data on the biological effects of low doses and dose rates of ionizing radiation and help in determining the dose and dose rate effectiveness factor.\n\nHuman VH10 skin fibroblasts exposed to 25, 50, and 100 mGy of 137Cs gamma radiation at 1.6, 8, 12 mGy/h, and at a high dose rate of 23.4 Gy/h, were analyzed for radiation-induced short- and long-term effects. Two sample cohorts, i.e., discovery (n = 30) and validation (n = 12), were subjected to RNA sequencing. The pool of the results from those six experiments with shared conditions (1.6 mGy/h; 24 h), together with an earlier time point (0 h), constituted a third cohort (n = 12).\n\nThe 100 mGy-exposed cells at all abovementioned dose rates, harvested at 0/24 h and 21 days after exposure, showed no strong gene expression changes. DMXL2, involved in the regulation of the NOTCH signaling pathway, presented a consistent upregulation among both the discovery and validation cohorts, and was validated by qPCR. Gene set enrichment analysis revealed that the NOTCH pathway was upregulated in the pooled cohort (p = 0.76, normalized enrichment score (NES) = 0.86). Apart from upregulated apical junction and downregulated DNA repair, few pathways were consistently changed across exposed cohorts. Concurringly, cell viability assays, performed 1, 3, and 6 days post irradiation, and colony forming assay, seeded just after exposure, did not reveal any statistically significant early effects on cell growth or survival patterns. Tendencies of increased viability (day 6) and reduced colony size (day 21) were observed at 12 mGy/h and 23.4 Gy/min. Furthermore, no long-term changes were observed in cell growth curves generated up to 70 days after exposure.\n\nIn conclusion, low doses of gamma radiation given at low dose rates had no strong cytotoxic effects on radioresistant VH10 cells.", "doi": "10.3389/fpubh.2023.1297942", "pmid": "38162630", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10755029"}], "notes": [], "created": "2024-03-14T11:23:49.129Z", "modified": "2024-11-25T10:33:30.483Z"}, {"entity": "publication", "iuid": "01767a010d784ab9aeff6a91140f9d16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01767a010d784ab9aeff6a91140f9d16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01767a010d784ab9aeff6a91140f9d16"}}, "title": "Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.", "authors": [{"family": "David", "given": "Dezs\u0151", "initials": "D"}, {"family": "Fino", "given": "Joana", "initials": "J"}, {"family": "Oliveira", "given": "Renata", "initials": "R"}, {"family": "D\u00f3ria", "given": "Sofia", "initials": "S"}, {"family": "Morton", "given": "Cynthia C", "initials": "CC"}], "type": "journal article", "published": "2023-12-15", "journal": {"title": "Gene", "issn": "1879-0038", "volume": "887", "pages": "147737", "issn-l": "0378-1119"}, "abstract": "Naturally occurring balanced, unbalanced, and complex chromosomal rearrangements have been reported to cause pathogenic genomic or genetic variants leading to infertility and recurrent miscarriage. Therefore, balanced chromosomal rearrangements were used as genomic signposts for identification of candidate genes or genomic loci associated with male infertility due to defects of spermatogenesis, or with recurrent miscarriage. In three male probands, structural chromosomal variants and copy number variants were identified at nucleotide resolution by long-insert genome sequencing approaches and Sanger sequencing. The pathogenic potential of these and affected candidate genes was assessed based on convergent genomic and genotype-phenotype correlation data. Identification of balanced chromosomal rearrangement breakpoints and interpretation in the context of their genomic background of structural and copy number variants led us to conclude that the infertility due to oligoasthenozoospermia and oligozoospermia is most likely associated with a position effect on YIPF5 and SPATC1L, respectively. In a third proband with intellectual disability and recurrent miscarriage, disruption of CAMK2B causing autosomal dominant, intellectual developmental disorder 54 and increased meiotic segregation during gametogenesis of a der(22) are responsible for the reported phenotype. Our data further support the existence of loci at 5q23 and 21q22.3 for these spermatogenesis defects and highlight the importance of the naturally occurring balanced chromosomal rearrangements for assessment of the pathogenic mechanisms. Furthermore, we show comorbidities due to the same balanced chromosomal rearrangement caused by different pathogenic mechanisms.", "doi": "10.1016/j.gene.2023.147737", "pmid": "37625567", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-1119(23)00578-4"}], "notes": [], "created": "2023-10-11T12:24:05.757Z", "modified": "2023-10-19T13:04:02.075Z"}, {"entity": "publication", "iuid": "10b805170fe94fe1acccfcec55db793d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10b805170fe94fe1acccfcec55db793d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10b805170fe94fe1acccfcec55db793d"}}, "title": "A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}, {"family": "Westerberg", "given": "Ivar", "initials": "I"}, {"family": "Galbraith", "given": "James", "initials": "J"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2023-12-13", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836"}, "abstract": "Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.", "doi": "10.1093/g3journal/jkad266", "pmid": "38092066", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7471854"}], "notes": [], "created": "2024-01-02T13:29:05.665Z", "modified": "2024-01-16T13:48:31.509Z"}, {"entity": "publication", "iuid": "a6edd515f3214f8594dc78220571aa36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6edd515f3214f8594dc78220571aa36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6edd515f3214f8594dc78220571aa36"}}, "title": "The formation of the Indo-Pacific montane avifauna.", "authors": [{"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Kennedy", "given": "Jonathan David", "initials": "JD"}, {"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA", "orcid": "0000-0001-8940-456X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f54d4c39cdd74208ad03500bd22b7609.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2023-12-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8215", "issn-l": "2041-1723"}, "abstract": "The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.", "doi": "10.1038/s41467-023-43964-y", "pmid": "38081809", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10713610"}, {"db": "pii", "key": "10.1038/s41467-023-43964-y"}], "notes": [], "created": "2024-01-02T13:39:08.815Z", "modified": "2024-11-25T10:16:06.008Z"}, {"entity": "publication", "iuid": "12e49eee38b34480aa21925cdd7fa0e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12e49eee38b34480aa21925cdd7fa0e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12e49eee38b34480aa21925cdd7fa0e5"}}, "title": "The functional and molecular impact of triamcinolone acetonide on primary human bone marrow mesenchymal stem cells.", "authors": [{"family": "Kumlin", "given": "Maritha", "initials": "M"}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J"}, {"family": "Cai", "given": "Huan", "initials": "H"}, {"family": "Leonard", "given": "Elory", "initials": "E"}, {"family": "Fell\u00e4nder-Tsai", "given": "Li", "initials": "L"}, {"family": "Qian", "given": "Hong", "initials": "H"}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "21787", "issn-l": "2045-2322"}, "abstract": "Traumatic or degenerative joint pain is abundant in the population. Symptom relief by intra- and periarticular glucocorticoid administration is frequently used, however may have potentially devastating effects, changing the normal healing process of the joint. Mesenchymal stem cells (MSCs) are important for wound-healing processes due to their multipotency in regenerating osteoblasts, chondrocytes and adipocytes but also have immunomodulatory properties. The aim of this study was to investigate the impact of triamcinolone acetonide (TA) a common glucocorticoid administrated intra- and periarticularly, on human bone marrow derived MSC viability, functionality, multi-lineage differentiation and transcriptomic output. We found that TA treatment induced apoptosis and promoted adipogenesis while impairing chondrogenesis of MSCs. RNA sequencing indicated that TA modulated the inflammatory response of MSCs, which may have an impact on the immunologic environment where the inflammatory phase is a physiological part of the natural healing process. These data indicate that triamcinolone acetonide should be used with consideration bearing the patient's outcome in mind, with the intention to optimize joint recovery and homeostasis.", "doi": "10.1038/s41598-023-48448-z", "pmid": "38066109", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10709330"}, {"db": "pii", "key": "10.1038/s41598-023-48448-z"}], "notes": [], "created": "2024-01-02T13:27:30.002Z", "modified": "2024-01-02T13:27:30.006Z"}, {"entity": "publication", "iuid": "aa7e2fd0de904b36aabb562ce819de11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa7e2fd0de904b36aabb562ce819de11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa7e2fd0de904b36aabb562ce819de11"}}, "title": "Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.", "authors": [{"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Lin", "given": "Qirong", "initials": "Q", "orcid": "0000-0001-5298-7861", "researcher": {"href": "https://publications.scilifelab.se/researcher/d10a182a9f0a4ec68ff809d1ac5a13a0.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A", "orcid": "0000-0002-4773-9975", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e483b7a04bd44d0ad31e15569ea7ea9.json"}}, {"family": "Toosi", "given": "Hosein", "initials": "H", "orcid": "0000-0002-5525-4724", "researcher": {"href": "https://publications.scilifelab.se/researcher/1024be99666a46cd97c75f9220f5b931.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Steiner", "given": "Embla", "initials": "E"}, {"family": "Lu", "given": "Chang", "initials": "C", "orcid": "0000-0001-6304-2820", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0204945479c4066896ba3643fa4229a.json"}}, {"family": "Mantovani", "given": "Giulia", "initials": "G", "orcid": "0000-0002-5307-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f8e781842747bb91bdb07e9d5c0cd8.json"}}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "Jangard", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3772-2026", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dafcc3cdede495aabccee445306fac1.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0043f77cad4f6e8ab9641d7f42c420.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba167f912244d879746ed60a3c19568.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "382", "issue": "6675", "pages": "eadf8486"}, "abstract": "The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.", "doi": "10.1126/science.adf8486", "pmid": "38060664", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-09T11:23:39.309Z", "modified": "2024-01-16T13:48:31.521Z"}, {"entity": "publication", "iuid": "0196c04488ee49cc8e0460edb6b46d2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0196c04488ee49cc8e0460edb6b46d2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0196c04488ee49cc8e0460edb6b46d2d"}}, "title": "Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network.", "authors": [{"family": "Xu", "given": "Xuechun", "initials": "X"}, {"family": "Bhalla", "given": "Nayanika", "initials": "N"}, {"family": "St\u00e5hl", "given": "Patrik", "initials": "P"}, {"family": "Jald\u00e9n", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2023-12-07", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "issn-l": "1471-2105", "volume": "24", "issue": "1", "pages": "461"}, "abstract": "Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov models (HMMs) that relied on pre-segmenting ion current measurements. However, the CTC-RNN model operates independently of prior biological and physical insights.\r\n\r\nWe present a novel basecaller named Lokatt: explicit duration Markov model and residual-LSTM network. It leverages an explicit duration HMM (EDHMM) designed to model the nanopore sequencing processes. Trained on a newly generated library with methylation-free Ecoli samples and MinION R9.4.1 chemistry, the Lokatt basecaller achieves basecalling performances with a median single read identity score of 0.930, a genome coverage ratio of 99.750%, on par with existing state-of-the-art structure when trained on the same datasets.\r\n\r\nOur research underlines the potential of incorporating prior knowledge into the basecalling processes, particularly through integrating HMMs and recurrent neural networks. The Lokatt basecaller showcases the efficacy of a hybrid approach, emphasizing its capacity to achieve high-quality basecalling performance while accommodating the nuances of nanopore sequencing. These outcomes pave the way for advanced basecalling methodologies, with potential implications for enhancing the accuracy and efficiency of nanopore-based DNA sequencing protocols.", "doi": "10.1186/s12859-023-05580-x", "pmid": "38062356", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": null, "NGI Long read": null}, "xrefs": [{"db": "pmc", "key": "PMC10704643"}, {"db": "pii", "key": "10.1186/s12859-023-05580-x"}], "notes": [], "created": "2024-03-14T11:32:10.692Z", "modified": "2024-03-14T11:32:28.610Z"}, {"entity": "publication", "iuid": "fee49a2ca1774790b27d5e0b2c8eda55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fee49a2ca1774790b27d5e0b2c8eda55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fee49a2ca1774790b27d5e0b2c8eda55"}}, "title": "Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex.", "authors": [{"family": "Johansson", "given": "Ulf S", "initials": "US"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "189", "pages": "107909", "issn-l": "1055-7903"}, "abstract": "Genetic isolation and morphological differentiation are two important factors in the speciation process that not always act in concert. A rapid morphological change in a lineage can hide its close relationship to another lineage, while slight morphological differentiation between two taxa can give the appearance of a closer relationship than is actually the case. The Dollarbird (Eurystomus orientalis) and the Azure Roller (Eurystomus azureus) is such an example. Today the Dollarbird and the Azure Roller are unanimously considered to constitute two distinct species, but in a recent genetic study it has been shown that the latter taxon, despite being larger and having a distinctly different coloration, is phylogenetically nested within the former. Its precise placement within this complex has not been determined, however. In this study, we investigate the phylogenetic relationships within the Dollarbird/Azure Roller complex. We estimate divergence times and infer phylogenetic relationships using sequence data from 6,475 genome-wide intronic regions, as well as complete mitochondrial genomes, using both concatenation and multispecies coalescence approaches. We find that within the Dollarbird/Azure Roller complex there are several examples of discrepancies between genetic and morphological differentiation. The Dollarbird is currently divided into between nine to twelve subspecies. Some of these subspecies are poorly differentiated, whereas others are morphologically more clearly discernable. Our data suggest that the complex consist of at least seven distinct genetic lineages that do not entirely match the morphological variation within the group. For instance, our results show that the subspecies solomonensis from the Solomon Islands, despite being morphologically very similar to its geographically closest neighbors, in fact is a highly distinct lineage that became isolated more than 700,000 years ago. In contrast, the morphologically distinct Azure Roller, which is currently treated as a distinct species, is nested within the Dollarbird and forms a slightly younger lineage than solomonensis and is the sister group to a clade with Australian and New Guinean Dollarbirds. Our results also show a deep genetic split within the Dollarbirds on the Asian mainland. This stands in contrast to the apparent clinal morphological variation reported for the birds on the Asian mainland. We also find support for the presence of a genetically distinct clade in the Wallacea region. The birds from the Wallacea region has previously been recognized as a distinct subspecies, connectens, but is currently placed in synonymy of other subspecies. Our results are thus at odds with the current division of the Dollarbird/Azure Roller complex into two species. Given that the species status of azureus is undisputed, the apparent genetic isolation of solomonensis and its clear separation from the other lineages suggests that this taxon also warrants species status. Based on the genetic and morphological variation observed within the Dollarbird/Azure Roller complex there is little doubt that even more taxa should regarded as species, but this require further examination.", "doi": "10.1016/j.ympev.2023.107909", "pmid": "37611647", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(23)00209-9"}], "notes": [], "created": "2023-10-11T09:10:51.017Z", "modified": "2024-11-25T10:14:58.166Z"}, {"entity": "publication", "iuid": "4587d673eeec438bb581a08cf7c0f9ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4587d673eeec438bb581a08cf7c0f9ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4587d673eeec438bb581a08cf7c0f9ca"}}, "title": "Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.", "authors": [{"family": "Hensen", "given": "Noah", "initials": "N"}, {"family": "Bonometti", "given": "Lucas", "initials": "L"}, {"family": "Westerberg", "given": "Ivar", "initials": "I"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Ioana Onut", "initials": "IO"}, {"family": "Guillou", "given": "Sonia", "initials": "S"}, {"family": "Cros-Aarteil", "given": "Sandrine", "initials": "S"}, {"family": "Calhoun", "given": "Sara", "initials": "S"}, {"family": "Haridas", "given": "Sajeet", "initials": "S"}, {"family": "Kuo", "given": "Alan", "initials": "A"}, {"family": "Mondo", "given": "Stephen", "initials": "S"}, {"family": "Pangilinan", "given": "Jasmyn", "initials": "J"}, {"family": "Riley", "given": "Robert", "initials": "R"}, {"family": "LaButti", "given": "Kurt", "initials": "K"}, {"family": "Andreopoulos", "given": "Bill", "initials": "B"}, {"family": "Lipzen", "given": "Anna", "initials": "A"}, {"family": "Chen", "given": "Cindy", "initials": "C"}, {"family": "Yan", "given": "Mi", "initials": "M"}, {"family": "Daum", "given": "Chris", "initials": "C"}, {"family": "Ng", "given": "Vivian", "initials": "V"}, {"family": "Clum", "given": "Alicia", "initials": "A"}, {"family": "Steindorff", "given": "Andrei", "initials": "A"}, {"family": "Ohm", "given": "Robin A", "initials": "RA"}, {"family": "Martin", "given": "Francis", "initials": "F"}, {"family": "Silar", "given": "Philippe", "initials": "P"}, {"family": "Natvig", "given": "Donald O", "initials": "DO"}, {"family": "Lalanne", "given": "Christophe", "initials": "C"}, {"family": "Gautier", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL"}, {"family": "Kruys", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Hutchinson", "given": "Miriam I", "initials": "MI"}, {"family": "Powell", "given": "Amy Jo", "initials": "AJ"}, {"family": "Barry", "given": "Kerrie", "initials": "K"}, {"family": "Miller", "given": "Andrew N", "initials": "AN"}, {"family": "Grigoriev", "given": "Igor V", "initials": "IV"}, {"family": "Debuchy", "given": "Robert", "initials": "R"}, {"family": "Gladieux", "given": "Pierre", "initials": "P"}, {"family": "Hiltunen Thor\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "189", "pages": "107938", "issn-l": "1055-7903"}, "abstract": "The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.", "doi": "10.1016/j.ympev.2023.107938", "pmid": "37820761", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(23)00238-5"}], "notes": [], "created": "2023-11-24T18:16:04.483Z", "modified": "2024-01-16T13:48:31.570Z"}, {"entity": "publication", "iuid": "ba84364ff43d4dcdaf6b28d76f58c594", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba84364ff43d4dcdaf6b28d76f58c594.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba84364ff43d4dcdaf6b28d76f58c594"}}, "title": "An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets.", "authors": [{"family": "Tatemoto", "given": "Patricia", "initials": "P"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Bernardino", "given": "Thiago", "initials": "T"}, {"family": "Zanella", "given": "Ricardo", "initials": "R"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Zanella", "given": "Adroaldo Jos\u00e9", "initials": "AJ"}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "18", "issue": "1", "pages": "2196656", "issn-l": "1559-2294"}, "abstract": "Epigenetic mechanisms are important modulators of neurodevelopmental outcomes in the offspring of animals challenged during pregnancy. Pregnant sows living in a confined environment are challenged with stress and lack of stimulation which may result in the expression of stereotypies (repetitive behaviours without an apparent function). Little attention has been devoted to the postnatal effects of maternal stereotypies in the offspring. We investigated how the environment and stereotypies of pregnant sows affected the neuro-epigenome of their piglets. We focused on the amygdala, frontal cortex, and hippocampus, brain regions related to emotionality, learning, memory, and stress response. Differentially methylated regions (DMRs) were investigated in these brain regions of male piglets born from sows kept in an enriched vs a barren environment. Within the latter group of piglets, we compared the brain methylomes of piglets born from sows expressing stereotypies vs sows not expressing stereotypies. DMRs emerged in each comparison. While the epigenome of the hippocampus and frontal cortex of piglets is mainly affected by the maternal environment, the epigenome of the amygdala is mainly affected by maternal stereotypies. The molecular pathways and mechanisms triggered in the brains of piglets by maternal environment or stereotypies are different, which is reflected on the differential gene function associated to the DMRs found in each piglets' brain region . The present study is the first to investigate the neuro-epigenomic effects of maternal enrichment in pigs' offspring and the first to investigate the neuro-epigenomic effects of maternal stereotypies in the offspring of a mammal.", "doi": "10.1080/15592294.2023.2196656", "pmid": "37192378", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10190189"}], "notes": [], "created": "2023-10-11T12:33:45.733Z", "modified": "2024-01-16T13:48:31.582Z"}, {"entity": "publication", "iuid": "f278321a964942c58d8fad97a3a8e229", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f278321a964942c58d8fad97a3a8e229.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f278321a964942c58d8fad97a3a8e229"}}, "title": "Ovarian ER\u03b2 cistrome and transcriptome reveal chromatin interaction with LRH-1.", "authors": [{"family": "Birgersson", "given": "Madeleine", "initials": "M"}, {"family": "Indukuri", "given": "Rajitha", "initials": "R"}, {"family": "Lindquist", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Stepanauskaite", "given": "Lina", "initials": "L"}, {"family": "Luo", "given": "Qing", "initials": "Q"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Archer", "given": "Amena", "initials": "A"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2023-11-29", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "21", "issue": "1", "pages": "277", "issn-l": "1741-7007"}, "abstract": "Estrogen receptor beta (ER\u03b2, Esr2) plays a pivotal role in folliculogenesis and ovulation, yet its exact mechanism of action is mainly uncharacterized.\n\nWe here performed ER\u03b2 ChIP-sequencing of mouse ovaries followed by complementary RNA-sequencing of wild-type and ER\u03b2 knockout ovaries. By integrating the ER\u03b2 cistrome and transcriptome, we identified its direct target genes and enriched biological functions in the ovary. This demonstrated its strong impact on genes regulating organism development, cell migration, lipid metabolism, response to hypoxia, and response to estrogen. Cell-type deconvolution analysis of the bulk RNA-seq data revealed a decrease in luteal cells and an increased proportion of theca cells and a specific type of cumulus cells upon ER\u03b2 loss. Moreover, we identified a significant overlap with the gene regulatory network of liver receptor homolog 1 (LRH-1, Nr5a2) and showed that ER\u03b2 and LRH-1 extensively bound to the same chromatin locations in granulosa cells. Using ChIP-reChIP, we corroborated simultaneous ER\u03b2 and LRH-1 co-binding at the ER\u03b2-repressed gene Greb1 but not at the ER\u03b2-upregulated genes Cyp11a1 and Fkbp5. Transactivation assay experimentation further showed that ER\u03b2 and LRH-1 can inhibit their respective transcriptional activity at classical response elements.\n\nBy characterizing the genome-wide endogenous ER\u03b2 chromatin binding, gene regulations, and extensive crosstalk between ER\u03b2 and LRH-1, along with experimental corroborations, our data offer genome-wide mechanistic underpinnings of ovarian physiology and fertility.", "doi": "10.1186/s12915-023-01773-1", "pmid": "38031019", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10688478"}, {"db": "pii", "key": "10.1186/s12915-023-01773-1"}], "notes": [], "created": "2024-01-02T13:30:47.361Z", "modified": "2024-01-16T13:48:31.622Z"}, {"entity": "publication", "iuid": "55a655ce643f48fa87e39fd46539cd1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55a655ce643f48fa87e39fd46539cd1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55a655ce643f48fa87e39fd46539cd1f"}}, "title": "Shotgun metagenomes from productive lakes in an urban region of Sweden.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1649-6894", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25dfecc53e94af0b79799621f131631.json"}}, {"family": "Hampel", "given": "Justyna J", "initials": "JJ", "orcid": "0000-0002-2869-5807", "researcher": {"href": "https://publications.scilifelab.se/researcher/6400f81d7ac04606abe86b28400576dd.json"}}, {"family": "Dharamshi", "given": "Jennah", "initials": "J", "orcid": "0000-0003-4563-3939", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c4fab7c00a48b29be068ac41016947.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}], "type": "dataset", "published": "2023-11-17", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "10", "issue": "1", "pages": "810", "issn-l": "2052-4463"}, "abstract": "Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake M\u00e4laren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake M\u00e4laren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.", "doi": "10.1038/s41597-023-02722-x", "pmid": "37978200", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10656542"}, {"db": "pii", "key": "10.1038/s41597-023-02722-x"}], "notes": [], "created": "2024-01-02T13:30:18.895Z", "modified": "2024-11-25T10:19:55.700Z"}, {"entity": "publication", "iuid": "3118c95ffa7b4c70841ecdc016754edd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3118c95ffa7b4c70841ecdc016754edd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3118c95ffa7b4c70841ecdc016754edd"}}, "title": "Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.", "authors": [{"family": "Estravis Barcala", "given": "Maximiliano", "initials": "M", "orcid": "0000-0002-0337-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5bde72d803c4eeab652acd0a354893c.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Chen", "given": "Zhiqiang", "initials": "Z", "orcid": "0000-0001-9725-8929", "researcher": {"href": "https://publications.scilifelab.se/researcher/4307cfe2c0094a0492e6b8b3cece1eb5.json"}}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chaudhary", "given": "Rajiv", "initials": "R"}, {"family": "Klingberg", "given": "Adam", "initials": "A"}, {"family": "Fundova", "given": "Irena", "initials": "I"}, {"family": "Suontama", "given": "Mari", "initials": "M"}, {"family": "Hallingb\u00e4ck", "given": "Henrik", "initials": "H"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Sherwood", "given": "Ellen", "initials": "E"}, {"family": "Street", "given": "Nathaniel", "initials": "N"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2023-11-10", "journal": {"title": "Plant J.", "issn": "1365-313X", "issn-l": "0960-7412", "volume": null, "issue": null, "pages": null}, "abstract": "Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.", "doi": "10.1111/tpj.16535", "pmid": "37947292", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-11-22T11:42:36.385Z", "modified": "2024-01-16T13:48:31.686Z"}, {"entity": "publication", "iuid": "2ebb264849874de29aaa681b573207bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ebb264849874de29aaa681b573207bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ebb264849874de29aaa681b573207bb"}}, "title": "Improving diagnostic precision in primary ovarian insufficiency using comprehensive genetic and autoantibody testing.", "authors": [{"family": "Vogt", "given": "Elinor Chelsom", "initials": "EC", "orcid": "0000-0001-9810-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0184e7eaeb8f44f3b787fc6604f83aae.json"}}, {"family": "Bratland", "given": "Eirik", "initials": "E", "orcid": "0000-0002-8359-9818", "researcher": {"href": "https://publications.scilifelab.se/researcher/be609ee07e8d485aa1bbd37d6ea26d00.json"}}, {"family": "Berland", "given": "Siren", "initials": "S"}, {"family": "Berentsen", "given": "Ragnhild", "initials": "R"}, {"family": "Lund", "given": "Agnethe", "initials": "A"}, {"family": "Bj\u00f6rnsdottir", "given": "Sigridur", "initials": "S"}, {"family": "Husebye", "given": "Eystein", "initials": "E"}, {"family": "\u00d8ksnes", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2023-11-09", "journal": {"title": "Hum. Reprod.", "issn": "1460-2350", "issn-l": "0268-1161", "volume": null, "issue": null, "pages": null}, "abstract": "Is it possible to find the cause of primary ovarian insufficiency (POI) in more women by extensive screening?\r\n\r\nAdding next generation sequencing techniques including a POI-associated gene panel, extended whole exome sequencing data, as well as specific autoantibody assays to the recommended diagnostic investigations increased the determination of a potential etiological diagnosis of POI from 11% to 41%.\r\n\r\nPOI affects \u223c1% of women. Clinical presentations and pathogenic mechanisms are heterogeneous and include genetic, autoimmune, and environmental factors, but the underlying etiology remains unknown in the majority of cases.\r\n\r\nProspective cross-sectional study of 100 women with newly diagnosed POI of unknown cause consecutively referred to Haukeland University Hospital, Bergen, Norway, January 2019 to December 2021.\r\n\r\nIn addition to standard recommended diagnostic investigations including screening for chromosomal anomalies and premutations in the fragile X mental retardation 1 gene (FMR1) we used whole exome sequencing, including targeted analysis of 103 ovarian-related genes, and assays of autoantibodies against steroid cell antigens.\r\n\r\nWe identified chromosomal aberrations in 8%, FMR1 premutations in 3%, genetic variants related to POI in 16%, and autoimmune POI in 3%. Furthermore in 11% we identified POI associated genetic Variants of unknown signifcance (VUS). A homozygous pathogenic variant in the ZSWIM7 gene (NM_001042697.2) was found in two women, corroborating this as a novel cause of monogenic POI. No associations between phenotypes and genotypes were found.\r\n\r\nUse of candidate genetic and autoimmune markers limit the possibility to discover new markers. To further investigate the genetic variants, family studies would have been useful. We found a relatively high proportion of genetic variants in women from Africa and lack of genetic diversity in the genomic databases can impact diagnostic accuracy.\r\n\r\nSince no specific clinical or biochemical markers predicted the underlying cause of POI discussion of which tests should be part of diagnostic screening in clinical practice remains open. New technology has altered the availability and effectiveness of genetic testing, and cost-effectiveness analyses are required to aid sustainable diagnostics.\r\n\r\nThe study was supported by grants and fellowships from Stiftelsen Kristian Gerhard Jebsen, the Novonordisk Foundation, the Norwegian Research Council, University of Bergen, and the Regional Health Authorities of Western Norway. The authors declare no conflict of interest.\r\n\r\nNCT04082169.", "doi": "10.1093/humrep/dead233", "pmid": "37953503", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "7404896"}, {"db": "ClinicalTrials.gov", "key": "NCT04082169"}], "notes": [], "created": "2023-11-24T18:06:39.382Z", "modified": "2024-01-02T13:41:38.991Z"}, {"entity": "publication", "iuid": "34ee2d9d31294024a4bd99218824e5c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34ee2d9d31294024a4bd99218824e5c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34ee2d9d31294024a4bd99218824e5c7"}}, "title": "The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.", "authors": [{"family": "Willink", "given": "Beatriz", "initials": "B", "orcid": "0000-0002-4579-6909", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2484b770760479aa8102b95268b2de5.json"}}, {"family": "Tunstr\u00f6m", "given": "Kalle", "initials": "K", "orcid": "0000-0002-5285-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd0ddb97d724542b6e7c46f782f3bbd.json"}}, {"family": "Nil\u00e9n", "given": "Sofie", "initials": "S", "orcid": "0009-0002-0996-0182", "researcher": {"href": "https://publications.scilifelab.se/researcher/19b63b7c5ebd4b90b6431b33882c2f14.json"}}, {"family": "Chikhi", "given": "Rayan", "initials": "R"}, {"family": "Lemane", "given": "T\u00e9o", "initials": "T"}, {"family": "Takahashi", "given": "Michihiko", "initials": "M", "orcid": "0009-0000-9572-4463", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff33a3b13f4e4a3d9a312d323f3ab2f4.json"}}, {"family": "Takahashi", "given": "Yuma", "initials": "Y", "orcid": "0000-0003-1490-7837", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aaa231bbcb9421a9bca56d8c1a9b86f.json"}}, {"family": "Svensson", "given": "Erik I", "initials": "EI", "orcid": "0000-0001-9006-016X", "researcher": {"href": "https://publications.scilifelab.se/researcher/975e1e8172f64aa78265e6c7772990af.json"}}, {"family": "Wheat", "given": "Christopher West", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}], "type": "journal article", "published": "2023-11-06", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "issn-l": "2397-334X", "volume": null, "issue": null, "pages": null}, "abstract": "Sex-limited morphs can provide profound insights into the evolution and genomic architecture of complex phenotypes. Inter-sexual mimicry is one particular type of sex-limited polymorphism in which a novel morph resembles the opposite sex. While inter-sexual mimics are known in both sexes and a diverse range of animals, their evolutionary origin is poorly understood. Here, we investigated the genomic basis of female-limited morphs and male mimicry in the common bluetail damselfly. Differential gene expression between morphs has been documented in damselflies, but no causal locus has been previously identified. We found that male mimicry originated in an ancestrally sexually dimorphic lineage in association with multiple structural changes, probably driven by transposable element activity. These changes resulted in ~900 kb of novel genomic content that is partly shared by male mimics in a close relative, indicating that male mimicry is a trans-species polymorphism. More recently, a third morph originated following the translocation of part of the male-mimicry sequence into a genomic position ~3.5 mb apart. We provide evidence of balancing selection maintaining male mimicry, in line with previous field population studies. Our results underscore how structural variants affecting a handful of potentially regulatory genes and morph-specific genes can give rise to novel and complex phenotypic polymorphisms.", "doi": "10.1038/s41559-023-02243-1", "pmid": "37932383", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-023-02243-1"}], "notes": [], "created": "2023-11-19T20:04:57.151Z", "modified": "2024-01-16T13:48:31.695Z"}, {"entity": "publication", "iuid": "2a63fab4f8d341be97dda6d47d09befb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a63fab4f8d341be97dda6d47d09befb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a63fab4f8d341be97dda6d47d09befb"}}, "title": "BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.", "authors": [{"family": "H\u00f6jer", "given": "Pontus", "initials": "P", "orcid": "0000-0001-8010-4755", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f901467fc54bb3a162e533248ebb70.json"}}, {"family": "Frick", "given": "Tobias", "initials": "T", "orcid": "0000-0002-3174-2096", "researcher": {"href": "https://publications.scilifelab.se/researcher/374b7074648048cdb0823281009f73ab.json"}}, {"family": "Siga", "given": "Humam", "initials": "H", "orcid": "0000-0003-1842-0882", "researcher": {"href": "https://publications.scilifelab.se/researcher/058b6ec6390a41929dc1288f71de63d4.json"}}, {"family": "Pourbozorgi", "given": "Parham", "initials": "P", "orcid": "0000-0002-5957-627X", "researcher": {"href": "https://publications.scilifelab.se/researcher/520886f23ef54f008bff773ebb86f7b1.json"}}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A", "orcid": "0000-0001-7837-8597", "researcher": {"href": "https://publications.scilifelab.se/researcher/67107191b3e4405697d0c110b1fa2735.json"}}], "type": "journal article", "published": "2023-11-06", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": null, "issue": null, "pages": null}, "abstract": "Linked-read sequencing promises a one-method approach for genome-wide insights including single nucleotide variants (SNVs), structural variants, and haplotyping. We introduce Barcode Linked Reads (BLR), an open-source haplotyping pipeline capable of handling millions of barcodes and data from multiple linked-read technologies including DBS, 10\u00d7 Genomics, TELL-seq and stLFR. Running BLR on DBS linked-reads yielded megabase-scale phasing with low (<0.2%) switch error rates. Of 13616 protein-coding genes phased in the GIAB benchmark set (v4.2.1), 98.6% matched the BLR phasing. In addition, large structural variants showed concordance with HPRC-HG002 reference assembly calls. Compared to diploid assembly with PacBio HiFi reads, BLR phasing was more continuous when considering switch errors. We further show that integrating long reads at low coverage (\u223c10\u00d7) can improve phasing contiguity and reduce switch errors in tandem repeats. When compared to Long Ranger on 10\u00d7 Genomics data, BLR showed an increase in phase block N50 with low switch-error rates. For TELL-Seq and stLFR linked reads, BLR generated longer or similar phase block lengths and low switch error rates compared to results presented in the original publications. In conclusion, BLR provides a flexible workflow for comprehensive haplotype analysis of linked reads from multiple platforms.", "doi": "10.1093/nar/gkad1010", "pmid": "37941142", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7369811"}], "notes": [], "created": "2023-11-22T16:12:00.786Z", "modified": "2024-03-14T11:35:08.948Z"}, {"entity": "publication", "iuid": "f4021b9df07f499b87174b36df9fc9c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4021b9df07f499b87174b36df9fc9c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4021b9df07f499b87174b36df9fc9c4"}}, "title": "Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Abdelgadir", "given": "Mohanad", "initials": "M"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}, {"family": "Forsberg", "given": "Sara C", "initials": "SC"}, {"family": "Wikstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Gunnarsson", "given": "Jonas S", "initials": "JS"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Sj\u00f6ling", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "86", "issue": "4", "pages": "2357-2372", "issn-l": "0095-3628"}, "abstract": "Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.", "doi": "10.1007/s00248-023-02241-7", "pmid": "37222807", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10640501"}, {"db": "pii", "key": "10.1007/s00248-023-02241-7"}], "notes": [], "created": "2023-10-11T10:27:50.998Z", "modified": "2024-01-16T13:48:31.791Z"}, {"entity": "publication", "iuid": "d13191fe287644429bdcf022135ef86a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d13191fe287644429bdcf022135ef86a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d13191fe287644429bdcf022135ef86a"}}, "title": "Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.", "authors": [{"family": "An", "given": "Yueqing", "initials": "Y"}, {"family": "Braga", "given": "Mariana P", "initials": "MP"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "86", "issue": "4", "pages": "2477-2487", "issn-l": "0095-3628"}, "abstract": "Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that \u03b1- and \u03b2-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities.", "doi": "10.1007/s00248-023-02251-5", "pmid": "37314477", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10640405"}, {"db": "pii", "key": "10.1007/s00248-023-02251-5"}], "notes": [], "created": "2023-10-11T09:14:35.456Z", "modified": "2024-01-16T13:48:31.799Z"}, {"entity": "publication", "iuid": "a267830f3ede4dacae9c701de3f6ddd8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a267830f3ede4dacae9c701de3f6ddd8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a267830f3ede4dacae9c701de3f6ddd8"}}, "title": "Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations.", "authors": [{"family": "Aksoylu", "given": "Inci S", "initials": "IS"}, {"family": "Martin", "given": "Pauline", "initials": "P"}, {"family": "Robert", "given": "Francis", "initials": "F"}, {"family": "Szkop", "given": "Krzysztof J", "initials": "KJ"}, {"family": "Redmond", "given": "Nicholas E", "initials": "NE"}, {"family": "Bhattacharyya", "given": "Srirupa", "initials": "S"}, {"family": "Wang", "given": "Jennifer", "initials": "J"}, {"family": "Chen", "given": "Shan", "initials": "S"}, {"family": "Beauchamp", "given": "Roberta L", "initials": "RL"}, {"family": "Nobeli", "given": "Irene", "initials": "I"}, {"family": "Pelletier", "given": "Jerry", "initials": "J"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Ramesh", "given": "Vijaya", "initials": "V"}], "type": "journal article", "published": "2023-10-25", "journal": {"title": "Mol Autism", "issn": "2040-2392", "volume": "14", "issue": "1", "pages": "39", "issn-l": null}, "abstract": "Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin.\n\nHere, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272.\n\nPolysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin.\n\nOur work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND.", "doi": "10.1186/s13229-023-00572-3", "pmid": "37880800", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10601155"}, {"db": "pii", "key": "10.1186/s13229-023-00572-3"}], "notes": [], "created": "2023-11-24T18:12:57.402Z", "modified": "2023-11-24T18:14:22.371Z"}, {"entity": "publication", "iuid": "28a8e085d9004e98b312750d425227bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28a8e085d9004e98b312750d425227bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28a8e085d9004e98b312750d425227bb"}}, "title": "Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ericsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ekblom", "given": "Robert", "initials": "R", "orcid": "0000-0003-2222-1966", "researcher": {"href": "https://publications.scilifelab.se/researcher/e326451a036042b89707ea3d68af0c5c.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2023-10-17", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "1035", "issn-l": "2399-3642"}, "abstract": "Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.", "doi": "10.1038/s42003-023-05385-x", "pmid": "37848497", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Collaborative", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582009"}, {"db": "pii", "key": "10.1038/s42003-023-05385-x"}], "notes": [], "created": "2023-11-25T05:31:13.184Z", "modified": "2024-01-16T13:48:31.935Z"}, {"entity": "publication", "iuid": "a7e0b03fda004e4082417192abe4d7eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7e0b03fda004e4082417192abe4d7eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7e0b03fda004e4082417192abe4d7eb"}}, "title": "Associations between the Bacterial Composition of Farm Bulk Milk and the Microbiota in the Resulting Swedish Long-Ripened Cheese.", "authors": [{"family": "Sun", "given": "Li", "initials": "L"}, {"family": "H\u00f6jer", "given": "Annika", "initials": "A"}, {"family": "Johansson", "given": "Monika", "initials": "M"}, {"family": "Saed\u00e9n", "given": "Karin Hallin", "initials": "KH"}, {"family": "Bernes", "given": "Gun", "initials": "G", "orcid": "0000-0002-3576-8752", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c535836076464abeaf184eca2c3aac.json"}}, {"family": "Hetta", "given": "M\u00e5rten", "initials": "M"}, {"family": "Gustafsson", "given": "Anders H", "initials": "AH", "orcid": "0000-0001-9735-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef2663ea30464d399d58a4740a7e457a.json"}}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Lundh", "given": "\u00c5se", "initials": "\u00c5", "orcid": "0000-0002-1626-7063", "researcher": {"href": "https://publications.scilifelab.se/researcher/a224c2dba7b64eb6926b1ae3b2a8f276.json"}}], "type": "journal article", "published": "2023-10-16", "journal": {"title": "Foods", "issn": "2304-8158", "volume": "12", "issue": "20", "issn-l": null}, "abstract": "The maturation of a traditional Swedish long-ripened cheese has shown increasing variation in recent years and the ripening time is now generally longer than in the past. While the cheese is reliant on non-starter lactic acid bacteria for the development of its characteristic flavour, we hypothesised that the observed changes could be due to variations in the microbiota composition and number of bacteria in the raw milk used for production of the cheese. To evaluate associations between microbiota in the raw milk and the resulting cheese, three clusters of commercial farms were created to increase variation in the microbiota of dairy silo milk used for cheese production. Cheese production was performed in three periods over one year. Within each period, milk from the three farm clusters was collected separately and transported to the cheese production facility. Following pasteurisation, the milk was processed into the granular-eyed cheese and matured at a dedicated cheese-ripening facility. For each cheese batch, farm bulk and dairy silo milk samples, a starter culture, early process samples and cheese samples from different stages of maturation (7-20 months) were collected and their microbiota characterised using 16S rRNA amplicon sequencing. The microbiota in the farm bulk milk differed significantly between periods and clusters. Differences in microbiota in dairy silo milk were observed between periods, but not between farm clusters, while the cheese microbiota differed between periods and clusters. The top 13 amplicon sequence variants were dominant in early process samples and the resulting cheese, making up at least 93.3% of the relative abundance (RA). Lactococcus was the dominant genus in the early process samples and, together with Leuconostoc, also dominated in the cheese samples. Contradicting expectations, the RA of the aroma-producing genus Lactobacillus was low in cheese during ripening and there was an unexpected dominance of starter lactic acid bacteria even at the later stages of cheese ripening. To identify factors behind the recent variations in ripening time of this cheese, future studies should address the effects of process variables and the dairy environment.", "doi": "10.3390/foods12203796", "pmid": "37893689", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10606660"}, {"db": "pii", "key": "foods12203796"}], "notes": [], "created": "2023-11-24T18:11:33.105Z", "modified": "2023-11-24T18:11:33.190Z"}, {"entity": "publication", "iuid": "838e0b3db3344e009deafc5bec93347c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/838e0b3db3344e009deafc5bec93347c"}}, "title": "Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.", "authors": [{"family": "Rancilhac", "given": "Lo\u00efs", "initials": "L", "orcid": "0000-0002-9859-1448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3a53ef0421c4c0990fbf9ef20f6bd3b.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED"}, {"family": "Harris", "given": "Rebecca", "initials": "R"}, {"family": "Saitoh", "given": "Takema", "initials": "T"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "issn-l": "1063-5157", "volume": null, "issue": null, "pages": null}, "abstract": "Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the \"black-and-white wagtails\", a group of five species in the songbird genus Motacilla: one species, Motacilla alba, shows wide intra-specific plumage variation, while the four others form two pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the two species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a \"complete evidence\" phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome, to quantify the extent of discordance across genomic regions, and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investigation of genome-wide patterns of gene tree heterogeneity to help understanding the mechanisms underlying phenotypic evolution.", "doi": "10.1093/sysbio/syad062", "pmid": "37801684", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7294611"}], "notes": [], "created": "2023-10-19T13:54:24.722Z", "modified": "2024-01-16T13:48:32.004Z"}, {"entity": "publication", "iuid": "45375ebcae4042dd915bd6b469846869", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45375ebcae4042dd915bd6b469846869.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45375ebcae4042dd915bd6b469846869"}}, "title": "Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures.", "authors": [{"family": "Figiel", "given": "Sandy", "initials": "S"}, {"family": "Yin", "given": "Wencheng", "initials": "W"}, {"family": "Doultsinos", "given": "Dimitrios", "initials": "D"}, {"family": "Erickson", "given": "Andrew", "initials": "A"}, {"family": "Poulose", "given": "Ninu", "initials": "N"}, {"family": "Singh", "given": "Reema", "initials": "R"}, {"family": "Magnussen", "given": "Anette", "initials": "A"}, {"family": "Anbarasan", "given": "Thineskrishna", "initials": "T"}, {"family": "Teague", "given": "Renuka", "initials": "R"}, {"family": "He", "given": "Mengxiao", "initials": "M"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}, {"family": "Loda", "given": "Massimo", "initials": "M"}, {"family": "Verrill", "given": "Clare", "initials": "C"}, {"family": "Colling", "given": "Richard", "initials": "R"}, {"family": "Gill", "given": "Pelvender S", "initials": "PS"}, {"family": "Bryant", "given": "Richard J", "initials": "RJ"}, {"family": "Hamdy", "given": "Freddie C", "initials": "FC"}, {"family": "Woodcock", "given": "Dan J", "initials": "DJ"}, {"family": "Mills", "given": "Ian G", "initials": "IG"}, {"family": "Cussenot", "given": "Olivier", "initials": "O"}, {"family": "Lamb", "given": "Alastair D", "initials": "AD"}], "type": "letter", "published": "2023-10-03", "journal": {"title": "Mol. Cancer", "issn": "1476-4598", "issn-l": "1476-4598", "volume": "22", "issue": "1", "pages": "162"}, "abstract": "Genetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx\u00ae, Decipher\u00ae, Prostadiag\u00ae) using a step-wise approach with increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses.", "doi": "10.1186/s12943-023-01863-2", "pmid": "37789377", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10546768"}, {"db": "pii", "key": "10.1186/s12943-023-01863-2"}], "notes": [], "created": "2023-10-19T13:12:00.630Z", "modified": "2023-11-25T05:36:45.833Z"}, {"entity": "publication", "iuid": "b6fc0f9d7a044833846df2ea3ca6b15b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6fc0f9d7a044833846df2ea3ca6b15b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6fc0f9d7a044833846df2ea3ca6b15b"}}, "title": "A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo.", "authors": [{"family": "Giannakopoulou", "given": "Eirini", "initials": "E"}, {"family": "Lehander", "given": "Madeleine", "initials": "M"}, {"family": "Virding Culleton", "given": "Stina", "initials": "S"}, {"family": "Yang", "given": "Weiwen", "initials": "W"}, {"family": "Li", "given": "Yingqian", "initials": "Y"}, {"family": "Karpanen", "given": "Terhi", "initials": "T", "orcid": "0000-0002-2803-083X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6013dbea3045e798ce756d45b9777f.json"}}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T"}, {"family": "Rustad", "given": "Even H", "initials": "EH"}, {"family": "Nielsen", "given": "Morten Milek", "initials": "MM"}, {"family": "Bollineni", "given": "Ravi Chand", "initials": "RC"}, {"family": "Tran", "given": "Trung T", "initials": "TT"}, {"family": "Delic-Sarac", "given": "Marina", "initials": "M"}, {"family": "Gjerdingen", "given": "Thea Johanne", "initials": "TJ"}, {"family": "Douvlataniotis", "given": "Karolos", "initials": "K"}, {"family": "Laos", "given": "Maarja", "initials": "M"}, {"family": "Ali", "given": "Muhammad", "initials": "M"}, {"family": "Hillen", "given": "Amy", "initials": "A", "orcid": "0000-0002-8567-1545", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba7f6c5a2f04d71816a8381ede8a615.json"}}, {"family": "Mazzi", "given": "Stefania", "initials": "S"}, {"family": "Chin", "given": "Desmond Wai Loon", "initials": "DWL"}, {"family": "Mehta", "given": "Adi", "initials": "A"}, {"family": "Holm", "given": "Jeppe Sejer\u00f8", "initials": "JS"}, {"family": "Bentzen", "given": "Amalie Kai", "initials": "AK"}, {"family": "Bill", "given": "Marie", "initials": "M"}, {"family": "Griffioen", "given": "Marieke", "initials": "M", "orcid": "0000-0002-3001-4441", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb97023cdb84dd0aaecc659eca5d6a3.json"}}, {"family": "Gedde-Dahl", "given": "Tobias", "initials": "T"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fc5e4f49e4330b095c26cd965cc98.json"}}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ae0c1d2cf5461894c6d0d80ed42f68.json"}}, {"family": "Olweus", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1898-3100", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bbcafcada6a4586948b50153464ec60.json"}}], "type": "journal article", "published": "2023-10-02", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "issn-l": null}, "abstract": "Acute myeloid leukemia (AML), the most frequent leukemia in adults, is driven by recurrent somatically acquired genetic lesions in a restricted number of genes. Treatment with tyrosine kinase inhibitors has demonstrated that targeting of prevalent FMS-related receptor tyrosine kinase 3 (FLT3) gain-of-function mutations can provide significant survival benefits for patients, although the efficacy of FLT3 inhibitors in eliminating FLT3-mutated clones is variable. We identified a T cell receptor (TCR) reactive to the recurrent D835Y driver mutation in the FLT3 tyrosine kinase domain (TCRFLT3D/Y). TCRFLT3D/Y-redirected T cells selectively eliminated primary human AML cells harboring the FLT3D835Y mutation in vitro and in vivo. TCRFLT3D/Y cells rejected both CD34+ and CD34- AML in mice engrafted with primary leukemia from patients, reaching minimal residual disease-negative levels, and eliminated primary CD34+ AML leukemia-propagating cells in vivo. Thus, T cells targeting a single shared mutation can provide efficient immunotherapy toward selective elimination of clonally involved primary AML cells in vivo.", "doi": "10.1038/s43018-023-00642-8", "pmid": "37783807", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s43018-023-00642-8"}], "notes": [], "created": "2023-10-19T13:55:47.476Z", "modified": "2023-10-19T13:55:47.704Z"}, {"entity": "publication", "iuid": "b5b5c7255f784a05bc6f42ac2af8a6a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b5c7255f784a05bc6f42ac2af8a6a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b5c7255f784a05bc6f42ac2af8a6a1"}}, "title": "The dynamics of touch-responsive gene expression in cereals.", "authors": [{"family": "Darwish", "given": "Essam", "initials": "E"}, {"family": "Ghosh", "given": "Ritesh", "initials": "R"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Tsardakas Renhuldt", "given": "Nikos", "initials": "N"}, {"family": "Proux-Wera", "given": "Estelle", "initials": "E"}, {"family": "Kamal", "given": "Nadia", "initials": "N"}, {"family": "Spannagl", "given": "Manuel", "initials": "M"}, {"family": "Hause", "given": "Bettina", "initials": "B"}, {"family": "Sirijovski", "given": "Nick", "initials": "N"}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Plant J.", "issn": "1365-313X", "issn-l": "0960-7412", "volume": "116", "issue": "1", "pages": "282-302"}, "abstract": "Wind, rain, herbivores, obstacles, neighbouring plants, etc. provide important mechanical cues to steer plant growth and survival. Mechanostimulation to stimulate yield and stress resistance of crops is of significant research interest, yet a molecular understanding of transcriptional responses to touch is largely absent in cereals. To address this, we performed whole-genome transcriptomics following mechanostimulation of wheat, barley, and the recent genome-sequenced oat. The largest transcriptome changes occurred \u00b125 min after touching, with most of the genes being upregulated. While most genes returned to basal expression level by 1-2 h in oat, many genes retained high expression even 4 h post-treatment in barley and wheat. Functional categories such as transcription factors, kinases, phytohormones, and Ca2+ regulation were affected. In addition, cell wall-related genes involved in (hemi)cellulose, lignin, suberin, and callose biosynthesis were touch-responsive, providing molecular insight into mechanically induced changes in cell wall composition. Furthermore, several cereal-specific transcriptomic footprints were identified that were not observed in Arabidopsis. In oat and barley, we found evidence for systemic spreading of touch-induced signalling. Finally, we provide evidence that both the jasmonic acid-dependent and the jasmonic acid-independent pathways underlie touch-signalling in cereals, providing a detailed framework and marker genes for further study of (a)biotic stress responses in cereals.", "doi": "10.1111/tpj.16269", "pmid": "37159480", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-05-16T13:33:51.071Z", "modified": "2023-10-19T12:14:37.586Z"}, {"entity": "publication", "iuid": "8c04317c16bd45aa87bc68c221982ad6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c04317c16bd45aa87bc68c221982ad6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c04317c16bd45aa87bc68c221982ad6"}}, "title": "Similarity in milk microbiota in replicates.", "authors": [{"family": "Dahlberg", "given": "Josef", "initials": "J", "orcid": "0000-0001-8131-6725", "researcher": {"href": "https://publications.scilifelab.se/researcher/090cf8219ee047be97d9b75b104d8b7c.json"}}, {"family": "Pelve", "given": "Erik", "initials": "E"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Microbiologyopen", "issn": "2045-8827", "issn-l": "2045-8827", "volume": "12", "issue": "5", "pages": "e1383"}, "abstract": "Receiving the same results from repeated analysis of the same sample is a basic principle in science. The inability to reproduce previously published results has led to discussions of a reproducibility crisis within science. For studies of microbial communities, the problem of reproducibility is more pronounced and has, in some fields, led to a discussion on the very existence of a constantly present microbiota. In this study, DNA from 44 bovine milk samples were extracted twice and the V3-V4 region of the 16S rRNA gene was sequenced in two separate runs. The FASTQ files from the two data sets were run through the same bioinformatics pipeline using the same settings and results from the two data sets were compared. Milk samples collected maximally 2 h apart were used as replicates and permitted comparisons to be made within the same run. Results show a significant difference in species richness between the two sequencing runs although Shannon and Simpson's diversity was the same. Multivariate analyses of all samples demonstrate that the sequencing run was a driver for variation. Direct comparison of similarity between samples and sequencing run showed an average similarity of 42%-45% depending on whether binary or abundance-based similarity indices were used. Within-run comparisons of milk samples collected maximally 2 h apart showed an average similarity of 39%-47% depending on the similarity index used and that similarity differed significantly between runs. We conclude that repeated DNA extraction and sequencing significantly can affect the results of a low microbial biomass microbiota study.", "doi": "10.1002/mbo3.1383", "pmid": "37877657", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10542097"}], "notes": [], "created": "2023-11-24T18:10:29.818Z", "modified": "2024-01-16T13:48:32.027Z"}, {"entity": "publication", "iuid": "231837a3a0dd4323b22402ea267145b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/231837a3a0dd4323b22402ea267145b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/231837a3a0dd4323b22402ea267145b0"}}, "title": "Single-cell sequencing of tumor-associated macrophages in a Drosophila model.", "authors": [{"family": "Khalili", "given": "Dilan", "initials": "D"}, {"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Kunc", "given": "Martin", "initials": "M"}, {"family": "Sindlerova", "given": "Martina", "initials": "M"}, {"family": "Ankarklev", "given": "Johan", "initials": "J"}, {"family": "Theopold", "given": "Ulrich", "initials": "U"}], "type": "journal article", "published": "2023-09-19", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "14", "pages": "1243797", "issn-l": "1664-3224"}, "abstract": "Tumor-associated macrophages may act to either limit or promote tumor growth, yet the molecular basis for either path is poorly characterized.\n\nWe use a larval Drosophila model that expresses a dominant-active version of the Ras-oncogene (RasV12) to study dysplastic growth during early tumor progression. We performed single-cell RNA-sequencing of macrophage-like hemocytes to characterize these cells in tumor- compared to wild-type larvae. Hemocytes included manually extracted tumor-associated- and circulating cells.\n\nWe identified five distinct hemocyte clusters. In addition to RasV12 larvae, we included a tumor model where the activation of effector caspases was inhibited, mimicking an apoptosis-resistant setting. Circulating hemocytes from both tumor models differ qualitatively from control wild-type cells-they display an enrichment for genes involved in cell division, which was confirmed using proliferation assays. Split analysis of the tumor models further reveals that proliferation is strongest in the caspase-deficient setting. Similarly, depending on the tumor model, hemocytes that attach to tumors activate different sets of immune effectors-antimicrobial peptides dominate the response against the tumor alone, while caspase inhibition induces a shift toward members of proteolytic cascades. Finally, we provide evidence for transcript transfer between hemocytes and possibly other tissues. Taken together, our data support the usefulness of Drosophila to study the response against tumors at the organismic level.", "doi": "10.3389/fimmu.2023.1243797", "pmid": "37795097", "labels": {"Microbial Single Cell Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10546068"}], "notes": [], "created": "2023-10-06T12:18:26.110Z", "modified": "2024-01-16T13:48:32.229Z"}, {"entity": "publication", "iuid": "fd07d95de9ab4362b25137d754c76efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd07d95de9ab4362b25137d754c76efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd07d95de9ab4362b25137d754c76efa"}}, "title": "Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick.", "authors": [{"family": "Rahlff", "given": "Janina", "initials": "J", "orcid": "0000-0002-2132-2709", "researcher": {"href": "https://publications.scilifelab.se/researcher/e809f7c550ab411cbb5f861dbb104a81.json"}}, {"family": "Wietz", "given": "Matthias", "initials": "M"}, {"family": "Giebel", "given": "Helge-Ansgar", "initials": "HA", "orcid": "0000-0002-9452-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e5f611e48b4488b8cb33f393f83d1ac.json"}}, {"family": "Bayfield", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1421-7780", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb071bf951644667b670a0c00f869e46.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K"}, {"family": "Kieft", "given": "Kristopher", "initials": "K"}, {"family": "Anantharaman", "given": "Karthik", "initials": "K", "orcid": "0000-0002-9584-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/607abfd9013345a7965b5ade8d16c317.json"}}, {"family": "Ribas-Ribas", "given": "Mariana", "initials": "M", "orcid": "0000-0003-3318-5462", "researcher": {"href": "https://publications.scilifelab.se/researcher/40d063dbf04843998bba87236c5a4e77.json"}}, {"family": "Schweitzer", "given": "Hannah D", "initials": "HD"}, {"family": "Wurl", "given": "Oliver", "initials": "O"}, {"family": "Hoetzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-1932-6479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6324668ed1db48a787d75bd996d5358c.json"}}, {"family": "Antson", "given": "Alfred", "initials": "A"}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}], "type": "journal article", "published": "2023-09-18", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "3", "issue": "1", "pages": "97", "issn-l": null}, "abstract": "Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.", "doi": "10.1038/s43705-023-00307-8", "pmid": "37723220", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10507051"}, {"db": "pii", "key": "10.1038/s43705-023-00307-8"}], "notes": [], "created": "2023-10-19T13:56:47.904Z", "modified": "2024-01-16T13:48:32.239Z"}, {"entity": "publication", "iuid": "a7779ca0e6794082a6fb16d84f023606", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7779ca0e6794082a6fb16d84f023606.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7779ca0e6794082a6fb16d84f023606"}}, "title": "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.", "authors": [{"family": "Mihali\u010d", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Benz", "given": "Caroline", "initials": "C", "orcid": "0000-0002-5166-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/86628e15252f4dd98f08759d59fad848.json"}}, {"family": "Kassa", "given": "Eszter", "initials": "E"}, {"family": "Lindqvist", "given": "Richard", "initials": "R"}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Inturi", "given": "Raviteja", "initials": "R"}, {"family": "Aronsson", "given": "Hanna", "initials": "H"}, {"family": "Andersson", "given": "Eva", "initials": "E"}, {"family": "Chi", "given": "Celestine N", "initials": "CN"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "\u00d6verby", "given": "Anna K", "initials": "AK", "orcid": "0000-0001-6553-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/506b0e2b2d884f868df73c7663b9ffb7.json"}}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2023-09-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5636", "issn-l": "2041-1723"}, "abstract": "The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD \u223c 7-300 \u03bcM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.", "doi": "10.1038/s41467-023-41312-8", "pmid": "37704626", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10499821"}, {"db": "pii", "key": "10.1038/s41467-023-41312-8"}], "notes": [], "created": "2023-10-19T13:57:45.671Z", "modified": "2024-11-12T10:39:14.679Z"}, {"entity": "publication", "iuid": "523f80968c724e2f908f578a52fd9495", "links": {"self": {"href": "https://publications.scilifelab.se/publication/523f80968c724e2f908f578a52fd9495.json"}, "display": {"href": "https://publications.scilifelab.se/publication/523f80968c724e2f908f578a52fd9495"}}, "title": "A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration.", "authors": [{"family": "S\u00f8rensen", "given": "Megan E S", "initials": "MES"}, {"family": "Zlatogursky", "given": "Vasily V", "initials": "VV"}, {"family": "Onu\u0163-Br\u00e4nnstr\u00f6m", "given": "Ioana", "initials": "I"}, {"family": "Walraven", "given": "Anne", "initials": "A"}, {"family": "Foster", "given": "Rachel A", "initials": "RA"}, {"family": "Burki", "given": "Fabien", "initials": "F"}], "type": "journal article", "published": "2023-09-11", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "33", "issue": "17", "pages": "3571-3584.e6", "issn-l": "0960-9822"}, "abstract": "Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems and for understanding the evolution of plastids. Kleptoplastidy, where the plastids of prey are temporarily retained and continuously re-acquired, provides opportunities to study the transitional states of plastid establishment. Here, we investigated the poorly studied marine centrohelid Meringosphaera and its previously unidentified symbionts using culture-independent methods from environmental samples. Investigations of the 18S rDNA from single-cell assembled genomes (SAGs) revealed uncharacterized genetic diversity within Meringosphaera that likely represents multiple species. We found that Meringosphaera harbors plastids of Dictyochophyceae origin (stramenopiles), for which we recovered six full plastid genomes and found evidence of two distinct subgroups that are congruent with host identity. Environmental monitoring by qPCR and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) revealed seasonal dynamics of both host and plastid. In particular, we did not detect the plastids for 6 months of the year, which, combined with the lack of plastids in some SAGs, suggests that the plastids are temporary and the relationship is kleptoplastidic. Importantly, we found evidence of genetic integration of the kleptoplasts as we identified host-encoded plastid-associated genes, with evolutionary origins likely from the plastid source as well as from other alga sources. This is only the second case where host-encoded kleptoplast-targeted genes have been predicted in an ancestrally plastid-lacking group. Our results provide evidence for gene transfers and protein re-targeting as relatively early events in the evolution of plastid symbioses.", "doi": "10.1016/j.cub.2023.07.017", "pmid": "37536342", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "EMS186826"}, {"db": "pmc", "key": "PMC7615077"}, {"db": "pii", "key": "S0960-9822(23)00924-7"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.6313464"}], "notes": [], "created": "2023-10-11T12:15:06.299Z", "modified": "2024-01-16T13:48:32.315Z"}, {"entity": "publication", "iuid": "755e7f7e5104445e87f7735a04e84157", "links": {"self": {"href": "https://publications.scilifelab.se/publication/755e7f7e5104445e87f7735a04e84157.json"}, "display": {"href": "https://publications.scilifelab.se/publication/755e7f7e5104445e87f7735a04e84157"}}, "title": "Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development.", "authors": [{"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Zhou", "given": "Chikai", "initials": "C"}, {"family": "H\u00e4neke", "given": "Timm", "initials": "T"}, {"family": "Xiao", "given": "Yao", "initials": "Y"}, {"family": "Huang", "given": "Xiaoting", "initials": "X"}, {"family": "Rohner", "given": "Eduarde", "initials": "E", "orcid": "0000-0001-8411-3720", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7bb51a667fd4c79968aec99cf52ff58.json"}}, {"family": "Sohlm\u00e9r", "given": "Jesper", "initials": "J", "orcid": "0000-0003-2607-7500", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e770e2f774bb68ed8059bc6aa2aef.json"}}, {"family": "Grote Beverborg", "given": "Niels", "initials": "N", "orcid": "0000-0003-4629-9960", "researcher": {"href": "https://publications.scilifelab.se/researcher/4209163c007f4c7cb94cdf9777ee90cc.json"}}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}, {"family": "Sahara", "given": "Makoto", "initials": "M", "orcid": "0000-0002-6281-5454", "researcher": {"href": "https://publications.scilifelab.se/researcher/db8ed12692374718a5a07fc52e9c5c33.json"}}], "type": "journal article", "published": "2023-09-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5435", "issn-l": "2041-1723"}, "abstract": "Cardiogenic growth factors play important roles in heart development. Placental growth factor (PLGF) has previously been reported to have angiogenic effects; however, its potential role in cardiogenesis has not yet been determined. We analyze single-cell RNA-sequencing data derived from human and primate embryonic hearts and find PLGF shows a biphasic expression pattern, as it is expressed specifically on ISL1+ second heart field progenitors at an earlier stage and on vascular smooth muscle cells (SMCs) and endothelial cells (ECs) at later stages. Using chemically modified mRNAs (modRNAs), we generate a panel of cardiogenic growth factors and test their effects on enhancing cardiomyocyte (CM) and EC induction during different stages of human embryonic stem cell (hESC) differentiations. We discover that only the application of PLGF modRNA at early time points of hESC-CM differentiation can increase both CM and EC production. Conversely, genetic deletion of PLGF reduces generation of CMs, SMCs and ECs in vitro. We also confirm in vivo beneficial effects of PLGF modRNA for development of human heart progenitor-derived cardiac muscle grafts on murine kidney capsules. Further, we identify the previously unrecognized PLGF-related transcriptional networks driven by EOMES and SOX17. These results shed light on the dual cardiomyogenic and vasculogenic effects of PLGF during heart development.", "doi": "10.1038/s41467-023-41305-7", "pmid": "37669989", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10480216"}, {"db": "pii", "key": "10.1038/s41467-023-41305-7"}], "notes": [], "created": "2023-10-11T09:07:02.839Z", "modified": "2023-10-19T12:34:41.339Z"}, {"entity": "publication", "iuid": "27e5410cdd1f47228b9aa1c4b75dea54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27e5410cdd1f47228b9aa1c4b75dea54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27e5410cdd1f47228b9aa1c4b75dea54"}}, "title": "The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees.", "authors": [{"family": "Everitt", "given": "Turid", "initials": "T"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Hoffmann", "given": "Wolfgang", "initials": "W"}, {"family": "Neumann", "given": "Peter", "initials": "P"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2023-09-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "9", "issn-l": "1759-6653"}, "abstract": "A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.", "doi": "10.1093/gbe/evad157", "pmid": "37625795", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10484329"}, {"db": "pii", "key": "7251443"}], "notes": [], "created": "2023-10-11T09:08:46.279Z", "modified": "2024-01-16T13:48:32.323Z"}, {"entity": "publication", "iuid": "1aec5594a6404fb690c42c9ade3b8ffc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1aec5594a6404fb690c42c9ade3b8ffc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1aec5594a6404fb690c42c9ade3b8ffc"}}, "title": "Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer.", "authors": [{"family": "Burnett", "given": "Hamish A", "initials": "HA", "orcid": "0000-0002-1868-4944", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd65df3d6770435eaa0199cb7e679c17.json"}}, {"family": "Bieker", "given": "Vanessa C", "initials": "VC", "orcid": "0000-0002-2061-9041", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4a4bac15f0242b49d53423af4b9d420.json"}}, {"family": "Le Moullec", "given": "Mathilde", "initials": "M", "orcid": "0000-0002-3290-7091", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a561187f64f4909be869cef4cf45057.json"}}, {"family": "Peeters", "given": "Bart", "initials": "B", "orcid": "0000-0002-2341-1035", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fa56b2acf01481082a822d439f4dc0d.json"}}, {"family": "Rosvold", "given": "J\u00f8rgen", "initials": "J", "orcid": "0000-0001-9555-5217", "researcher": {"href": "https://publications.scilifelab.se/researcher/07e37674cc254b699db8aa7e0c0999cf.json"}}, {"family": "Pedersen", "given": "\u00c5shild \u00d8nvik", "initials": "\u00c5\u00d8"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Loe", "given": "Leif Egil", "initials": "LE", "orcid": "0000-0003-4804-2253", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d5922ae20d2430e88ded17dc444248e.json"}}, {"family": "Jensen", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7804-1564", "researcher": {"href": "https://publications.scilifelab.se/researcher/27e3fe8ca67c4bfea44b8bff1f996f8c.json"}}, {"family": "Hansen", "given": "Brage B", "initials": "BB", "orcid": "0000-0001-8763-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/46766648cff847ea8a82d52d02744c1d.json"}}, {"family": "Martin", "given": "Michael D", "initials": "MD", "orcid": "0000-0002-2010-5139", "researcher": {"href": "https://publications.scilifelab.se/researcher/2498075af1374bafbeefec3b208f86ff.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "9", "pages": "1531-1548", "issn-l": "1752-4571"}, "abstract": "Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.", "doi": "10.1111/eva.13585", "pmid": "37752961", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10519417"}, {"db": "pii", "key": "EVA13585"}], "notes": [], "created": "2023-10-19T13:19:05.975Z", "modified": "2023-10-19T13:19:06.280Z"}, {"entity": "publication", "iuid": "e817890e5774451c8e6fa35656545217", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e817890e5774451c8e6fa35656545217.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e817890e5774451c8e6fa35656545217"}}, "title": "Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation.", "authors": [{"family": "Brink", "given": "Daniel P", "initials": "DP"}, {"family": "Mierke", "given": "Friederike", "initials": "F"}, {"family": "Norbeck", "given": "Joakim", "initials": "J"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "Andlid", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2023-08-19", "journal": {"title": "Microb. Cell Fact.", "issn": "1475-2859", "volume": "22", "issue": "1", "pages": "160", "issn-l": "1475-2859"}, "abstract": "The non-conventional yeast Rhodotorula toruloides is an emerging host organism in biotechnology by merit of its natural capacity to accumulate high levels of carotenoids and intracellular storage lipids from a variety of carbon sources. While the number of genetic engineering strategies that employ R. toruloides is increasing, the lack of genetic tools available for modification of this yeast is still limiting strain development. For instance, several strong, constitutive R. toruloides promoters have been characterized, but to date, only five inducible promoters have been identified. Although nitrogen-limited cultivation conditions are commonly used to induce lipid accumulation in this yeast, no promoters regulated by nitrogen starvation have been described for R. toruloides.\n\nIn this study, we used a combination of genomics and transcriptomics methods to identify novel R. toruloides promoter sequences that are either inducible or repressible by nitrogen starvation. RNA sequencing was used to assess gene expression in the recently isolated strain R. toruloides BOT-A2 during exponential growth and during nitrogen starvation, when cultivated with either glucose or xylose as the carbon source. The genome of BOT-A2 was sequenced using a combination of long- and short-read sequencing and annotated with support of the RNAseq data. Differential expression analysis was used to identify genes with a |log2 fold change|\u2265 2 when comparing their expression during nitrogen depletion to that during exponential growth. The promoter regions from 16 of these genes were evaluated for their ability to drive the expression of a fluorescent reporter gene. Three promoters that were clearly upregulated under nitrogen starvation and three that were downregulated were selected and further characterized. One promoter, derived from gene RTBOTA2_003877, was found to function like an on-off switch, as it was only upregulated under full nitrogen depletion and downregulated in the presence of the nitrogen source.\n\nSix new R. toruloides promoters that were either upregulated or downregulated under nitrogen-starvation were identified. These substantially contribute to the available promoters when engineering this organism and are foreseen to be particularly useful for future engineering strategies requiring specific regulation of target genes in accordance with nitrogen availability.", "doi": "10.1186/s12934-023-02175-2", "pmid": "37598166", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10440040"}, {"db": "pii", "key": "10.1186/s12934-023-02175-2"}], "notes": [], "created": "2023-10-11T08:44:17.242Z", "modified": "2023-10-19T12:31:22.249Z"}, {"entity": "publication", "iuid": "a8d5b60301664b87994aad1147569a52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8d5b60301664b87994aad1147569a52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8d5b60301664b87994aad1147569a52"}}, "title": "Multiplexed Guide RNA Expression Leads to Increased Mutation Frequency in Targeted Window Using a CRISPR-Guided Error-Prone DNA Polymerase in Saccharomyces cerevisiae.", "authors": [{"family": "Gossing", "given": "Michael", "initials": "M", "orcid": "0000-0001-6794-0900", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c99f63c080e45de8e9f77bc605e7769.json"}}, {"family": "Limeta", "given": "Angelo", "initials": "A"}, {"family": "Skrekas", "given": "Christos", "initials": "C", "orcid": "0000-0003-2510-495X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c86ebf426834c62a60da866f01f604b.json"}}, {"family": "Wigglesworth", "given": "Mark", "initials": "M"}, {"family": "Davis", "given": "Andrew", "initials": "A"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "David", "given": "Florian", "initials": "F"}], "type": "letter", "published": "2023-08-18", "journal": {"title": "ACS Synth Biol", "issn": "2161-5063", "volume": "12", "issue": "8", "pages": "2271-2277", "issn-l": null}, "abstract": "Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology, with its ability to target a specific DNA locus using guide RNAs (gRNAs), is particularly suited for targeted mutagenesis. The targeted diversification of nucleotides in Saccharomyces cerevisiae using a CRISPR-guided error-prone DNA polymerase\u2500called yEvolvR\u2500was recently reported. Here, we investigate the effect of multiplexed expression of gRNAs flanking a short stretch of DNA on reversion and mutation frequencies using yEvolvR. Phenotypic assays demonstrate that higher reversion frequencies are observed when expressing multiple gRNAs simultaneously. Next generation sequencing reveals a synergistic effect of multiple gRNAs on mutation frequencies, which is more pronounced in a mutant with a partially defective DNA mismatch repair system. Additionally, we characterize a galactose-inducible yEvolvR, which enables temporal control of mutagenesis. This study demonstrates that multiplex expression of gRNAs and induction of mutagenesis greatly improves the capabilities of yEvolvR for generation of genetic libraries in vivo.", "doi": "10.1021/acssynbio.2c00689", "pmid": "37486342", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10443033"}], "notes": [], "created": "2023-10-11T08:45:26.264Z", "modified": "2024-01-16T13:48:32.472Z"}, {"entity": "publication", "iuid": "20ef745a74824ae895660affb2537907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20ef745a74824ae895660affb2537907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20ef745a74824ae895660affb2537907"}}, "title": "Decoding pancreatic endocrine cell differentiation and \u03b2 cell regeneration in zebrafish.", "authors": [{"family": "Mi", "given": "Jiarui", "initials": "J", "orcid": "0000-0001-6498-3817", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca048a5e8eb24bbbb09d6ea07475dad5.json"}}, {"family": "Liu", "given": "Ka-Cheuk", "initials": "KC", "orcid": "0000-0001-6082-8801", "researcher": {"href": "https://publications.scilifelab.se/researcher/5495387725884c8a969b53cad833258a.json"}}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f796ff515c95491e9cd47018e02220c0.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "33", "pages": "eadf5142", "issn-l": "2375-2548"}, "abstract": "In contrast to mice, zebrafish have an exceptional yet elusive ability to replenish lost \u03b2 cells in adulthood. Understanding this framework would provide mechanistic insights for \u03b2 cell regeneration, which may be extrapolated to humans. Here, we characterize a krt4-expressing ductal cell type, which is distinct from the putative Notch-responsive cells, showing neogenic competence and giving rise to the majority of endocrine cells during postembryonic development. Furthermore, we demonstrate a marked ductal remodeling process featuring a Notch-responsive to krt4+ luminal duct transformation during late development, indicating several origins of krt4+ ductal cells displaying similar transcriptional patterns. Single-cell transcriptomics upon a series of time points during \u03b2 cell regeneration unveil a previously unrecognized dlb+ transitional endocrine precursor cell, distinct regulons, and a differentiation trajectory involving cellular shuffling through differentiation and dedifferentiation dynamics. These results establish a model of zebrafish pancreatic endocrinogenesis and highlight key values of zebrafish for translational studies of \u03b2 cell regeneration.", "doi": "10.1126/sciadv.adf5142", "pmid": "37595046", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10438462"}], "notes": [], "created": "2024-10-15T11:03:41.228Z", "modified": "2024-10-15T11:03:41.918Z"}, {"entity": "publication", "iuid": "36f146b5c7b14bbca774b45612b1d3ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36f146b5c7b14bbca774b45612b1d3ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36f146b5c7b14bbca774b45612b1d3ec"}}, "title": "An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver.", "authors": [{"family": "Fern\u00e1ndez Moro", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6863-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/216d382919954ccfb4b47458bb3d9b08.json"}}, {"family": "Geyer", "given": "Natalie", "initials": "N"}, {"family": "Harrizi", "given": "Sara", "initials": "S"}, {"family": "Hamidi", "given": "Yousra", "initials": "Y"}, {"family": "S\u00f6derqvist", "given": "Sara", "initials": "S"}, {"family": "Kuznyecov", "given": "Danyil", "initials": "D", "orcid": "0009-0007-8218-557X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b48e050665d04e4da8484bcf6da5cc96.json"}}, {"family": "Tidholm Qvist", "given": "Evelina", "initials": "E"}, {"family": "Salmonson Schaad", "given": "Media", "initials": "M"}, {"family": "Hermann", "given": "Laura", "initials": "L"}, {"family": "Lindberg", "given": "Amanda", "initials": "A"}, {"family": "Heuchel", "given": "Rainer L", "initials": "RL", "orcid": "0000-0002-2782-585X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf96c4ef4e8c4d64bcbffdcaa994258b.json"}}, {"family": "Mart\u00edn-Bernab\u00e9", "given": "Alfonso", "initials": "A"}, {"family": "Dhanjal", "given": "Soniya", "initials": "S"}, {"family": "Navis", "given": "Anna C", "initials": "AC", "orcid": "0000-0002-5267-4678", "researcher": {"href": "https://publications.scilifelab.se/researcher/e89ad1a255984dd2ba50d83c3c0c628f.json"}}, {"family": "Villard", "given": "Christina", "initials": "C"}, {"family": "Del Valle", "given": "Andrea C", "initials": "AC", "orcid": "0000-0002-1698-9533", "researcher": {"href": "https://publications.scilifelab.se/researcher/52990e30c09c48cbbd0f39f90ab25994.json"}}, {"family": "Boz\u00f3ky", "given": "Lorand", "initials": "L"}, {"family": "Sparrelid", "given": "Ernesto", "initials": "E"}, {"family": "Dirix", "given": "Luc", "initials": "L", "orcid": "0000-0002-6248-1677", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1a10889290412e9257e79899aef2e9.json"}}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "\u00d6stman", "given": "Arne", "initials": "A", "orcid": "0000-0003-3993-0021", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa382835e9554f5db45fa6cd86f04eab.json"}}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Vermeulen", "given": "Peter B", "initials": "PB"}, {"family": "Engstrand", "given": "Jennie", "initials": "J", "orcid": "0000-0003-1123-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef6292473b94b3b90e78745841cdeaa.json"}}, {"family": "Boz\u00f3ky", "given": "B\u00e9la", "initials": "B"}, {"family": "Gerling", "given": "Marco", "initials": "M", "orcid": "0000-0002-1810-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f9aa5d37124e379eb160737d657bab.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5024", "issn-l": "2041-1723"}, "abstract": "A perimetastatic capsule is a strong positive prognostic factor in liver metastases, but its origin remains unclear. Here, we systematically quantify the capsule's extent and cellular composition in 263 patients with colorectal cancer liver metastases to investigate its clinical significance and origin. We show that survival improves proportionally with increasing encapsulation and decreasing tumor-hepatocyte contact. Immunostaining reveals the gradual zonation of the capsule, transitioning from benign-like NGFRhigh stroma at the liver edge to FAPhigh stroma towards the tumor. Encapsulation correlates with decreased tumor viability and preoperative chemotherapy. In mice, chemotherapy and tumor cell ablation induce capsule formation. Our results suggest that encapsulation develops where tumor invasion into the liver plates stalls, representing a reparative process rather than tumor-induced desmoplasia. We propose a model of metastases growth, where the efficient tumor colonization of the liver parenchyma and a reparative liver injury reaction are opposing determinants of metastasis aggressiveness.", "doi": "10.1038/s41467-023-40688-x", "pmid": "37596278", "labels": {"CRISPR Functional Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10439160"}, {"db": "pii", "key": "10.1038/s41467-023-40688-x"}], "notes": [], "created": "2023-08-20T11:51:56.440Z", "modified": "2023-10-19T12:56:35.044Z"}, {"entity": "publication", "iuid": "3e5c425e90cd4b8e82e9a2d6e76fb874", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e5c425e90cd4b8e82e9a2d6e76fb874.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e5c425e90cd4b8e82e9a2d6e76fb874"}}, "title": "Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration.", "authors": [{"family": "Munguba", "given": "Hermany", "initials": "H"}, {"family": "Nikouei", "given": "Kasra", "initials": "K"}, {"family": "Hochgerner", "given": "Hannah", "initials": "H"}, {"family": "Oberst", "given": "Polina", "initials": "P"}, {"family": "Kouznetsova", "given": "Alexandra", "initials": "A"}, {"family": "Ryge", "given": "Jesper", "initials": "J"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana Bel\u00e9n", "initials": "AB"}, {"family": "Close", "given": "Jennie", "initials": "J"}, {"family": "Batista-Brito", "given": "Renata", "initials": "R"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2023-08-15", "journal": {"title": "Neuron", "issn": "1097-4199", "issn-l": "0896-6273"}, "abstract": "Although cardinal cortical interneuron identity is established upon cell-cycle exit, it remains unclear whether specific interneuron subtypes are pre-established, and if so, how their identity is maintained prior to circuit integration. We conditionally removed Sox6 (Sox6-cKO) in migrating somatostatin (Sst+) interneurons and assessed the effects on their mature identity. In adolescent mice, five of eight molecular Sst+ subtypes were nearly absent in the Sox6-cKO cortex without a reduction in cell number. Sox6-cKO cells displayed electrophysiological maturity and expressed genes enriched within the broad class of Sst+ interneurons. Furthermore, we could infer subtype identity prior to cortical integration (embryonic day 18.5), suggesting that the loss in subtype was due to disrupted subtype maintenance. Conversely, Sox6 removal at postnatal day 7 did not disrupt marker expression in the mature cortex. Therefore, Sox6 is necessary during migration for maintenance of Sst+ subtype identity, indicating that subtype maintenance requires active transcriptional programs.", "doi": "10.1016/j.neuron.2023.07.018", "pmid": "37625400", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-6273(23)00580-9"}], "notes": [], "created": "2023-10-11T08:47:37.057Z", "modified": "2023-10-19T12:32:19.357Z"}, {"entity": "publication", "iuid": "5389ad128863443393f9abe4e554b58c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5389ad128863443393f9abe4e554b58c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5389ad128863443393f9abe4e554b58c"}}, "title": "Molecular and spatial landmarks of early mouse skin development.", "authors": [{"family": "Jacob", "given": "Tina", "initials": "T"}, {"family": "Annusver", "given": "Karl", "initials": "K"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P"}, {"family": "Dalessandri", "given": "Tim", "initials": "T"}, {"family": "Kalk", "given": "Christina", "initials": "C"}, {"family": "Levra Levron", "given": "Chiara", "initials": "C"}, {"family": "Campam\u00e0 Sanz", "given": "Nil", "initials": "N"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Mikkola", "given": "Marja L", "initials": "ML"}, {"family": "Rendl", "given": "Michael", "initials": "M"}, {"family": "Lichtenberger", "given": "Beate M", "initials": "BM"}, {"family": "Donati", "given": "Giacomo", "initials": "G"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Kasper", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2023-08-13", "journal": {"title": "Dev. Cell", "issn": "1878-1551", "issn-l": "1534-5807", "volume": null, "issue": null, "pages": null}, "abstract": "A wealth of specialized cell populations within the skin facilitates its hair-producing, protective, sensory, and thermoregulatory functions. How the vast cell-type diversity and tissue architecture develops is largely unexplored. Here, with single-cell transcriptomics, spatial cell-type assignment, and cell-lineage tracing, we deconstruct early embryonic mouse skin during the key transitions from seemingly uniform developmental precursor states to a multilayered, multilineage epithelium, and complex dermal identity. We identify the spatiotemporal emergence of hair-follicle-inducing, muscle-supportive, and fascia-forming fibroblasts. We also demonstrate the formation of the panniculus carnosus muscle (PCM), sprouting blood vessels without pericyte coverage, and the earliest residence of mast and dendritic immune cells in skin. Finally, we identify an unexpected epithelial heterogeneity within the early single-layered epidermis and a signaling-rich periderm layer. Overall, this cellular and molecular blueprint of early skin development-which can be explored at https://kasperlab.org/tools-establishes histological landmarks and highlights unprecedented dynamic interactions among skin cells.", "doi": "10.1016/j.devcel.2023.07.015", "pmid": "37591247", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1534-5807(23)00362-3"}], "notes": [], "created": "2023-10-11T10:50:48.867Z", "modified": "2023-11-16T14:35:02.978Z"}, {"entity": "publication", "iuid": "d1c6bed351434c519178da6c6291753d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1c6bed351434c519178da6c6291753d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1c6bed351434c519178da6c6291753d"}}, "title": "Graded expression of the chemokine receptor CX3CR1 marks differentiation states of human and murine T cells and enables cross-species interpretation.", "authors": [{"family": "Zwijnenburg", "given": "Anthonie Johan", "initials": "AJ"}, {"family": "Pokharel", "given": "Jyoti", "initials": "J"}, {"family": "Varnait\u0117", "given": "Renata", "initials": "R"}, {"family": "Zheng", "given": "Wenning", "initials": "W"}, {"family": "Hoffer", "given": "Elena", "initials": "E"}, {"family": "Shryki", "given": "Iman", "initials": "I"}, {"family": "Comet", "given": "Natalia Ramirez", "initials": "NR"}, {"family": "Ehrstr\u00f6m", "given": "Marcus", "initials": "M"}, {"family": "Gredmark-Russ", "given": "Sara", "initials": "S"}, {"family": "Eidsmo", "given": "Liv", "initials": "L"}, {"family": "Gerlach", "given": "Carmen", "initials": "C"}], "type": "journal article", "published": "2023-08-08", "journal": {"title": "Immunity", "issn": "1097-4180", "volume": "56", "issue": "8", "pages": "1955-1974.e10", "issn-l": "1074-7613"}, "abstract": "T cells differentiate into functionally distinct states upon antigen encounter. These states are delineated by different cell surface markers for murine and human T cells, which hamper cross-species translation of T cell properties. We aimed to identify surface markers that reflect the graded nature of CD8+ T cell differentiation and delineate functionally comparable states in mice and humans. CITEseq analyses revealed that graded expression of CX3CR1, encoding the chemokine receptor CX3CR1, correlated with the CD8+ T cell differentiation gradient. CX3CR1 expression distinguished human and murine CD8+ and CD4+ T cell states, as defined by migratory and functional properties. Graded CX3CR1 expression, refined with CD62L, accurately captured the high-dimensional T cell differentiation continuum. Furthermore, the CX3CR1 expression gradient delineated states with comparable properties in humans and mice in steady state and on longitudinally tracked virus-specific CD8+ T cells in both species. Thus, graded CX3CR1 expression provides a strategy to translate the behavior of distinct T cell differentiation states across species.", "doi": "10.1016/j.immuni.2023.06.025", "pmid": "37490909", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(23)00282-0"}], "notes": [], "created": "2023-10-11T12:34:48.216Z", "modified": "2024-10-15T13:15:22.239Z"}, {"entity": "publication", "iuid": "b2824cda334744f899eacc0cdc21ac12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2824cda334744f899eacc0cdc21ac12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2824cda334744f899eacc0cdc21ac12"}}, "title": "Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds.", "authors": [{"family": "Tan", "given": "Hui Zhen", "initials": "HZ", "orcid": "0000-0002-6750-7506", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1f78cf9a2b7486c909019461b1d253e.json"}}, {"family": "Jansen", "given": "Justin J F J", "initials": "JJFJ"}, {"family": "Allport", "given": "Gary A", "initials": "GA", "orcid": "0000-0003-2261-6386", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad69006dd1df47d881e05cf41c506b22.json"}}, {"family": "Garg", "given": "Kritika M", "initials": "KM", "orcid": "0000-0003-3510-3408", "researcher": {"href": "https://publications.scilifelab.se/researcher/90e08ad42b224e5c9d42f5dc4046795e.json"}}, {"family": "Chattopadhyay", "given": "Balaji", "initials": "B"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Pang", "given": "Sean E H", "initials": "SEH"}, {"family": "Chilton", "given": "Glen", "initials": "G"}, {"family": "Gwee", "given": "Chyi Yin", "initials": "CY", "orcid": "0000-0003-1706-0520", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e69fbd57957405c8174c18385fdb214.json"}}, {"family": "Rheindt", "given": "Frank E", "initials": "FE", "orcid": "0000-0001-8946-7085", "researcher": {"href": "https://publications.scilifelab.se/researcher/744276ae56e24e7295f672854fbaf3d9.json"}}], "type": "journal article", "published": "2023-08-07", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Understanding the relative contributions of historical and anthropogenic factors to declines in genetic diversity is important for informing conservation action. Using genome-wide DNA of fresh and historic specimens, including that of two species widely thought to be extinct, we investigated fluctuations in genetic diversity and present the first complete phylogenomic tree for all nine species of the threatened shorebird genus Numenius, known as whimbrels and curlews. Most species faced sharp declines in effective population size, a proxy for genetic diversity, soon after the Last Glacial Maximum (around 20,000 years ago). These declines occurred prior to the Anthropocene and in spite of an increase in the breeding area predicted by environmental niche modeling, suggesting that they were not caused by climatic or recent anthropogenic factors. Crucially, these genetic diversity declines coincide with mass extinctions of mammalian megafauna in the Northern Hemisphere. Among other factors, the demise of ecosystem-engineering megafauna which maintained open habitats may have been detrimental for grassland and tundra-breeding Numenius shorebirds. Our work suggests that the impact of historical factors such as megafaunal extinction may have had wider repercussions on present-day population dynamics of open habitat biota than previously appreciated.", "doi": "10.7554/eLife.85422", "pmid": "37549057", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10406428"}, {"db": "pii", "key": "85422"}], "notes": [], "created": "2023-10-11T10:25:33.739Z", "modified": "2023-10-19T12:45:36.995Z"}, {"entity": "publication", "iuid": "9c09757e502b4f28bedeb9e4e9f351d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c09757e502b4f28bedeb9e4e9f351d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c09757e502b4f28bedeb9e4e9f351d9"}}, "title": "Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.", "authors": [{"family": "Almamoun", "given": "Radwa", "initials": "R"}, {"family": "Pierozan", "given": "Paula", "initials": "P"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L"}, {"family": "Karlsson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2023-08-05", "journal": {"title": "Ecotoxicol Environ Saf", "issn": "1090-2414", "volume": "262", "pages": "115321", "issn-l": null}, "abstract": "Di-n-butyl phthalate (DBP) is a ubiquitous environmental contaminant linked with various adverse health effects, including immune system dysfunction. Gut microbial dysbiosis can contribute to a wide range of pathogenesis, particularly immune disease. Here, we investigated the impact of DBP on the gut microbiome and examined correlations with immune system changes after five weeks oral exposure (10 or 100 mg/kg/day) in adult male mice. The fecal microbiome composition was characterized using 16S rRNA sequencing. DBP-treated mice displayed a significantly distinct microbial community composition, indicated by Bray-Curtis distance. Numerous amplicon sequence variants (ASVs) at the genus level were altered. Compared to the vehicle control group, the 10 mg/kg/day DBP group had 63 more abundant and 65 less abundant ASVs, while 60 ASVs were increased and 76 ASVs were decreased in the 100 mg/kg/day DBP group. Both DBP treatment groups showed higher abundances of ASVs assigned to Desulfovibrio (Proteobacteria phylum) and Enterorhabdus genera, while ASVs belonging to Parabacteroides, Lachnospiraceae UCG-006 and Lachnoclostridium were less common compared to the control group. Interestingly, an ASV belonging to Rumniniclostridium 6, which was less abundant in DBP-treated mice, demonstrated a negative correlation with the increased number of non-classical monocytes observed in the blood of DBP-treated animals. In addition, an ASV from Lachnospiraceae UCG-001, which was more abundant in the DBP-treated animals, showed a positive correlation with the non-classical monocyte increase. This study shows that DBP exposure greatly modifies the gut bacterial microbiome and indicates a potential contribution of microbial dysbiosis to DBP-induced immune system impairment, illustrating the importance of investigating how interactions between exposome components can affect health.", "doi": "10.1016/j.ecoenv.2023.115321", "pmid": "37549549", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0147-6513(23)00825-4"}], "notes": [], "created": "2023-08-16T13:14:28.168Z", "modified": "2024-01-16T13:48:32.526Z"}, {"entity": "publication", "iuid": "cac2b2a5dca44746b91a68788dce04df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df"}}, "title": "Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.", "authors": [{"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Ehler", "given": "Edvard", "initials": "E", "orcid": "0000-0003-1774-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d5e30a4e46e47d8b800d5242e23d7de.json"}}, {"family": "Breszka", "given": "Agnieszka", "initials": "A"}, {"family": "G\u00f3rski", "given": "Jacek", "initials": "J"}, {"family": "Taras", "given": "Halina", "initials": "H"}, {"family": "Szczepanek", "given": "Anita", "initials": "A"}, {"family": "Pola\u0144ska", "given": "Marta", "initials": "M"}, {"family": "W\u0142odarczak", "given": "Piotr", "initials": "P", "orcid": "0000-0003-0359-7386", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4581e4213be44969693180b26b3f263.json"}}, {"family": "Lasota-Ku\u015b", "given": "Anna", "initials": "A", "orcid": "0000-0002-0603-846X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8716e836f3894e28bee1bcacffb7245a.json"}}, {"family": "W\u00f3jcik", "given": "Irena", "initials": "I"}, {"family": "Romaniszyn", "given": "Jan", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Ko\u015bko", "given": "Aleksander", "initials": "A"}, {"family": "Ignaczak", "given": "Marcin", "initials": "M"}, {"family": "Sadowski", "given": "Sylwester", "initials": "S"}, {"family": "Matoga", "given": "Andrzej", "initials": "A"}, {"family": "Grossman", "given": "Anna", "initials": "A"}, {"family": "Ilchyshyn", "given": "Vasyl", "initials": "V"}, {"family": "Yahodinska", "given": "Maryna O", "initials": "MO"}, {"family": "Roma\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Tunia", "given": "Krzysztof", "initials": "K"}, {"family": "Przyby\u0142a", "given": "Marcin", "initials": "M"}, {"family": "Grygiel", "given": "Ryszard", "initials": "R"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "historical article", "published": "2023-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4395"}, "abstract": "The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.", "doi": "10.1038/s41467-023-40072-9", "pmid": "37528090", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10393988"}, {"db": "pii", "key": "10.1038/s41467-023-40072-9"}], "notes": [], "created": "2023-10-19T12:43:53.699Z", "modified": "2024-01-16T13:48:32.641Z"}, {"entity": "publication", "iuid": "5f11a08653594e8c886a55b8c87b663d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f11a08653594e8c886a55b8c87b663d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f11a08653594e8c886a55b8c87b663d"}}, "title": "Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.", "authors": [{"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2023-08-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "8", "issn-l": "1759-6653"}, "abstract": "Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage.", "doi": "10.1093/gbe/evad150", "pmid": "37565492", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10462419"}, {"db": "pii", "key": "7241093"}], "notes": [], "created": "2023-10-11T09:12:00.794Z", "modified": "2024-01-16T13:48:32.669Z"}, {"entity": "publication", "iuid": "304ba3fee9f04c1d8cdb461622cc3344", "links": {"self": {"href": "https://publications.scilifelab.se/publication/304ba3fee9f04c1d8cdb461622cc3344.json"}, "display": {"href": "https://publications.scilifelab.se/publication/304ba3fee9f04c1d8cdb461622cc3344"}}, "title": "Solid-phase capture and profiling of open chromatin by spatial ATAC.", "authors": [{"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications.scilifelab.se/researcher/3144601c466246cfa70acbe8c7ee00ee.json"}}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f196173b40b4819a5fcd11bf76a4e6e.json"}}, {"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a238f7adbc242398a46fd24190a2811.json"}}, {"family": "Bhalla", "given": "Nayanika", "initials": "N", "orcid": "0000-0002-6800-0432", "researcher": {"href": "https://publications.scilifelab.se/researcher/add89d1454ce490ab138768993411d70.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "41", "issue": "8", "pages": "1085-1088"}, "abstract": "Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.", "doi": "10.1038/s41587-022-01603-9", "pmid": "36604544", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Spatial omics": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10421738"}, {"db": "pii", "key": "10.1038/s41587-022-01603-9"}], "notes": [], "created": "2023-01-13T13:02:50.766Z", "modified": "2024-01-16T13:48:32.685Z"}, {"entity": "publication", "iuid": "21acaa69979c4e2cbe8dd6a3a61c1fb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21acaa69979c4e2cbe8dd6a3a61c1fb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21acaa69979c4e2cbe8dd6a3a61c1fb1"}}, "title": "Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements.", "authors": [{"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L", "orcid": "0000-0003-0104-4796", "researcher": {"href": "https://publications.scilifelab.se/researcher/a45738fda5954b73a28e47430c4b1f20.json"}}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "19", "issue": "8", "pages": "e1010717", "issn-l": "1553-7390"}, "abstract": "Reshuffling of genetic variation occurs both by independent assortment of chromosomes and by homologous recombination. Such reshuffling can generate novel allele combinations and break linkage between advantageous and deleterious variants which increases both the potential and the efficacy of natural selection. Here we used high-density linkage maps to characterize global and regional recombination rate variation in two populations of the wood white butterfly (Leptidea sinapis) that differ considerably in their karyotype as a consequence of at least 27 chromosome fissions and fusions. The recombination data were compared to estimates of genetic diversity and measures of selection to assess the relationship between chromosomal rearrangements, crossing over, maintenance of genetic diversity and adaptation. Our data show that the recombination rate is influenced by both chromosome size and number, but that the difference in the number of crossovers between karyotypes is reduced as a consequence of a higher frequency of double crossovers in larger chromosomes. As expected from effects of selection on linked sites, we observed an overall positive association between recombination rate and genetic diversity in both populations. Our results also revealed a significant effect of chromosomal rearrangements on the rate of intergenic diversity change between populations, but limited effects on polymorphisms in coding sequence. We conclude that chromosomal rearrangements can have considerable effects on the recombination landscape and consequently influence both maintenance of genetic diversity and efficiency of selection in natural populations.", "doi": "10.1371/journal.pgen.1010717", "pmid": "37549188", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10434929"}, {"db": "pii", "key": "PGENETICS-D-23-00339"}], "notes": [], "created": "2023-10-11T09:12:41.322Z", "modified": "2024-01-16T13:48:32.739Z"}, {"entity": "publication", "iuid": "2d9f608223ca4943b796ebbb3a671d0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d9f608223ca4943b796ebbb3a671d0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d9f608223ca4943b796ebbb3a671d0c"}}, "title": "Methylation of lysine 36 on histone H3 is required to control transposon activities in somatic cells.", "authors": [{"family": "Lindehell", "given": "Henrik", "initials": "H", "orcid": "0000-0003-1195-2341", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffc62dbca3145d8849c0dbbb16d44b3.json"}}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB"}, {"family": "Larsson", "given": "Jan", "initials": "J", "orcid": "0000-0003-4373-6790", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6f8e41628d4534879edaf229575dec.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "6", "issue": "8", "issn-l": "2575-1077"}, "abstract": "Transposable elements constitute a substantial portion of most eukaryotic genomes and their activity can lead to developmental and neuronal defects. In the germline, transposon activity is antagonized by the PIWI-interacting RNA pathway tasked with repression of transposon transcription and degrading transcripts that have already been produced. However, most of the genes required for transposon control are not expressed outside the germline, prompting the question: what causes deleterious transposons activity in the soma and how is it managed? Here, we show that disruptions of the Histone 3 lysine 36 methylation machinery led to increased transposon transcription in Drosophila melanogaster brains and that there is division of labour for the repression of transposable elements between the different methyltransferases Set2, NSD, and Ash1. Furthermore, we show that disruption of methylation leads to somatic activation of key genes in the PIWI-interacting RNA pathway and the preferential production of RNA from dual-strand piRNA clusters.", "doi": "10.26508/lsa.202201832", "pmid": "37169594", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10176111"}, {"db": "pii", "key": "6/8/e202201832"}], "notes": [], "created": "2023-10-04T12:51:01.650Z", "modified": "2024-01-16T13:48:32.747Z"}, {"entity": "publication", "iuid": "345d335f75d34a9c989df5d83cc38c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/345d335f75d34a9c989df5d83cc38c93"}}, "title": "Historical RNA expression profiles from the extinct Tasmanian tiger.", "authors": [{"family": "M\u00e1rmol-S\u00e1nchez", "given": "Emilio", "initials": "E", "orcid": "0000-0002-4393-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d902a4dab4e48499f7e941ab4c6417f.json"}}, {"family": "Fromm", "given": "Bastian", "initials": "B", "orcid": "0000-0003-0352-3037", "researcher": {"href": "https://publications.scilifelab.se/researcher/f29dd3593b894c5e9d233da6049d59e8.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kalogeropoulos", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6717-5011", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9e4e4366bb94239b2635da3f2a510de.json"}}, {"family": "Eriksson", "given": "Eli", "initials": "E", "orcid": "0000-0002-0340-3062", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb10331c72f24f2291455003f81a7a98.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V", "orcid": "0000-0002-6810-1591", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8bb2f06511f4c3695c1e84dac62e6bb.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2975-9400", "researcher": {"href": "https://publications.scilifelab.se/researcher/db755021d4474a7c836bdb418b5d12ca.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "33", "issue": "8", "pages": "1299-1316"}, "abstract": "Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a \u223c130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.", "doi": "10.1101/gr.277663.123", "pmid": "37463752", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10552650"}, {"db": "pii", "key": "gr.277663.123"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2023-09-20T16:48:10.289Z", "modified": "2024-01-16T13:48:32.754Z"}, {"entity": "publication", "iuid": "953e70aba81b4127939f42ea17f61c21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/953e70aba81b4127939f42ea17f61c21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/953e70aba81b4127939f42ea17f61c21"}}, "title": "Evaluation of genetic demultiplexing of single-cell sequencing data from model species.", "authors": [{"family": "Cardiello", "given": "Joseph F", "initials": "JF", "orcid": "0000-0001-7212-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/f66dfd07566947b68638630de5b8e807.json"}}, {"family": "Joven Araus", "given": "Alberto", "initials": "A", "orcid": "0000-0002-0926-4665", "researcher": {"href": "https://publications.scilifelab.se/researcher/11c7df4727464e1c95bdaa9372ce7409.json"}}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S"}, {"family": "Helsens", "given": "Clement", "initials": "C", "orcid": "0000-0002-9243-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c293306f5704b2eb524f1e195dc6113.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}, {"family": "Leigh", "given": "Nicholas D", "initials": "ND", "orcid": "0000-0002-6978-6254", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7856432de344f3a2443bea13e157f8.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "6", "issue": "8", "pages": "e202301979"}, "abstract": "Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address these problems is pooling cells from multiple individuals into one sc-seq library. In humans, genotype-based computational separation (i.e., demultiplexing) of pooled sc-seq samples is common. This approach would be instrumental for studying non-isogenic model organisms. We set out to determine whether genotype-based demultiplexing could be more broadly applied among species ranging from zebrafish to non-human primates. Using such non-isogenic species, we benchmark genotype-based demultiplexing of pooled sc-seq datasets against various ground truths. We demonstrate that genotype-based demultiplexing of pooled sc-seq samples can be used with confidence in several non-isogenic model organisms and uncover limitations of this method. Importantly, the only genomic resource required for this approach is sc-seq data and a de novo transcriptome. The incorporation of pooling into sc-seq study designs will decrease cost while simultaneously increasing the reproducibility and experimental options in non-isogenic model organisms.", "doi": "10.26508/lsa.202301979", "pmid": "37197983", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10192724"}, {"db": "pii", "key": "6/8/e202301979"}], "notes": [], "created": "2022-12-01T13:53:09.953Z", "modified": "2024-10-16T13:17:03.038Z"}, {"entity": "publication", "iuid": "1d3400d45b8b493d905352f554009969", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d3400d45b8b493d905352f554009969.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d3400d45b8b493d905352f554009969"}}, "title": "Characterisation of a low methane emission rice cultivar suitable for cultivation in high latitude light and temperature conditions.", "authors": [{"family": "Hu", "given": "Jia", "initials": "J", "orcid": "0000-0002-5829-2638", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3313b4e4add403ea9242b01eef55796.json"}}, {"family": "Bettembourg", "given": "Mathilde", "initials": "M"}, {"family": "Moreno", "given": "Silvana", "initials": "S"}, {"family": "Zhang", "given": "Ai", "initials": "A"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Chuanxin", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Jens", "initials": "J"}, {"family": "Jin", "given": "Yunkai", "initials": "Y"}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Environ Sci Pollut Res", "issn": "1614-7499", "issn-l": "0944-1344", "volume": "30", "issue": "40", "pages": "92950-92962"}, "abstract": "Rice cultivation on paddy soil is commonly associated with emissions of methane, a greenhouse gas, but rice varieties may differ in their actual level of emissions. This study analysed methane emissions associated with 22 distinct rice genotypes, using gas chromatography, and identified the cultivar Heijing 5 from northern China as a potential low-methane rice variety. To confirm this and to examine whether Heijing 5 can perform similarly at higher latitudes, Heijing 5 was cultivated in field trials in China (lat. 32\u00b0 N) and Sweden (lat. 59\u00b0 N) where (i) methane emissions were measured, (ii) methanogen abundance in the rhizosphere was determined using quantitative PCR, and (iii) the concentrations of nutrients in water and of heavy metals in rice grain and paddy soil were analysed. The results demonstrated that the low-methane rice cultivar Heijing 5 can successfully complete an entire growth period at high-latitude locations such as central Sweden. Massively parallel sequencing of mRNAs identified candidate genes involved in day length and cold acclimatisation. Cultivation of Heijing 5 in central Sweden was also associated with relatively low heavy metal accumulation in rice grains and lowered nutrient losses to neighbouring water bodies.", "doi": "10.1007/s11356-023-28985-w", "pmid": "37501024", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10447601"}, {"db": "pii", "key": "10.1007/s11356-023-28985-w"}], "notes": [], "created": "2023-10-19T12:57:19.310Z", "modified": "2024-01-16T13:48:32.778Z"}, {"entity": "publication", "iuid": "c8226e5702b44441b8271c4d5639dbc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8226e5702b44441b8271c4d5639dbc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8226e5702b44441b8271c4d5639dbc6"}}, "title": "scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics.", "authors": [{"family": "Hildebrandt", "given": "Franziska", "initials": "F"}, {"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Bhandage", "given": "Amol K", "initials": "AK"}, {"family": "Divne", "given": "Anna-Maria", "initials": "AM"}, {"family": "Barren\u00e4s", "given": "Fredrik", "initials": "F"}, {"family": "Barragan", "given": "Antonio", "initials": "A"}, {"family": "Henriksson", "given": "Johan", "initials": "J"}, {"family": "Ankarklev", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-07-27", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "14", "pages": "1224591", "issn-l": "1664-3224"}, "abstract": "Dendritic cells and macrophages are integral parts of the innate immune system and gatekeepers against infection. The protozoan pathogen, Toxoplasma gondii, is known to hijack host immune cells and modulate their immune response, making it a compelling model to study host-pathogen interactions. Here we utilize single cell Dual RNA-seq to parse out heterogeneous transcription of mouse bone marrow-derived dendritic cells (BMDCs) infected with two distinct genotypes of T. gondii parasites, over multiple time points post infection. We show that the BMDCs elicit differential responses towards T. gondii infection and that the two parasite lineages distinctly manipulate subpopulations of infected BMDCs. Co-expression networks define host and parasite genes, with implications for modulation of host immunity. Integrative analysis validates previously established immune pathways and additionally, suggests novel candidate genes involved in host-pathogen interactions. Altogether, this study provides a comprehensive resource for characterizing host-pathogen interplay at high-resolution.", "doi": "10.3389/fimmu.2023.1224591", "pmid": "37575232", "labels": {"Microbial Single Cell Genomics": "Technology development", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10415529"}], "notes": [], "created": "2023-10-06T12:18:00.948Z", "modified": "2024-01-16T13:48:32.842Z"}, {"entity": "publication", "iuid": "30a1386e02c149b68921f0515981458f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30a1386e02c149b68921f0515981458f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30a1386e02c149b68921f0515981458f"}}, "title": "Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper.", "authors": [{"family": "Fridolfsson", "given": "Emil", "initials": "E", "orcid": "0000-0003-4871-7441", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f9f3d44ed8b46729bf6c3d9984bfbe6.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C", "orcid": "0000-0002-0683-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb255e90d0584d3e8128c5288a715c97.json"}}, {"family": "Lindehoff", "given": "Elin", "initials": "E", "orcid": "0000-0002-1149-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca95ca733ed448d3894e83739d758419.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K", "orcid": "0000-0002-6570-5525", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bcd7d3b7b47405185ba0d0062111a13.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Legrand", "given": "Catherine", "initials": "C", "orcid": "0000-0001-7155-3604", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2287e0a4ced4bb49ca18a67867a8815.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}], "type": "journal article", "published": "2023-07-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "11865", "issn-l": "2045-2322"}, "abstract": "The planktonic realm from bacteria to zooplankton provides the baseline for pelagic aquatic food webs. However, multiple trophic levels are seldomly included in time series studies, hampering a holistic understanding of the influence of seasonal dynamics and species interactions on food web structure and biogeochemical cycles. Here, we investigated plankton community composition, focusing on bacterio-, phyto- and large mesozooplankton, and how biotic and abiotic factors correlate at the Linnaeus Microbial Observatory (LMO) station in the Baltic Sea from 2011 to 2018. Plankton communities structures showed pronounced dynamic shifts with recurring patterns. Summarizing the parts of the planktonic microbial food web studied here to total carbon, a picture emerges with phytoplankton consistently contributing > 39% while bacterio- and large mesozooplankton contributed ~ 30% and ~ 7%, respectively, during summer. Cyanophyceae, Actinobacteria, Bacteroidetes, and Proteobacteria were important groups among the prokaryotes. Importantly, Dinophyceae, and not Bacillariophyceae, dominated the autotrophic spring bloom whereas Litostomatea (ciliates) and Appendicularia contributed significantly to the consumer entities together with the more traditionally observed mesozooplankton, Copepoda and Cladocera. Our findings of seasonality in both plankton composition and carbon stocks emphasize the importance of time series analyses of food web structure for characterizing the regulation of biogeochemical cycles and appropriately constraining ecosystem models.", "doi": "10.1038/s41598-023-38816-0", "pmid": "37481661", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10363133"}, {"db": "pii", "key": "10.1038/s41598-023-38816-0"}], "notes": [], "created": "2023-10-04T13:23:17.104Z", "modified": "2023-10-19T12:25:13.624Z"}, {"entity": "publication", "iuid": "527e3d8b82bc4ccfa7770f2835197693", "links": {"self": {"href": "https://publications.scilifelab.se/publication/527e3d8b82bc4ccfa7770f2835197693.json"}, "display": {"href": "https://publications.scilifelab.se/publication/527e3d8b82bc4ccfa7770f2835197693"}}, "title": "Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.", "authors": [{"family": "Ginja", "given": "Catarina", "initials": "C"}, {"family": "Guimar\u00e3es", "given": "Silvia", "initials": "S"}, {"family": "da Fonseca", "given": "Rute R", "initials": "RR"}, {"family": "Rasteiro", "given": "Rita", "initials": "R"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG"}, {"family": "Sarmento", "given": "Cindy", "initials": "C"}, {"family": "Belarte", "given": "Maria Carme", "initials": "MC"}, {"family": "Kallala", "given": "Nabil", "initials": "N"}, {"family": "Torres", "given": "Joan Ramon", "initials": "JR"}, {"family": "Sanmart\u00ed", "given": "Joan", "initials": "J"}, {"family": "Arruda", "given": "Ana Margarida", "initials": "AM"}, {"family": "Detry", "given": "Cleia", "initials": "C"}, {"family": "Davis", "given": "Simon", "initials": "S"}, {"family": "Matos", "given": "Jos\u00e9", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Pires", "given": "Ana Elisabete", "initials": "AE"}, {"family": "Valenzuela-Lamas", "given": "Silvia", "initials": "S"}], "type": "journal article", "published": "2023-07-21", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "26", "issue": "7", "pages": "107196", "issn-l": "2589-0042"}, "abstract": "The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (\u223c2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.", "doi": "10.1016/j.isci.2023.107196", "pmid": "37485357", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10359934"}, {"db": "pii", "key": "S2589-0042(23)01273-7"}, {"db": "Dryad", "key": "10.5061/dryad.v9s4mw71n"}], "notes": [], "created": "2023-10-11T09:18:50.650Z", "modified": "2023-10-19T12:44:38.068Z"}, {"entity": "publication", "iuid": "df7b818acd8048ebad937340458fca60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df7b818acd8048ebad937340458fca60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df7b818acd8048ebad937340458fca60"}}, "title": "FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples.", "authors": [{"family": "Iwaszkiewicz-Eggebrecht", "given": "Elzbieta", "initials": "E"}, {"family": "\u0141ukasik", "given": "Piotr", "initials": "P"}, {"family": "Buczek", "given": "Mateusz", "initials": "M"}, {"family": "Deng", "given": "Junchen", "initials": "J", "orcid": "0000-0003-3669-7172", "researcher": {"href": "https://publications.scilifelab.se/researcher/1349455ce24243e6be1abf71e3698f61.json"}}, {"family": "Hartop", "given": "Emily A", "initials": "EA"}, {"family": "Havn\u00e5s", "given": "Harald", "initials": "H"}, {"family": "Prus-Frankowska", "given": "Monika", "initials": "M"}, {"family": "Ugarph", "given": "Carina R", "initials": "CR"}, {"family": "Viteri", "given": "Paulina", "initials": "P"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}, {"family": "Miraldo", "given": "Andreia", "initials": "A"}], "type": "journal article", "published": "2023-07-19", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "18", "issue": "7", "pages": "e0286272", "issn-l": "1932-6203"}, "abstract": "Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.", "doi": "10.1371/journal.pone.0286272", "pmid": "37467453", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10356154"}, {"db": "pii", "key": "PONE-D-23-08476"}], "notes": [], "created": "2023-10-11T08:38:17.103Z", "modified": "2024-01-16T13:48:32.873Z"}, {"entity": "publication", "iuid": "295aef354d21417f9b1d254f7f751005", "links": {"self": {"href": "https://publications.scilifelab.se/publication/295aef354d21417f9b1d254f7f751005.json"}, "display": {"href": "https://publications.scilifelab.se/publication/295aef354d21417f9b1d254f7f751005"}}, "title": "Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature.", "authors": [{"family": "Lihavainen", "given": "Jenna", "initials": "J", "orcid": "0000-0001-7979-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab4d87f8aed74a9794dea29912031a93.json"}}, {"family": "\u0160imura", "given": "Jan", "initials": "J"}, {"family": "Bag", "given": "Pushan", "initials": "P", "orcid": "0000-0003-3858-4606", "researcher": {"href": "https://publications.scilifelab.se/researcher/033b97dc712047a294d3e801ba750787.json"}}, {"family": "Fataftah", "given": "Nazeer", "initials": "N"}, {"family": "Robinson", "given": "Kathryn Megan", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Ljung", "given": "Karin", "initials": "K", "orcid": "0000-0003-2901-189X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f91b1e1f90c24559b915ebcd265804a4.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "4288", "issn-l": "2041-1723"}, "abstract": "Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive \"switches\"; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.", "doi": "10.1038/s41467-023-39564-5", "pmid": "37463905", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10354028"}, {"db": "pii", "key": "10.1038/s41467-023-39564-5"}], "notes": [], "created": "2023-08-30T07:04:20.536Z", "modified": "2025-10-17T13:03:13.717Z"}, {"entity": "publication", "iuid": "54a263eed46a4d8ca6dbb82ac886808a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54a263eed46a4d8ca6dbb82ac886808a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54a263eed46a4d8ca6dbb82ac886808a"}}, "title": "Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants.", "authors": [{"family": "Hanifah", "given": "Nurul Atilia Shafienaz Binti", "initials": "NASB"}, {"family": "Ghadamgahi", "given": "Farideh", "initials": "F"}, {"family": "Ghosh", "given": "Samrat", "initials": "S"}, {"family": "Ortiz", "given": "Rodomiro", "initials": "R"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Kalyandurg", "given": "Pruthvi B", "initials": "PB"}], "type": "journal article", "published": "2023-07-18", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "14", "pages": "1141692", "issn-l": "1664-462X"}, "abstract": "The use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains: Pseudomonas fluorescens SLU99, Serratia plymuthica S412, S. rubidaea AV10, and S. rubidaea EV23. Greenhouse and in vitro experiments showed that P. fluorescens SLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield.", "doi": "10.3389/fpls.2023.1141692", "pmid": "37534284", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10393259"}], "notes": [], "created": "2023-10-11T12:16:52.510Z", "modified": "2023-10-19T13:01:31.991Z"}, {"entity": "publication", "iuid": "917f69c53a0c42acb20c8b50676c0cde", "links": {"self": {"href": "https://publications.scilifelab.se/publication/917f69c53a0c42acb20c8b50676c0cde.json"}, "display": {"href": "https://publications.scilifelab.se/publication/917f69c53a0c42acb20c8b50676c0cde"}}, "title": "Irradiation and lithium treatment alter the global DNA methylation pattern and gene expression underlying a shift from gliogenesis towards neurogenesis in human neural progenitors.", "authors": [{"family": "Neofytou", "given": "Christina", "initials": "C", "orcid": "0000-0002-1547-7085", "researcher": {"href": "https://publications.scilifelab.se/researcher/757792036d8040e8bebe763443aab360.json"}}, {"family": "Backlund", "given": "Alexandra", "initials": "A"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}, {"family": "Hermanson", "given": "Ola", "initials": "O", "orcid": "0000-0001-9320-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/127407b365334524be30de6c31aec5ba.json"}}], "type": "journal article", "published": "2023-07-13", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "volume": "13", "issue": "1", "pages": "258", "issn-l": "2158-3188"}, "abstract": "Central nervous system (CNS) tumors account for almost a third of pediatric cancers and are the largest contributor to cancer-related death in children. Cranial radiation therapy (CRT) is, often in combination with chemotherapy and surgery, effective in the treatment of high-grade childhood brain cancers, but it has been associated with late complications in 50-90% of survivors, such as decline in cognition and mood, decreased social competence, and fatigue. A leading hypothesis to explain the decline in cognition, at least partially, is injury to the neural stem and progenitor cells (NSPCs), which leads to apoptosis and altered fate choice, favoring gliogenesis over neurogenesis. Hence, treatments harnessing neurogenesis are of great relevance in this context. Lithium, a well-known mood stabilizer, has neuroprotective and antitumor effects and has been found to reverse irradiation-induced damage in rodents, at least in part by regulating the expression of the glutamate decarboxylase 2 gene (Gad2) via promoter demethylation in rat NSPCs. Additionally, lithium was shown to rescue irradiation-induced cognitive defects in mice. Here, we show that irradiation (IR) alone or in combination with lithium chloride (LiCl) caused major changes in gene expression and global DNA methylation in iPSC-derived human NSPCs (hNSPCs) compared to untreated cells, as well as LiCl-only-treated cells. The pattern of DNA methylation changes after IR-treatment alone was stochastic and observed across many different gene groups, whereas differences in DNA methylation after LiCl-treatment of irradiated cells were more directed to specific promoters of genes, including genes associated with neurogenesis, for example GAD2. Interestingly, IR and IR + LiCl treatment affected the promoter methylation and expression of several genes encoding factors involved in BMP signaling, including the BMP antagonist gremlin1. We propose that lithium in addition to promoting neuronal differentiation, also represses glial differentiation in hNSPCs with DNA methylation regulation being a key mechanism of action.", "doi": "10.1038/s41398-023-02560-w", "pmid": "37443041", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10345108"}, {"db": "pii", "key": "10.1038/s41398-023-02560-w"}], "notes": [], "created": "2023-10-11T10:47:25.231Z", "modified": "2023-10-19T12:53:20.882Z"}, {"entity": "publication", "iuid": "d01d821e756b4e1fa367a57db292c956", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d01d821e756b4e1fa367a57db292c956.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d01d821e756b4e1fa367a57db292c956"}}, "title": "Proteomic and transcriptomic screening demonstrates increased mast cell-derived CCL23 in systemic mastocytosis.", "authors": [{"family": "S\u00f6derlund", "given": "Stina", "initials": "S"}, {"family": "Boey", "given": "Daryl", "initials": "D"}, {"family": "van Midden", "given": "Wouter", "initials": "W"}, {"family": "Kjellander", "given": "Matilda", "initials": "M"}, {"family": "Ax", "given": "Kajsa", "initials": "K"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Dahlin", "given": "Joakim S", "initials": "JS"}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J"}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "J. Allergy Clin. Immunol.", "issn": "1097-6825", "volume": "152", "issue": "1", "pages": "205-213", "issn-l": "0091-6749"}, "abstract": "Systemic mastocytosis (SM) is a heterogeneous group of mast cell-driven diseases diagnosed by bone marrow sampling. However, there are a limited number of available blood disease biomarkers.\n\nOur aim was to identify mast cell-derived proteins that could potentially serve as blood biomarkers for indolent and advanced forms of SM.\n\nWe performed a plasma proteomics screening coupled with single-cell transcriptomic analysis in SM patients and healthy subjects.\n\nPlasma proteomics screening identified 19 proteins upregulated in indolent disease compared to healthy, and 16 proteins in advanced disease compared to indolent. Among these, 5 proteins, CCL19, CCL23, CXCL13, IL-10, and IL-12R\u03b21, were higher in indolent relative to healthy and in advanced disease compared to indolent. Single-cell RNA sequencing demonstrated that CCL23, IL-10, and IL-6 were selectively produced by mast cells. Notably, plasma CCL23 levels correlated positively with known markers of SM disease severity, namely tryptase levels, percentage bone marrow mast cell infiltration, and IL-6.\n\nCCL23 is produced predominantly by mast cells in SM, and CCL23 plasma levels are associated with disease severity, correlating positively with established markers of disease burden, thus suggesting that CCL23 is a specific SM biomarker. In addition, the combination of CCL19, CCL23, CXCL13, IL-10, and IL-12R\u03b21 may be useful for defining disease stage.", "doi": "10.1016/j.jaci.2023.01.033", "pmid": "36813186", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(23)00214-2"}], "notes": [], "created": "2024-10-16T13:44:32.011Z", "modified": "2024-10-16T13:44:32.016Z"}, {"entity": "publication", "iuid": "5abb89f902dd4f478a43fe12a321bd55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5abb89f902dd4f478a43fe12a321bd55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5abb89f902dd4f478a43fe12a321bd55"}}, "title": "Esr1+ hypothalamic-habenula neurons shape aversive states.", "authors": [{"family": "Calvigioni", "given": "Daniela", "initials": "D"}, {"family": "Fuzik", "given": "Janos", "initials": "J", "orcid": "0000-0002-5408-4882", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8c003b45e3f4acf82ac123a0b7cef56.json"}}, {"family": "Le Merre", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4205-7411", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba592e9aa93b433cb85ff11a786b0a71.json"}}, {"family": "Slashcheva", "given": "Marina", "initials": "M"}, {"family": "Jung", "given": "Felix", "initials": "F", "orcid": "0000-0002-7565-977X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a9c9171dd6640f98fd55823ce57515c.json"}}, {"family": "Ortiz", "given": "Cantin", "initials": "C"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/e282901d24c64b16a540eff0d57776f4.json"}}, {"family": "Csillag", "given": "Veronika", "initials": "V"}, {"family": "Graziano", "given": "Marta", "initials": "M"}, {"family": "Nikolakopoulou", "given": "Ifigeneia", "initials": "I"}, {"family": "Weglage", "given": "Moritz", "initials": "M", "orcid": "0000-0002-9173-7459", "researcher": {"href": "https://publications.scilifelab.se/researcher/38cc5154b85541b6bc790cf8ae69d37b.json"}}, {"family": "Lazaridis", "given": "Iakovos", "initials": "I", "orcid": "0000-0002-4578-2347", "researcher": {"href": "https://publications.scilifelab.se/researcher/59bbc8044d78498eb2350a89a65cd01f.json"}}, {"family": "Kim", "given": "Hoseok", "initials": "H"}, {"family": "Lenzi", "given": "Irene", "initials": "I", "orcid": "0000-0002-9229-7301", "researcher": {"href": "https://publications.scilifelab.se/researcher/b047b6697d874c02bdc01269a93e5359.json"}}, {"family": "Park", "given": "Hyunsoo", "initials": "H", "orcid": "0000-0001-5754-9617", "researcher": {"href": "https://publications.scilifelab.se/researcher/654b5c1af2434c30ad7fed7323f3e6f6.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb82c502293d424cb266e1c4e405485f.json"}}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications.scilifelab.se/researcher/88931dd9e39c48e2820b89080c3945ad.json"}}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications.scilifelab.se/researcher/56822ffe0341444297c820580f52dfd0.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "26", "issue": "7", "pages": "1245-1255", "issn-l": "1097-6256"}, "abstract": "Excitatory projections from the lateral hypothalamic area (LHA) to the lateral habenula (LHb) drive aversive responses. We used patch-sequencing (Patch-seq) guided multimodal classification to define the structural and functional heterogeneity of the LHA-LHb pathway. Our classification identified six glutamatergic neuron types with unique electrophysiological properties, molecular profiles and projection patterns. We found that genetically defined LHA-LHb neurons signal distinct aspects of emotional or naturalistic behaviors, such as estrogen receptor 1-expressing (Esr1+) LHA-LHb neurons induce aversion, whereas neuropeptide Y-expressing (Npy+) LHA-LHb neurons control rearing behavior. Repeated optogenetic drive of Esr1+ LHA-LHb neurons induces a behaviorally persistent aversive state, and large-scale recordings showed a region-specific neural representation of the aversive signals in the prelimbic region of the prefrontal cortex. We further found that exposure to unpredictable mild shocks induced a sex-specific sensitivity to develop a stress state in female mice, which was associated with a specific shift in the intrinsic properties of bursting-type Esr1+ LHA-LHb neurons. In summary, we describe the diversity of LHA-LHb neuron types and provide evidence for the role of Esr1+ neurons in aversion and sexually dimorphic stress sensitivity.", "doi": "10.1038/s41593-023-01367-8", "pmid": "37349481", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10322719"}, {"db": "pii", "key": "10.1038/s41593-023-01367-8"}], "notes": [], "created": "2023-10-11T12:27:06.512Z", "modified": "2023-10-11T12:27:06.757Z"}, {"entity": "publication", "iuid": "c7a01707163a492680ecdd4294d2c2b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7a01707163a492680ecdd4294d2c2b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7a01707163a492680ecdd4294d2c2b0"}}, "title": "Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui).", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Zhu", "given": "Yishu", "initials": "Y"}, {"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L"}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "13", "pages": "3513-3523"}, "abstract": "Seasonal environmental fluctuations provide formidable challenges for living organisms, especially small ectotherms such as butterflies. A common strategy to cope with harsh environments is to enter diapause, but some species avoid unsuitable conditions by migrating. Despite a growing understanding of migration in the life cycles of some butterfly species, it remains unknown how individuals register and store environmental cues to determine whether and where to migrate. Here, we explored how competition and host plant availability during larval development affect patterns of DNA methylation in the migratory painted lady (Vanessa cardui) butterfly. We identify a set of potentially functional methylome shifts associated with differences in the environment, indicating that DNA methylation is involved in the response to different conditions during larval development. By analysing the transcriptome for the same samples used for methylation profiling, we also uncovered a non-monotonic relationship between gene body methylation and gene expression. Our results provide a starting point for understanding the interplay between DNA methylation and gene expression in butterflies in general and how differences in environmental conditions during development can trigger unique epigenetic marks that might be important for behavioural decisions in the adult stage.", "doi": "10.1111/mec.16957", "pmid": "37088782", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-04T12:44:28.636Z", "modified": "2024-01-16T13:48:33.060Z"}, {"entity": "publication", "iuid": "7d77baf270e942c6aa5141e432d1ed00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d77baf270e942c6aa5141e432d1ed00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d77baf270e942c6aa5141e432d1ed00"}}, "title": "Actionable cancer vulnerability due to translational arrest, p53 aggregation and ribosome biogenesis stress evoked by the disulfiram metabolite CuET.", "authors": [{"family": "Kanellis", "given": "Dimitris C", "initials": "DC"}, {"family": "Zisi", "given": "Asimina", "initials": "A"}, {"family": "Skrott", "given": "Zdenek", "initials": "Z", "orcid": "0000-0001-6004-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4918c99b9f44668c2346c8b89dea0f.json"}}, {"family": "Lemmens", "given": "Bennie", "initials": "B"}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA"}, {"family": "Kosar", "given": "Martin", "initials": "M"}, {"family": "Bj\u00f6rkman", "given": "Andrea", "initials": "A"}, {"family": "Li", "given": "Xuexin", "initials": "X"}, {"family": "Arampatzis", "given": "Stefanos", "initials": "S"}, {"family": "Bartkova", "given": "Jirina", "initials": "J"}, {"family": "And\u00fajar-S\u00e1nchez", "given": "Miguel", "initials": "M"}, {"family": "Fernandez-Capetillo", "given": "Oscar", "initials": "O"}, {"family": "Mistrik", "given": "Martin", "initials": "M", "orcid": "0000-0002-2321-0348", "researcher": {"href": "https://publications.scilifelab.se/researcher/48c6999c35c746e08495daea2381874b.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Cell Death Differ.", "issn": "1476-5403", "volume": "30", "issue": "7", "pages": "1666-1678", "issn-l": "1350-9047"}, "abstract": "Drug repurposing is a versatile strategy to improve current therapies. Disulfiram has long been used in the treatment of alcohol dependency and multiple clinical trials to evaluate its clinical value in oncology are ongoing. We have recently reported that the disulfiram metabolite diethyldithiocarbamate, when combined with copper (CuET), targets the NPL4 adapter of the p97VCP segregase to suppress the growth of a spectrum of cancer cell lines and xenograft models in vivo. CuET induces proteotoxic stress and genotoxic effects, however important issues concerning the full range of the CuET-evoked tumor cell phenotypes, their temporal order, and mechanistic basis have remained largely unexplored. Here, we have addressed these outstanding questions and show that in diverse human cancer cell models, CuET causes a very early translational arrest through the integrated stress response (ISR), later followed by features of nucleolar stress. Furthermore, we report that CuET entraps p53 in NPL4-rich aggregates leading to elevated p53 protein and its functional inhibition, consistent with the possibility of CuET-triggered cell death being p53-independent. Our transcriptomics profiling revealed activation of pro-survival adaptive pathways of ribosomal biogenesis (RiBi) and autophagy upon prolonged exposure to CuET, indicating potential feedback responses to CuET treatment. The latter concept was validated here by simultaneous pharmacological inhibition of RiBi and/or autophagy that further enhanced CuET's tumor cytotoxicity, using both cell culture and zebrafish in vivo preclinical models. Overall, these findings expand the mechanistic repertoire of CuET's anti-cancer activity, inform about the temporal order of responses and identify an unorthodox new mechanism of targeting p53. Our results are discussed in light of cancer-associated endogenous stresses as exploitable tumor vulnerabilities and may inspire future clinical applications of CuET in oncology, including combinatorial treatments and focus on potential advantages of using certain validated drug metabolites, rather than old, approved drugs with their, often complex, metabolic profiles.", "doi": "10.1038/s41418-023-01167-4", "pmid": "37142656", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10307793"}, {"db": "pii", "key": "10.1038/s41418-023-01167-4"}], "notes": [], "created": "2023-10-04T12:55:20.897Z", "modified": "2023-10-19T12:09:43.478Z"}, {"entity": "publication", "iuid": "9ac67eefe49643bc80efb1022d8ed2ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ac67eefe49643bc80efb1022d8ed2ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ac67eefe49643bc80efb1022d8ed2ce"}}, "title": "Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics.", "authors": [{"family": "Arora", "given": "Abishek", "initials": "A"}, {"family": "Becker", "given": "Martin", "initials": "M"}, {"family": "Marques", "given": "C\u00e1tia", "initials": "C"}, {"family": "Oksanen", "given": "Marika", "initials": "M"}, {"family": "Li", "given": "Danyang", "initials": "D"}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F"}, {"family": "Watts", "given": "Michelle Evelyn", "initials": "ME"}, {"family": "Arora", "given": "Manish", "initials": "M"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Daub", "given": "Carsten Oliver", "initials": "CO"}, {"family": "Lanekoff", "given": "Ingela", "initials": "I"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K"}], "type": "journal article", "published": "2023-06-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "10519", "issn-l": "2045-2322"}, "abstract": "Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, we investigate a highly efficient and multiplexable, fractional factorial experimental design (FFED) to study six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine hydrochloride and zinc deficiency) and four human induced pluripotent stem cell line derived differentiating human neural progenitors. We showcase the FFED coupled with RNA-sequencing to identify the effects of low-grade exposures to these environmental factors and analyse the results in the context of autism spectrum disorder (ASD). We performed this after 5-day exposures on differentiating human neural progenitors accompanied by a layered analytical approach and detected several convergent and divergent, gene and pathway level responses. We revealed significant upregulation of pathways related to synaptic function and lipid metabolism following lead and fluoxetine exposure, respectively. Moreover, fluoxetine exposure elevated several fatty acids when validated using mass spectrometry-based metabolomics. Our study demonstrates that the FFED can be used for multiplexed transcriptomic analyses to detect relevant pathway-level changes in human neural development caused by low-grade environmental risk factors. Future studies will require multiple cell lines with different genetic backgrounds for characterising the effects of environmental exposures in ASD.", "doi": "10.1038/s41598-023-37488-0", "pmid": "37386098", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10310850"}, {"db": "pii", "key": "10.1038/s41598-023-37488-0"}], "notes": [], "created": "2023-10-11T08:41:00.302Z", "modified": "2024-01-16T13:48:33.099Z"}, {"entity": "publication", "iuid": "1f2831f32b964f84bb685abb64d185f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f2831f32b964f84bb685abb64d185f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f2831f32b964f84bb685abb64d185f6"}}, "title": "Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community.", "authors": [{"family": "Massing", "given": "Jana C", "initials": "JC"}, {"family": "Fahimipour", "given": "Ashkaan K", "initials": "AK", "orcid": "0000-0001-9138-3593", "researcher": {"href": "https://publications.scilifelab.se/researcher/6316daaa82ff4cebb59b829374b8abb1.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Gross", "given": "Thilo", "initials": "T"}], "type": "journal article", "published": "2023-06-29", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "8", "issue": "3", "pages": "e0002823", "issn-l": "2379-5077"}, "abstract": "Progress in molecular methods has enabled the monitoring of bacterial populations in time. Nevertheless, understanding community dynamics and its links with ecosystem functioning remains challenging due to the tremendous diversity of microorganisms. Conceptual frameworks that make sense of time series of taxonomically rich bacterial communities, regarding their potential ecological function, are needed. A key concept for organizing ecological functions is the niche, the set of strategies that enable a population to persist and define its impacts on the surroundings. Here we present a framework based on manifold learning to organize genomic information into potentially occupied bacterial metabolic niches over time. Manifold learning tries to uncover low-dimensional data structures in high-dimensional data sets that can be used to describe the data in reduced dimensions. We apply the method to re-construct the dynamics of putatively occupied metabolic niches using a long-term bacterial time series from the Baltic Sea, the Linnaeus Microbial Observatory (LMO). The results reveal a relatively low-dimensional space of occupied metabolic niches comprising groups of taxa with similar functional capabilities. Time patterns of occupied niches were strongly driven by seasonality. Some metabolic niches were dominated by one bacterial taxon, whereas others were occupied by multiple taxa, depending on the season. These results illustrate the power of manifold learning approaches to advance our understanding of the links between community composition and functioning in microbial systems. IMPORTANCE The increase in data availability of bacterial communities highlights the need for conceptual frameworks to advance our understanding of these complex and diverse communities alongside the production of such data. To understand the dynamics of these tremendously diverse communities, we need tools to identify overarching strategies and describe their role and function in the ecosystem in a comprehensive way. Here, we show that a manifold learning approach can coarse grain bacterial communities in terms of their metabolic strategies and that we can thereby quantitatively organize genomic information in terms of potentially occupied niches over time. This approach, therefore, advances our understanding of how fluctuations in bacterial abundances and species composition can relate to ecosystem functions and it can facilitate the analysis, monitoring, and future predictions of the development of microbial communities.", "doi": "10.1128/msystems.00028-23", "pmid": "37255288", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10312292"}], "notes": [], "created": "2023-10-19T12:27:19.965Z", "modified": "2023-10-19T12:27:20.010Z"}, {"entity": "publication", "iuid": "6bc894ab362d4c51895c8168a173f43e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6bc894ab362d4c51895c8168a173f43e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6bc894ab362d4c51895c8168a173f43e"}}, "title": "A Highly Substituted Ring-Fused 2-Pyridone Compound Targeting PrfA and the Efflux Regulator BrtA in Listeria monocytogenes.", "authors": [{"family": "T\u00fckenmez", "given": "Hasan", "initials": "H", "orcid": "0000-0002-2259-6883", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e2a6e729c344f2a9ea0c76ff9366fe.json"}}, {"family": "Singh", "given": "Pardeep", "initials": "P"}, {"family": "Sarkar", "given": "Souvik", "initials": "S"}, {"family": "\u00c7ak\u0131r", "given": "Melike", "initials": "M"}, {"family": "Oliveira", "given": "Ana H", "initials": "AH"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C"}, {"family": "Vaitkevicius", "given": "Karolis", "initials": "K"}, {"family": "Bonde", "given": "Mari", "initials": "M"}, {"family": "Sauer-Eriksson", "given": "A Elisabeth", "initials": "AE"}, {"family": "Almqvist", "given": "Fredrik", "initials": "F"}, {"family": "Johansson", "given": "J\u00f6rgen", "initials": "J", "orcid": "0000-0002-0904-497X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ee079f1c15549c1a2cdfad88c07f6ad.json"}}], "type": "journal article", "published": "2023-06-27", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "14", "issue": "3", "pages": "e0044923", "issn-l": null}, "abstract": "Listeria monocytogenes is a facultative Gram-positive bacterium that causes listeriosis, a severe foodborne disease. We previously discovered that ring-fused 2-pyridone compounds can decrease virulence factor expression in Listeria by binding and inactivating the PrfA virulence activator. In this study, we tested PS900, a highly substituted 2-pyridone that was recently discovered to be bactericidal to other Gram-positive pathogenic bacteria, such as Staphylococcus aureus and Enterococcus faecalis. We show that PS900 can interact with PrfA and reduce the expression of virulence factors. Unlike previous ring-fused 2-pyridones shown to inactivate PrfA, PS900 had an additional antibacterial activity and was found to potentiate sensitivity toward cholic acid. Two PS900-tolerant mutants able to grow in the presence of PS900 carried mutations in the brtA gene, encoding the BrtA repressor. In wild-type (WT) bacteria, cholic acid binds and inactivates BrtA, thereby alleviating the expression of the multidrug transporter MdrT. Interestingly, we found that PS900 also binds to BrtA and that this interaction causes BrtA to dissociate from its binding site in front of the mdrT gene. In addition, we observed that PS900 potentiated the effect of different osmolytes. We suggest that the increased potency of cholic acid and osmolytes to kill bacteria in the presence of PS900 is due to the ability of the latter to inhibit general efflux, through a yet-unknown mechanism. Our data indicate that thiazolino 2-pyridones constitute an attractive scaffold when designing new types of antibacterial agents. IMPORTANCE Bacteria resistant to one or several antibiotics are a very large problem, threatening not only treatment of infections but also surgery and cancer treatments. Thus, new types of antibacterial drugs are desperately needed. In this work, we show that a new generation of substituted ring-fused 2-pyridones not only inhibit Listeria monocytogenes virulence gene expression, presumably by inactivating the PrfA virulence regulator, but also potentiate the bactericidal effects of cholic acid and different osmolytes. We identified a multidrug repressor as a second target of 2-pyridones. The repressor-2-pyridone interaction displaces the repressor from DNA, thus increasing the expression of a multidrug transporter. In addition, our data suggest that the new class of ring-fused 2-pyridones are efficient efflux inhibitors, possibly explaining why the simultaneous addition of 2-pyridones together with cholic acid or osmolytes is detrimental for the bacterium. This work proves conclusively that 2-pyridones constitute a promising scaffold to build on for future antibacterial drug design.", "doi": "10.1128/mbio.00449-23", "pmid": "37120759", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10294697"}], "notes": [], "created": "2023-11-25T05:42:11.077Z", "modified": "2023-11-25T05:42:11.122Z"}, {"entity": "publication", "iuid": "6cc5f2c5c1484b96afa941595c6b80b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cc5f2c5c1484b96afa941595c6b80b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cc5f2c5c1484b96afa941595c6b80b6"}}, "title": "Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield.", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M", "orcid": "0000-0003-3588-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c5d5c765980461997541605f7512623.json"}}, {"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2023-06-22", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "9", "issue": "1", "pages": "41", "issn-l": "2055-5008"}, "abstract": "Biofilm formation is a common adaptation for microbes in energy-limited conditions such as those prevalent in the vast deep terrestrial biosphere. However, due to the low biomass and the inaccessible nature of subsurface groundwaters, the microbial populations and genes involved in its formation are understudied. Here, a flow-cell system was designed to investigate biofilm formation under in situ conditions in two groundwaters of contrasting age and geochemistry at the \u00c4sp\u00f6 Hard Rock Laboratory, Sweden. Metatranscriptomes showed Thiobacillus, Sideroxydans, and Desulforegula to be abundant and together accounted for 31% of the transcripts in the biofilm communities. Differential expression analysis highlighted Thiobacillus to have a principal role in biofilm formation in these oligotrophic groundwaters by being involved in relevant processes such as the formation of extracellular matrix, quorum sensing, and cell motility. The findings revealed an active biofilm community with sulfur cycling as a prominent mode of energy conservation in the deep biosphere.", "doi": "10.1038/s41522-023-00408-1", "pmid": "37349512", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10287647"}, {"db": "pii", "key": "10.1038/s41522-023-00408-1"}], "notes": [], "created": "2023-10-11T08:48:35.928Z", "modified": "2024-01-16T13:48:33.128Z"}, {"entity": "publication", "iuid": "2c65d20ec1de42e5b486342f5520c9c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c65d20ec1de42e5b486342f5520c9c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c65d20ec1de42e5b486342f5520c9c4"}}, "title": "Human skin-resident CD8+ T cells require RUNX2 and RUNX3 for induction of cytotoxicity and expression of the integrin CD49a.", "authors": [{"family": "Zitti", "given": "Beatrice", "initials": "B"}, {"family": "Hoffer", "given": "Elena", "initials": "E"}, {"family": "Zheng", "given": "Wenning", "initials": "W"}, {"family": "Pandey", "given": "Ram Vinay", "initials": "RV"}, {"family": "Schlums", "given": "Heinrich", "initials": "H"}, {"family": "Perinetti Casoni", "given": "Giovanna", "initials": "G"}, {"family": "Fusi", "given": "Irene", "initials": "I"}, {"family": "Nguyen", "given": "Lien", "initials": "L"}, {"family": "K\u00e4rner", "given": "Jaanika", "initials": "J"}, {"family": "Kokkinou", "given": "Efthymia", "initials": "E"}, {"family": "Carrasco", "given": "Anna", "initials": "A"}, {"family": "Gahm", "given": "Jessica", "initials": "J"}, {"family": "Ehrstr\u00f6m", "given": "Marcus", "initials": "M"}, {"family": "Happaniemi", "given": "Staffan", "initials": "S"}, {"family": "Keita", "given": "\u00c5sa V", "initials": "\u00c5V"}, {"family": "Hedin", "given": "Charlotte R H", "initials": "CRH"}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}, {"family": "Eidsmo", "given": "Liv", "initials": "L"}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT"}], "type": "journal article", "published": "2023-06-13", "journal": {"title": "Immunity", "issn": "1097-4180", "volume": "56", "issue": "6", "pages": "1285-1302.e7", "issn-l": "1074-7613"}, "abstract": "The integrin CD49a marks highly cytotoxic epidermal-tissue-resident memory (TRM) cells, but their differentiation from circulating populations remains poorly defined. We demonstrate enrichment of RUNT family transcription-factor-binding motifs in human epidermal CD8+CD103+CD49a+ TRM cells, paralleled by high RUNX2 and RUNX3 protein expression. Sequencing of paired skin and blood samples revealed clonal overlap between epidermal CD8+CD103+CD49a+ TRM cells and circulating memory CD8+CD45RA-CD62L+ T cells. In vitro stimulation of circulating CD8+CD45RA-CD62L+ T cells with IL-15 and TGF-\u03b2 induced CD49a expression and cytotoxic transcriptional profiles in a RUNX2- and RUNX3-dependent manner. We therefore identified a reservoir of circulating cells with cytotoxic TRM potential. In melanoma patients, high RUNX2, but not RUNX3, transcription correlated with a cytotoxic CD8+CD103+CD49a+ TRM cell signature and improved patient survival. Together, our results indicate that combined RUNX2 and RUNX3 activity promotes the differentiation of cytotoxic CD8+CD103+CD49a+ TRM cells, providing immunosurveillance of infected and malignant cells.", "doi": "10.1016/j.immuni.2023.05.003", "pmid": "37269830", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S1074-7613(23)00220-0"}], "notes": [], "created": "2023-10-11T12:37:29.638Z", "modified": "2023-10-19T13:10:17.377Z"}, {"entity": "publication", "iuid": "4b07c83ed5af41b69a48efde712ace79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b07c83ed5af41b69a48efde712ace79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b07c83ed5af41b69a48efde712ace79"}}, "title": "Absence of changes in the milk microbiota during Escherichia coli endotoxin induced experimental bovine mastitis.", "authors": [{"family": "Dahlberg", "given": "Josef", "initials": "J", "orcid": "0000-0001-8131-6725", "researcher": {"href": "https://publications.scilifelab.se/researcher/090cf8219ee047be97d9b75b104d8b7c.json"}}, {"family": "Johnzon", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"family": "\u00d6stensson", "given": "Karin", "initials": "K"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-06-08", "journal": {"title": "Vet Res", "issn": "1297-9716", "volume": "54", "issue": "1", "pages": "46", "issn-l": null}, "abstract": "Changes in the milk microbiota during the course of mastitis are due to the nature of a sporadic occurring disease difficult to study. In this study we experimentally induced mastitis by infusion of Escherichia coli endotoxins in one udder quarter each of nine healthy lactating dairy cows and assessed the bacteriological dynamics and the milk microbiota at four time points before and eight time points after infusion. As control, saline was infused in one udder quarter each of additionally nine healthy cows that followed the same sampling protocol. The milk microbiota was assessed by sequencing of the 16 S rRNA gene and a range of positive and negative controls were included for methodological evaluation. Two different data filtration models were used to identify and cure data from contaminating taxa. Endotoxin infused quarters responded with transient clinical signs of inflammation and increased SCC while no response was observed in the control cows. In the milk microbiota data no response to inflammation was identified. The data analysis of the milk microbiota was largely hampered by laboratory and reagent contamination. Application of the filtration models caused a marked reduction in data but did not reveal any associations with the inflammatory reaction. Our results indicate that the microbiota in milk from healthy cows is unaffected by inflammation.", "doi": "10.1186/s13567-023-01179-5", "pmid": "37291624", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10251687"}, {"db": "pii", "key": "10.1186/s13567-023-01179-5"}], "notes": [], "created": "2023-10-11T10:31:25.919Z", "modified": "2023-10-19T12:51:44.623Z"}, {"entity": "publication", "iuid": "a4df06e9148b4e4a95aae401ff4a8016", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4df06e9148b4e4a95aae401ff4a8016.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4df06e9148b4e4a95aae401ff4a8016"}}, "title": "Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (G\u00fcnther, 1874) from the Balearic Islands (Spain).", "authors": [{"family": "Gomez-Garrido", "given": "Jessica", "initials": "J"}, {"family": "Cruz", "given": "Fernando", "initials": "F"}, {"family": "Alioto", "given": "Tyler S", "initials": "TS"}, {"family": "Feiner", "given": "Nathalie", "initials": "N"}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications.scilifelab.se/researcher/6346267a5c3e41c6a6825b7b20a53fa5.json"}}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Sanchez Escudero", "given": "Ignacio", "initials": "I"}, {"family": "Tavecchia", "given": "Giacomo", "initials": "G"}, {"family": "Rotger", "given": "Andreu", "initials": "A"}, {"family": "Otalora Acevedo", "given": "Katherin Eliana", "initials": "KE"}, {"family": "Baldo", "given": "Laura", "initials": "L", "orcid": "0000-0003-4528-6674", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c72ce0ae73a4909a4bdeb49ab722d58.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "DNA Res.", "issn": "1756-1663", "issn-l": "1340-2838", "volume": "30", "issue": "3", "pages": null}, "abstract": "The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.", "doi": "10.1093/dnares/dsad008", "pmid": "37137526", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10214862"}, {"db": "pii", "key": "7151100"}], "notes": [], "created": "2023-10-10T08:47:32.990Z", "modified": "2023-11-29T11:43:27.568Z"}, {"entity": "publication", "iuid": "2c9906a7c1a0408f8006e723a38f488c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c9906a7c1a0408f8006e723a38f488c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c9906a7c1a0408f8006e723a38f488c"}}, "title": "An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Olsen", "given": "Remi Andr\u00e9", "initials": "RA"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "13", "issue": "6", "pages": null}, "abstract": "Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.", "doi": "10.1093/g3journal/jkad088", "pmid": "37097035", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10234393"}, {"db": "pii", "key": "7141353"}], "notes": [], "created": "2023-08-15T06:59:21.634Z", "modified": "2024-01-16T13:48:33.264Z"}, {"entity": "publication", "iuid": "30653c13c25141e2995dd5ba6d7d7e07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30653c13c25141e2995dd5ba6d7d7e07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30653c13c25141e2995dd5ba6d7d7e07"}}, "title": "The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.", "authors": [{"family": "Yazdi", "given": "Homa Papoli", "initials": "HP", "orcid": "0000-0001-8667-6279", "researcher": {"href": "https://publications.scilifelab.se/researcher/608729115444421b8c6db7eb852a059a.json"}}, {"family": "Olito", "given": "Colin", "initials": "C", "orcid": "0000-0001-6883-0367", "researcher": {"href": "https://publications.scilifelab.se/researcher/458a918560b048d68236db4b00cec58d.json"}}, {"family": "Kawakami", "given": "Takeshi", "initials": "T", "orcid": "0000-0002-9204-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/424031a0011f4e77bbb6f64a1d369b8b.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1cd4d11f8d443e8ff305f923b8fbb0.json"}}, {"family": "Schou", "given": "Mads F", "initials": "MF", "orcid": "0000-0001-5521-5269", "researcher": {"href": "https://publications.scilifelab.se/researcher/6efaf36be9d14564bd6e18344d55832e.json"}}, {"family": "Cloete", "given": "Schalk W P", "initials": "SWP", "orcid": "0000-0002-4548-5633", "researcher": {"href": "https://publications.scilifelab.se/researcher/034596fb7f8b427f9f153ebb55ef1850.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Cornwallis", "given": "Charlie K", "initials": "CK", "orcid": "0000-0003-1308-3995", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d766d021df4fbeba0d52a624df866d.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "19", "issue": "6", "pages": "e1010801", "issn-l": "1553-7390"}, "abstract": "Sex chromosomes have evolved repeatedly across the tree of life and often exhibit extreme size dimorphism due to genetic degeneration of the sex-limited chromosome (e.g. the W chromosome of some birds and Y chromosome of mammals). However, in some lineages, ancient sex-limited chromosomes have escaped degeneration. Here, we study the evolutionary maintenance of sex chromosomes in the ostrich (Struthio camelus), where the W remains 65% the size of the Z chromosome, despite being more than 100 million years old. Using genome-wide resequencing data, we show that the population scaled recombination rate of the pseudoautosomal region (PAR) is higher than similar sized autosomes and is correlated with pedigree-based recombination rate in the heterogametic females, but not homogametic males. Genetic variation within the sex-linked region (SLR) (\u03c0 = 0.001) was significantly lower than in the PAR, consistent with recombination cessation. Conversely, genetic variation across the PAR (\u03c0 = 0.0016) was similar to that of autosomes and dependent on local recombination rates, GC content and to a lesser extent, gene density. In particular, the region close to the SLR was as genetically diverse as autosomes, likely due to high recombination rates around the PAR boundary restricting genetic linkage with the SLR to only ~50Kb. The potential for alleles with antagonistic fitness effects in males and females to drive chromosome degeneration is therefore limited. While some regions of the PAR had divergent male-female allele frequencies, suggestive of sexually antagonistic alleles, coalescent simulations showed this was broadly consistent with neutral genetic processes. Our results indicate that the degeneration of the large and ancient sex chromosomes of the ostrich may have been slowed by high recombination in the female PAR, reducing the scope for the accumulation of sexually antagonistic variation to generate selection for recombination cessation.", "doi": "10.1371/journal.pgen.1010801", "pmid": "37390104", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10343094"}, {"db": "pii", "key": "PGENETICS-D-22-01416"}], "notes": [], "created": "2023-08-15T09:51:56.763Z", "modified": "2024-01-16T13:48:33.279Z"}, {"entity": "publication", "iuid": "50ebba759c9b46de865a47f18bd85eb2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50ebba759c9b46de865a47f18bd85eb2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50ebba759c9b46de865a47f18bd85eb2"}}, "title": "Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag.", "authors": [{"family": "Bartosovic", "given": "Marek", "initials": "M", "orcid": "0000-0003-2057-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce3c36916eb844e7bc10f73b95f6494a.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "41", "issue": "6", "pages": "794-805", "issn-l": "1087-0156"}, "abstract": "Probing histone modifications at a single-cell level in thousands of cells has been enabled by technologies such as single-cell CUT&Tag. Here we describe nano-CUT&Tag (nano-CT), which allows simultaneous mapping of up to three epigenomic modalities at single-cell resolution using nanobody-Tn5 fusion proteins. Multimodal nano-CT is compatible with starting materials as low as 25,000-200,000 cells and has significantly higher sensitivity and number of fragments per cell than single-cell CUT&Tag. We use nano-CT to simultaneously profile chromatin accessibility, H3K27ac, and H3K27me3 in juvenile mouse brain, allowing for discrimination of more cell types and states than unimodal single-cell CUT&Tag. We also infer chromatin velocity between assay for transposase-accessible chromatin (ATAC) and H3K27ac in the oligodendrocyte lineage and deconvolute H3K27me3 repressive states, finding two sequential waves of H3K27me3 repression at distinct gene modules during oligodendrocyte lineage progression. Given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in complex biological systems at the single-cell level.", "doi": "10.1038/s41587-022-01535-4", "pmid": "36536148", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10264246"}, {"db": "pii", "key": "10.1038/s41587-022-01535-4"}], "notes": [], "created": "2023-10-04T11:58:23.047Z", "modified": "2024-01-16T13:48:33.301Z"}, {"entity": "publication", "iuid": "cd448ce0b19746f38c1fe9249ff70662", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd448ce0b19746f38c1fe9249ff70662.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd448ce0b19746f38c1fe9249ff70662"}}, "title": "Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer.", "authors": [{"family": "Wadensten", "given": "Elisabeth", "initials": "E"}, {"family": "Wessman", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2035-2092", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4680125750b4d949d691a745818a6f7.json"}}, {"family": "Abel", "given": "Frida", "initials": "F", "orcid": "0000-0001-6958-4487", "researcher": {"href": "https://publications.scilifelab.se/researcher/957445dd84024bac8cc6b1cca2f07473.json"}}, {"family": "Diaz De St\u00e5hl", "given": "Teresita", "initials": "T", "orcid": "0000-0001-5933-6623", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f51158ce6e14f3b96bf16a214689d1d.json"}}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Orsmark Pietras", "given": "Christina", "initials": "C"}, {"family": "Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Fransson", "given": "Susanne", "initials": "S", "orcid": "0000-0002-9713-3074", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3f155163dae47478aae39b9c47fdadc.json"}}, {"family": "Vogt", "given": "Hartmut", "initials": "H", "orcid": "0000-0001-6009-7789", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e08eceec8ff418a961e32d0518ab97a.json"}}, {"family": "Poluha", "given": "Anna", "initials": "A", "orcid": "0000-0002-4716-9423", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7c9d843ebd549a7875bf10d4a16ee8b.json"}}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Hellberg", "given": "Maria", "initials": "M"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Raj Somarajan", "given": "Praveen", "initials": "P", "orcid": "0009-0005-5981-2286", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a17539de3840108fa5d4bb9f454bab.json"}}, {"family": "Samuelsson", "given": "Sofie", "initials": "S"}, {"family": "Orrsj\u00f6", "given": "Sara", "initials": "S", "orcid": "0009-0008-9223-3923", "researcher": {"href": "https://publications.scilifelab.se/researcher/acd6e5385a7b4406b973a3adbed96245.json"}}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea06b85057744018f754c373fef3ca5.json"}}, {"family": "Henning", "given": "Karin", "initials": "K"}, {"family": "Strid", "given": "Tobias", "initials": "T"}, {"family": "Ek", "given": "Torben", "initials": "T", "orcid": "0000-0002-0518-983X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce340b203a7840b786b73fb94c12c49a.json"}}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Olsson Bontell", "given": "Thomas", "initials": "T"}, {"family": "Martinsson", "given": "Tommy", "initials": "T", "orcid": "0000-0002-9403-3123", "researcher": {"href": "https://publications.scilifelab.se/researcher/90deb3f5dd5446e5853da797411dfd5d.json"}}, {"family": "Puls", "given": "Florian", "initials": "F", "orcid": "0000-0002-9841-4230", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2d41b4d47c41e89d675a438efd9095.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ", "orcid": "0000-0002-0073-9660", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e42ba48d824aa0b42e871e9f11b00a.json"}}, {"family": "Wille", "given": "Joakim", "initials": "J", "orcid": "0009-0008-6426-9830", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b06137add284e3ca519eb0af7bf52d4.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}, {"family": "Sabel", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3072-657X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2378bd05915d47eca234fff49fb69289.json"}}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U", "orcid": "0000-0001-5606-5442", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f7a89bc35d4e72b4b2c0d4252b69f0.json"}}, {"family": "Grillner", "given": "Pernilla", "initials": "P"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Sandgren", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6776-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d5b6b16fdbe470f83de8748227f8987.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3653582762b14f9a9ad2fe6aba511115.json"}}, {"family": "Genomic Medicine Sweden Childhood Cancer Working Group", "given": "", "initials": ""}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "JCO Precision Oncology", "issn": "2473-4284", "issn-l": "2473-4284", "volume": "7", "issue": null, "pages": "e2300039"}, "abstract": "Several studies have indicated that broad genomic characterization of childhood cancer provides diagnostically and/or therapeutically relevant information in selected high-risk cases. However, the extent to which such characterization offers clinically actionable data in a prospective broadly inclusive setting remains largely unexplored.\n\nWe implemented prospective whole-genome sequencing (WGS) of tumor and germline, complemented by whole-transcriptome sequencing (RNA-Seq) for all children diagnosed with a primary or relapsed solid malignancy in Sweden. Multidisciplinary molecular tumor boards were set up to integrate genomic data in the clinical decision process along with a medicolegal framework enabling secondary use of sequencing data for research purposes.\n\nDuring the study's first 14 months, 118 solid tumors from 117 patients were subjected to WGS, with complementary RNA-Seq for fusion gene detection in 52 tumors. There was no significant geographic bias in patient enrollment, and the included tumor types reflected the annual national incidence of pediatric solid tumor types. Of the 112 tumors with somatic mutations, 106 (95%) exhibited alterations with a clear clinical correlation. In 46 of 118 tumors (39%), sequencing only corroborated histopathological diagnoses, while in 59 cases (50%), it contributed to additional subclassification or detection of prognostic markers. Potential treatment targets were found in 31 patients (26%), most commonly ALK mutations/fusions (n = 4), RAS/RAF/MEK/ERK pathway mutations (n = 14), FGFR1 mutations/fusions (n = 5), IDH1 mutations (n = 2), and NTRK2 gene fusions (n = 2). In one patient, the tumor diagnosis was revised based on sequencing. Clinically relevant germline variants were detected in 8 of 94 patients (8.5%).\n\nUp-front, large-scale genomic characterization of pediatric solid malignancies provides diagnostically valuable data in the majority of patients also in a largely unselected cohort.", "doi": "10.1200/PO.23.00039", "pmid": "37384868", "labels": {"NGI Short read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10581599"}], "notes": [], "created": "2023-10-11T08:39:38.509Z", "modified": "2024-11-21T07:53:59.877Z"}, {"entity": "publication", "iuid": "89802b086c134753af299e2d595aeba0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89802b086c134753af299e2d595aeba0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89802b086c134753af299e2d595aeba0"}}, "title": "Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L", "orcid": "0000-0002-2620-914X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0923436cd0a42cea933771b57ae8c94.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C", "orcid": "0000-0001-8302-5710", "researcher": {"href": "https://publications.scilifelab.se/researcher/28271fe98d59405b92dc026d1740dd9a.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Forsman", "given": "Anders", "initials": "A", "orcid": "0000-0001-9598-7618", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a605b671cd3414d9c75c2408b74d3de.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "17", "issue": "6", "pages": "855-869", "issn-l": "1751-7362"}, "abstract": "Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6-35 \u00b0C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.", "doi": "10.1038/s41396-023-01395-z", "pmid": "36977742", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10202955"}, {"db": "pii", "key": "10.1038/s41396-023-01395-z"}], "notes": [], "created": "2023-10-04T12:16:42.203Z", "modified": "2024-01-16T13:48:33.316Z"}, {"entity": "publication", "iuid": "ec8c55c51bce43cfa4a366478f780959", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec8c55c51bce43cfa4a366478f780959.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec8c55c51bce43cfa4a366478f780959"}}, "title": "Triazole fungicides induce adipogenesis and repress osteoblastogenesis in zebrafish.", "authors": [{"family": "Thrikawala", "given": "Savini", "initials": "S"}, {"family": "Mesmar", "given": "Fahmi", "initials": "F"}, {"family": "Bhattacharya", "given": "Beas", "initials": "B"}, {"family": "Muhsen", "given": "Maram", "initials": "M"}, {"family": "Mukhopadhyay", "given": "Srijita", "initials": "S"}, {"family": "Flores", "given": "Sara", "initials": "S"}, {"family": "Upadhyay", "given": "Sanat", "initials": "S"}, {"family": "Vergara", "given": "Leoncio", "initials": "L"}, {"family": "Gustafsson", "given": "Jan-\u00c5ke", "initials": "J\u00c5"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}, {"family": "Bondesson", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2023-05-31", "journal": {"title": "Toxicol. Sci.", "issn": "1096-0929", "volume": "193", "issue": "2", "pages": "119-130", "issn-l": null}, "abstract": "Triazoles are a major group of azole fungicides commonly used in agriculture, and veterinary and human medicine. Maternal exposure to certain triazole antifungal medication causes congenital malformations, including skeletal malformations. We hypothesized that triazoles used as pesticides in agriculture also pose a risk of causing skeletal malformations in developing embryos. In this study, teratogenic effects of three commonly used triazoles, cyproconazole, paclobutrazol, and triadimenol, were investigated in zebrafish, Danio rerio. Exposure to the triazole fungicides caused bone and cartilage malformations in developing zebrafish larvae. Data from whole-embryo transcriptomics with cyproconazole suggested that exposure to this compound induces adipogenesis while repressing skeletal development. Confirming this finding, the expression of selected bone and cartilage marker genes were significantly downregulated with triazoles exposure as determined by quantitative PCR. The expression of selected adipogenic genes was upregulated by the triazoles. Furthermore, exposure to each of the three triazoles induced adipogenesis and lipid droplet formation in vitro in 3T3-L1 pre-adipocyte cells. In vivo in zebrafish larvae, cyproconazole exposure caused lipid accumulation. These results suggest that exposure to triazoles promotes adipogenesis at the expense of skeletal development, and thus they expand the chemical group of bona fide bone to fat switchers.", "doi": "10.1093/toxsci/kfad031", "pmid": "36951524", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10230286"}, {"db": "pii", "key": "7084784"}], "notes": [], "created": "2023-10-11T08:34:53.943Z", "modified": "2023-10-19T12:07:50.145Z"}, {"entity": "publication", "iuid": "f6d5f37259274f449de8357acc898dc0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6d5f37259274f449de8357acc898dc0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6d5f37259274f449de8357acc898dc0"}}, "title": "Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein.", "authors": [{"family": "Watts", "given": "Michelle E", "initials": "ME"}, {"family": "Oksanen", "given": "Marika", "initials": "M"}, {"family": "Lejerkrans", "given": "Sanna", "initials": "S"}, {"family": "Mastropasqua", "given": "Francesca", "initials": "F"}, {"family": "Gorospe", "given": "Myriam", "initials": "M"}, {"family": "Tammimies", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-8324-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba19ec07147743c6942ea10c9a92482a.json"}}], "type": "journal article", "published": "2023-05-26", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "21", "issue": "1", "pages": "127", "issn-l": "1741-7007"}, "abstract": "Circular RNA (circRNA) molecules, generated through non-canonical back-splicing of exon-exon junctions, have recently been implicated in diverse biological functions including transcriptional regulation and modulation of protein interactions. CircRNAs are emerging as a key component of the complex neural transcriptome implicated in brain development. However, the specific expression patterns and functions of circRNAs in human neuronal differentiation have not been explored.\n\nUsing total RNA sequencing analysis, we identified expressed circRNAs during the differentiation of human neuroepithelial stem (NES) cells into developing neurons and discovered that many circRNAs originated from host genes associated with synaptic function. Interestingly, when assessing population data, exons giving rise to circRNAs in our dataset had a higher frequency of genetic variants. Additionally, screening for RNA-binding protein sites identified enrichment of Splicing Factor Proline and Glutamine Rich (SFPQ) motifs in increased circRNAs, several of which were reduced by SFPQ knockdown and enriched in SFPQ ribonucleoprotein complexes.\n\nOur study provides an in-depth characterisation of circRNAs in a human neuronal differentiation model and highlights SFPQ as both a regulator and binding partner of circRNAs elevated during neuronal maturation.", "doi": "10.1186/s12915-023-01627-w", "pmid": "37237280", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10224606"}, {"db": "pii", "key": "10.1186/s12915-023-01627-w"}], "notes": [], "created": "2023-10-11T08:42:02.695Z", "modified": "2024-01-16T13:48:33.362Z"}, {"entity": "publication", "iuid": "4b75ebd89eb8484b9e4587ef0e570612", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b75ebd89eb8484b9e4587ef0e570612.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b75ebd89eb8484b9e4587ef0e570612"}}, "title": "Balancing selection on the complement system of a wild rodent.", "authors": [{"family": "Nandakumar", "given": "Mridula", "initials": "M"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2023-05-25", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "23", "issue": "1", "pages": "21", "issn-l": null}, "abstract": "Selection pressure exerted by pathogens can influence patterns of genetic diversity in the host. In the immune system especially, numerous genes encode proteins involved in antagonistic interactions with pathogens, paving the way for coevolution that results in increased genetic diversity as a consequence of balancing selection. The complement system is a key component of innate immunity. Many complement proteins interact directly with pathogens, either by recognising pathogen molecules for complement activation, or by serving as targets of pathogen immune evasion mechanisms. Complement genes can therefore be expected to be important targets of pathogen-mediated balancing selection, but analyses of such selection on this part of the immune system have been limited.\n\nUsing a population sample of whole-genome resequencing data from wild bank voles (n = 31), we estimated the extent of genetic diversity and tested for signatures of balancing selection in multiple complement genes (n = 44). Complement genes showed higher values of standardised \u03b2 (a statistic expected to be high under balancing selection) than the genome-wide average of protein coding genes. One complement gene, FCNA, a pattern recognition molecule that interacts directly with pathogens, was found to have a signature of balancing selection, as indicated by the Hudson-Kreitman-Aguad\u00e9 test (HKA) test. Scans for localised signatures of balancing selection in this gene indicated that the target of balancing selection was found in exonic regions involved in ligand binding.\n\nThe present study adds to the growing evidence that balancing selection may be an important evolutionary force on components of the innate immune system. The identified target in the complement system typifies the expectation that balancing selection acts on genes encoding proteins involved in direct interactions with pathogens.", "doi": "10.1186/s12862-023-02122-0", "pmid": "37231383", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10214634"}, {"db": "pii", "key": "10.1186/s12862-023-02122-0"}], "notes": [], "created": "2023-10-11T08:50:27.738Z", "modified": "2024-01-16T13:48:33.370Z"}, {"entity": "publication", "iuid": "2ace00d184224d9a8da1fe7ded82ae91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ace00d184224d9a8da1fe7ded82ae91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ace00d184224d9a8da1fe7ded82ae91"}}, "title": "The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.", "authors": [{"family": "D\u00edaz de St\u00e5hl", "given": "Teresita", "initials": "T", "orcid": "0000-0001-5933-6623", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f51158ce6e14f3b96bf16a214689d1d.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Juhos", "given": "Szilvester", "initials": "S"}, {"family": "Basmaci", "given": "Elisa", "initials": "E"}, {"family": "Prochazka", "given": "Gabriela", "initials": "G"}, {"family": "Garcia", "given": "Maxime", "initials": "M"}, {"family": "Somarajan", "given": "Praveen Raj", "initials": "PR"}, {"family": "Zielinska-Chomej", "given": "Katarzyna", "initials": "K"}, {"family": "Illies", "given": "Christopher", "initials": "C"}, {"family": "\u00d8ra", "given": "Ingrid", "initials": "I"}, {"family": "Siesj\u00f6", "given": "Peter", "initials": "P"}, {"family": "Sandstr\u00f6m", "given": "Per-Erik", "initials": "P"}, {"family": "Stenman", "given": "Jakob", "initials": "J"}, {"family": "Sabel", "given": "Magnus", "initials": "M"}, {"family": "Gustavsson", "given": "Bengt", "initials": "B"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Pfeifer", "given": "Susan", "initials": "S"}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}], "type": "journal article", "published": "2023-05-23", "journal": {"title": "J Transl Med", "issn": "1479-5876", "issn-l": "1479-5876", "volume": "21", "issue": "1", "pages": "342"}, "abstract": "The Swedish Childhood Tumor Biobank (BTB) is a nonprofit national infrastructure for collecting tissue samples and genomic data from pediatric patients diagnosed with central nervous system (CNS) and other solid tumors. The BTB is built on a multidisciplinary network established to provide the scientific community with standardized biospecimens and genomic data, thereby improving knowledge of the biology, treatment and outcome of childhood tumors. As of 2022, over 1100 fresh-frozen tumor samples are available for researchers. We present the workflow of the BTB from sample collection and processing to the generation of genomic data and services offered. To determine the research and clinical utility of the data, we performed bioinformatics analyses on next-generation sequencing (NGS) data obtained from a subset of 82 brain tumors and patient blood-derived DNA combined with methylation profiling to enhance the diagnostic accuracy and identified germline and somatic alterations with potential biological or clinical significance. The BTB procedures for collection, processing, sequencing, and bioinformatics deliver high-quality data. We observed that the findings could impact patient management by confirming or clarifying the diagnosis in 79 of the 82 tumors and detecting known or likely driver mutations in 68 of 79 patients. In addition to revealing known mutations in a broad spectrum of genes implicated in pediatric cancer, we discovered numerous alterations that may represent novel driver events and specific tumor entities. In summary, these examples reveal the power of NGS to identify a wide number of actionable gene alterations. Making the power of NGS available in healthcare is a challenging task requiring the integration of the work of clinical specialists and cancer biologists; this approach requires a dedicated infrastructure, as exemplified here by the BTB.", "doi": "10.1186/s12967-023-04178-4", "pmid": "37221626", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Short read": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10204274"}, {"db": "pii", "key": "10.1186/s12967-023-04178-4"}], "notes": [], "created": "2023-07-07T10:40:17.052Z", "modified": "2024-01-16T13:48:33.377Z"}, {"entity": "publication", "iuid": "c763cc0d6be544df8e6de1820f63e0f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c763cc0d6be544df8e6de1820f63e0f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c763cc0d6be544df8e6de1820f63e0f9"}}, "title": "Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins.", "authors": [{"family": "Elliott", "given": "Kerryn", "initials": "K", "orcid": "0000-0001-9238-7879", "researcher": {"href": "https://publications.scilifelab.se/researcher/43d0bf4d07f44363ab3a0b97ecb22e36.json"}}, {"family": "Singh", "given": "Vinod Kumar", "initials": "VK", "orcid": "0000-0002-7556-2505", "researcher": {"href": "https://publications.scilifelab.se/researcher/944f79abc5034c889bf3086d20499997.json"}}, {"family": "Bostr\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0001-8199-8922", "researcher": {"href": "https://publications.scilifelab.se/researcher/22c73409ff7c49ccb84f63bb39480ec9.json"}}, {"family": "Larsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-1400-0119", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b196318c09a46d48ece9c8417be01ff.json"}}], "type": "journal article", "published": "2023-05-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "2701", "issn-l": "2041-1723"}, "abstract": "Decades ago, it was shown that proteins binding to DNA can quantitatively alter the formation of DNA damage by UV light. This established the principle of UV footprinting for non-intrusive study of protein-DNA contacts in living cells, albeit at limited scale and precision. Here, we perform deep base-resolution quantification of the principal UV damage lesion, the cyclobutane pyrimidine dimer (CPD), at select human promoter regions using targeted CPD sequencing. Several transcription factors exhibited distinctive and repeatable damage signatures indicative of site occupancy, involving strong (up to 17-fold) position-specific elevations and reductions in CPD formation frequency relative to naked DNA. Positive damage modulation at some ETS transcription factor binding sites coincided at base level with melanoma somatic mutation hotspots. Our work provides proof of concept for the study of protein-DNA interactions at individual loci using light and sequencing, and reveals widespread and potent modulation of UV damage in regulatory regions.", "doi": "10.1038/s41467-023-38266-2", "pmid": "37169761", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10175305"}, {"db": "pii", "key": "10.1038/s41467-023-38266-2"}], "notes": [], "created": "2023-10-04T12:37:44.184Z", "modified": "2023-10-19T11:55:43.881Z"}, {"entity": "publication", "iuid": "28c78159a7ca4f5dbfb9d579f9cc9598", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28c78159a7ca4f5dbfb9d579f9cc9598.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28c78159a7ca4f5dbfb9d579f9cc9598"}}, "title": "Warmer temperatures favor slower-growing bacteria in natural marine communities.", "authors": [{"family": "Abreu", "given": "Clare I", "initials": "CI", "orcid": "0000-0001-6728-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/885864b9a3b54e91a2f9a813e146a57e.json"}}, {"family": "Dal Bello", "given": "Martina", "initials": "M", "orcid": "0000-0003-3706-2929", "researcher": {"href": "https://publications.scilifelab.se/researcher/60679c34749940ea96e64664ff352dfe.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Gore", "given": "Jeff", "initials": "J", "orcid": "0000-0003-4583-8555", "researcher": {"href": "https://publications.scilifelab.se/researcher/656862ab75d4440aaad40680e80a384f.json"}}], "type": "journal article", "published": "2023-05-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "19", "pages": "eade8352", "issn-l": "2375-2548"}, "abstract": "Earth's life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.", "doi": "10.1126/sciadv.ade8352", "pmid": "37163596", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10171810"}], "notes": [], "created": "2023-10-04T12:12:30.689Z", "modified": "2023-10-19T10:04:58.150Z"}, {"entity": "publication", "iuid": "5e32a19715154d189357e4066464baed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e32a19715154d189357e4066464baed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e32a19715154d189357e4066464baed"}}, "title": "Effects of rye inclusion in dog food on fecal microbiota and short-chain fatty acids.", "authors": [{"family": "Palmqvist", "given": "Hanna", "initials": "H"}, {"family": "Ringmark", "given": "Sara", "initials": "S"}, {"family": "H\u00f6glund", "given": "Katja", "initials": "K"}, {"family": "Pelve", "given": "Erik", "initials": "E"}, {"family": "Lundh", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-05-10", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "volume": "19", "issue": "1", "pages": "70", "issn-l": null}, "abstract": "Rye intake has been associated with beneficial effects on health in human interventions, possibly due to dietary fiber in rye. In dogs, few studies have explored the effects on health of dietary fiber in general, and rye fiber in particular. The aim of this study was to investigate how inclusion of rye, compared with wheat, influenced fecal microbiota composition, short chain fatty acids (SCFA) and apparent total tract digestibility (ATTD) in dogs. Six male Beagle dogs (mean age 4.6 years, SEM 0.95 years; mean body weight 14.6 kg, SEM 0.32 kg) were fed three experimental diets, each for 21 days, including an adaptation period of six days and with 2-2.5 months between diet periods. The diets were similar regarding energy and protein, but had different carbohydrate sources (refined wheat (W), whole grain rye (R), or an equal mixture of both (RW)) comprising 50% of total weight on a dry matter (DM) basis. The diets were baked and titanium dioxide was added for ATTD determination. Fecal samples were collected before and in the end of each experimental period. Fecal microbiota was analyzed by sequencing 16S rRNA gene amplicons and fecal SCFA by high-performance liquid chromatography. Crude protein, crude fat, neutral detergent fiber, and gross energy (GE) in food and feces were analyzed and ATTD of each was determined. Univariate and multivariate statistical methods were applied in data evaluation.\n\nFaecal microbiota composition, differed depending on diet (P = 0.002), with samples collected after consumption of the R diet differing from baseline. This was primarily because of a shift in proportion of Prevotella, which increased significantly after consumption of the R diet (P < 0.001). No significant differences were found for SCFA, but there was a tendency (P < 0.06) for higher molar proportions of acetic acid following consumption of the R diet. The ATTD of crude protein, crude fat, neutral detergent fiber, and GE was lower after consumption of the R diet compared with the other diets (P < 0.05).\n\nConsumption of the R diet, but not RW or W diets, was associated with specific shifts in microbial community composition and function, but also with lower ATTD.", "doi": "10.1186/s12917-023-03623-2", "pmid": "37161401", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10170736"}, {"db": "pii", "key": "10.1186/s12917-023-03623-2"}], "notes": [], "created": "2023-10-04T12:53:24.604Z", "modified": "2023-10-19T12:06:17.464Z"}, {"entity": "publication", "iuid": "1fd41f8b0eca4b1287a6862547fe91fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fd41f8b0eca4b1287a6862547fe91fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fd41f8b0eca4b1287a6862547fe91fd"}}, "title": "The spatial landscape of gene expression isoforms in tissue sections.", "authors": [{"family": "Lebrigand", "given": "Kevin", "initials": "K", "orcid": "0000-0001-5604-7893", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb4fc2f3bb0848e2afe92c96c326617f.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications.scilifelab.se/researcher/56822ffe0341444297c820580f52dfd0.json"}}, {"family": "Barbry", "given": "Pascal", "initials": "P", "orcid": "0000-0001-9632-6483", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7a905ca05b34448a12858cea60ba1c6.json"}}, {"family": "Waldmann", "given": "Rainer", "initials": "R", "orcid": "0000-0002-4599-2926", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3ba1e7c02664cb49caee4007cfc7e61.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2023-05-08", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "51", "issue": "8", "pages": "e47"}, "abstract": "In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.", "doi": "10.1093/nar/gkad169", "pmid": "36928528", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Spatial omics": null}, "xrefs": [{"db": "pmc", "key": "PMC10164556"}, {"db": "pii", "key": "7079641"}], "notes": [], "created": "2023-10-04T12:11:14.358Z", "modified": "2023-10-19T10:03:46.014Z"}, {"entity": "publication", "iuid": "92bac20ff8b24a25b2ee57cb152d864b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92bac20ff8b24a25b2ee57cb152d864b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92bac20ff8b24a25b2ee57cb152d864b"}}, "title": "Genomics of adaptive evolution in the woolly mammoth.", "authors": [{"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Kanellidou", "given": "Foteini", "initials": "F"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Mortensen", "given": "Peter", "initials": "P"}, {"family": "Danilov", "given": "Gleb K", "initials": "GK"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2023-05-08", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "33", "issue": "9", "pages": "1753-1764.e4", "issn-l": "0960-9822"}, "abstract": "Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.", "doi": "10.1016/j.cub.2023.03.084", "pmid": "37030294", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(23)00404-9"}], "notes": [], "created": "2023-10-04T12:38:47.496Z", "modified": "2024-01-16T13:48:33.426Z"}, {"entity": "publication", "iuid": "e32fd724b739422db6fef1905f9b5493", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e32fd724b739422db6fef1905f9b5493.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e32fd724b739422db6fef1905f9b5493"}}, "title": "Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.", "authors": [{"family": "Li", "given": "Xiaofei", "initials": "X", "orcid": "0000-0002-9991-7534", "researcher": {"href": "https://publications.scilifelab.se/researcher/d90bb6581d134277924377269eef88b9.json"}}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Liu", "given": "Yang", "initials": "Y"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z"}, {"family": "Lee", "given": "Hower", "initials": "H"}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5471168acdf94b63b1eab431fd1e8442.json"}}, {"family": "Kallner", "given": "Helena Kopp", "initials": "HK"}, {"family": "\u00c5kesson", "given": "Elisabet", "initials": "E"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E", "orcid": "0000-0003-2931-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/594c030b77f348e98805ea71e06c1b4d.json"}}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "26", "issue": "5", "pages": "891-901"}, "abstract": "The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.", "doi": "10.1038/s41593-023-01312-9", "pmid": "37095395", "labels": {"BioImage Informatics": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10166856"}, {"db": "pii", "key": "10.1038/s41593-023-01312-9"}], "notes": [], "created": "2023-05-31T11:06:10.725Z", "modified": "2025-10-17T13:02:17.029Z"}, {"entity": "publication", "iuid": "ad566720b83f4be6a7bc41d77b622e6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad566720b83f4be6a7bc41d77b622e6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad566720b83f4be6a7bc41d77b622e6d"}}, "title": "Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates.", "authors": [{"family": "Mierke", "given": "Friederike", "initials": "F"}, {"family": "Brink", "given": "Daniel P", "initials": "DP"}, {"family": "Norbeck", "given": "Joakim", "initials": "J"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "Andlid", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Fungal Genet. Biol.", "issn": "1096-0937", "volume": "166", "pages": "103783", "issn-l": "1087-1845"}, "abstract": "Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log2 fold change| \u2265 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.", "doi": "10.1016/j.fgb.2023.103783", "pmid": "36870442", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S1087-1845(23)00014-2"}], "notes": [], "created": "2023-10-04T12:23:59.958Z", "modified": "2023-10-19T10:10:56.798Z"}, {"entity": "publication", "iuid": "1992fff5e6cc41f0934b9b39ee3b72f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1992fff5e6cc41f0934b9b39ee3b72f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1992fff5e6cc41f0934b9b39ee3b72f7"}}, "title": "Different spatial structure of plant-associated fungal communities above- and belowground.", "authors": [{"family": "Faticov", "given": "Maria", "initials": "M", "orcid": "0000-0001-8206-9332", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd00e5ee400e440ba76d1010f5cbe7d9.json"}}, {"family": "Abdelfattah", "given": "Ahmed", "initials": "A"}, {"family": "Hamb\u00e4ck", "given": "Peter", "initials": "P", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}, {"family": "Roslin", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2957-4791", "researcher": {"href": "https://publications.scilifelab.se/researcher/04d92328b67e47ab82257567c07cf12f.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "13", "issue": "5", "pages": "e10065", "issn-l": "2045-7758"}, "abstract": "The distribution and community assembly of above- and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant-microbe interactions and plant health. Depending on how microbial communities are structured, we can expect different effects of the microbial community on the health of individual plants and on ecosystem processes. Importantly, the relative role of different factors will likely differ with the scale examined. Here, we address the driving factors at a landscape level, where each individual unit (oak trees) is accessible to a joint species pool. This allowed to quantify the relative effect of environmental factors and dispersal on the distribution of two types of fungal communities: those associated with the leaves and those associated with the soil of Quercus robur trees in a landscape in southwestern Finland. Within each community type, we compared the role of microclimatic, phenological, and spatial variables, and across community types, we examined the degree of association between the respective communities. Most of the variation in the foliar fungal community was found within trees, whereas soil fungal community composition showed positive spatial autocorrelation up to 50 m. Microclimate, tree phenology, and tree spatial connectivity explained little variation in the foliar and soil fungal communities. Foliar and soil fungal communities differed strongly in community structure, with no significant concordance detected between them. We provide evidence that foliar and soil fungal communities assemble independent of each other and are structured by different ecological processes.", "doi": "10.1002/ece3.10065", "pmid": "37223309", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10200691"}, {"db": "pii", "key": "ECE310065"}, {"db": "figshare", "key": "10.6084/m9.figshare.22687594"}], "notes": [], "created": "2023-10-11T09:16:14.644Z", "modified": "2024-01-16T13:48:33.507Z"}, {"entity": "publication", "iuid": "69ff10bcb53f43ddbe6829f6a0b36b79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69ff10bcb53f43ddbe6829f6a0b36b79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69ff10bcb53f43ddbe6829f6a0b36b79"}}, "title": "An extracellular matrix stiffness-induced breast cancer cell transcriptome resembles the transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC).", "authors": [{"family": "G\u00f6ransson", "given": "Sara", "initials": "S"}, {"family": "Chen", "given": "Shan", "initials": "S"}, {"family": "Olofsson", "given": "Helene", "initials": "H"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Str\u00f6mblad", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2023-04-30", "journal": {"title": "Biochem. Biophys. Res. Commun.", "issn": "1090-2104", "volume": "654", "pages": "73-79", "issn-l": "0006-291X"}, "abstract": "Identifying mechanisms driving the transition from ductal carcinoma in situ (DCIS) to invasive breast cancer remains a challenge in breast cancer research. Breast cancer progression is accompanied by remodelling and stiffening of the extracellular matrix, leading to increased proliferation, survival, and migration. Here, we studied stiffness-dependent phenotypes in MCF10CA1a (CA1a) breast cancer cells cultured on hydrogels with stiffness corresponding to normal breast and breast cancer. This revealed a stiffness-associated morphology consistent with acquisition of an invasive phenotype in breast cancer cells. Surprisingly, this strong phenotypic switch was accompanied by relatively modest transcriptome-wide alterations in mRNA levels, as independently quantified using both DNA-microarrays and bulk RNA sequencing. Strikingly, however, the stiffness-dependent alterations in mRNA levels overlapped with those contrasting ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC). This supports a role of matrix stiffness in driving the pre-invasive to invasive transition and suggests that mechanosignalling may be a target for prevention of invasive breast cancer.", "doi": "10.1016/j.bbrc.2023.03.001", "pmid": "36893606", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-291X(23)00271-1"}], "notes": [], "created": "2023-10-04T12:30:50.492Z", "modified": "2024-01-16T13:48:33.532Z"}, {"entity": "publication", "iuid": "c6c3174c46c94cb89bc660b22e443717", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6c3174c46c94cb89bc660b22e443717.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6c3174c46c94cb89bc660b22e443717"}}, "title": "Age Rather Than Supplementation with Oat \u03b2-Glucan Influences Development of the Intestinal Microbiota and SCFA Concentrations in Suckling Piglets.", "authors": [{"family": "Arapovic", "given": "Lidija", "initials": "L"}, {"family": "Huang", "given": "Yi", "initials": "Y"}, {"family": "Manell", "given": "Elin", "initials": "E", "orcid": "0000-0002-4491-7609", "researcher": {"href": "https://publications.scilifelab.se/researcher/375db1ce4a074a65bd7f7706d57a0776.json"}}, {"family": "Verbeek", "given": "Else", "initials": "E", "orcid": "0000-0002-1223-3480", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd16e833652d4a21b469dd956781c4ca.json"}}, {"family": "Keeling", "given": "Linda", "initials": "L", "orcid": "0000-0003-2629-0117", "researcher": {"href": "https://publications.scilifelab.se/researcher/089e84cda2d8469ea654a00ee80628c1.json"}}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}, {"family": "Lundh", "given": "Torbj\u00f6rn", "initials": "T", "orcid": "0000-0002-2780-3263", "researcher": {"href": "https://publications.scilifelab.se/researcher/724c93d48be148d080c19e41a157f6db.json"}}, {"family": "Lindberg", "given": "Jan Erik", "initials": "JE"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-04-14", "journal": {"title": "Animals (Basel)", "issn": "2076-2615", "volume": "13", "issue": "8", "issn-l": null}, "abstract": "The effects of early supplementation with oat \u03b2-glucan during the suckling period on piglet gut microbiota composition, concentrations of short-chain fatty acids, and gut physiological markers were assessed. Fifty piglets from five litters, balanced for sex and birth weight, were divided within litters into two treatment groups: \u03b2-glucan and control. Piglets in the \u03b2-glucan group received the supplement three times/week from day 7 of age until weaning. Rectal swab samples were collected from 10 piglets per treatment group (balanced across litters) from week 1 to week 4, and plasma samples were collected at 1, 3, and 4 weeks of age. Additional samples of intestinal tissues and jugular and portal vein plasma were collected from 10 animals at weaning (one per treatment group and litter). The concentrations of short-chain fatty acids in plasma and the microbiota composition in rectal swabs were mainly influenced by piglet age, rather than the supplement. There were significant differences in microbiota composition between litters and several correlations between concentrations of short-chain fatty acids in plasma and specific microbial taxa in rectal swabs. Overall, \u03b2-glucan supplementation did not have any clear impact on the gut environment in suckling piglets, whereas a clear age-related pattern emerged.", "doi": "10.3390/ani13081349", "pmid": "37106912", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10135274"}, {"db": "pii", "key": "ani13081349"}], "notes": [], "created": "2023-05-24T05:53:08.401Z", "modified": "2023-10-19T11:54:33.915Z"}, {"entity": "publication", "iuid": "a447417a7c664b86a0308dd49ea05b31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a447417a7c664b86a0308dd49ea05b31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a447417a7c664b86a0308dd49ea05b31"}}, "title": "The genetic basis of wing spots in Pieris canidia butterflies.", "authors": [{"family": "Wee", "given": "Jocelyn Liang Qi", "initials": "JLQ"}, {"family": "Murugesan", "given": "Suriya Narayanan", "initials": "SN"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Monteiro", "given": "Ant\u00f3nia", "initials": "A"}], "type": "journal article", "published": "2023-04-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "169", "issn-l": "1471-2164"}, "abstract": "Spots in pierid butterflies and eyespots in nymphalid butterflies are likely non-homologous wing colour pattern elements, yet they share a few features in common. Both develop black scales that depend on the function of the gene spalt, and both might have central signalling cells. This suggests that both pattern elements may be sharing common genetic circuitry. Hundreds of genes have already been associated with the development of nymphalid butterfly eyespot patterns, but the genetic basis of the simpler spot patterns on the wings of pierid butterflies has not been investigated. To facilitate studies of pierid wing patterns, we report a high-quality draft genome assembly for Pieris canidia, the Indian cabbage white. We then conducted transcriptomic analyses of pupal wing tissues sampled from the spot and non-spot regions of P. canidia at 3-6 h post-pupation. A total of 1352 genes were differentially regulated between wing tissues with and without the black spot, including spalt, Kr\u00fcppel-like factor 10, genes from the Toll, Notch, TGF-\u03b2, and FGFR signalling pathways, and several genes involved in the melanin biosynthetic pathway. We identified 14 genes that are up-regulated in both pierid spots and nymphalid eyespots and propose that spots and eyespots share regulatory modules despite their likely independent origins.", "doi": "10.1186/s12864-023-09261-0", "pmid": "37016295", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10074818"}, {"db": "pii", "key": "10.1186/s12864-023-09261-0"}], "notes": [], "created": "2024-03-14T12:56:18.609Z", "modified": "2024-03-14T12:56:18.614Z"}, {"entity": "publication", "iuid": "10500fb8067541b5a9afef93fd90136a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10500fb8067541b5a9afef93fd90136a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10500fb8067541b5a9afef93fd90136a"}}, "title": "Red clover root-associated microbiota is shaped by geographic location and choice of farming system.", "authors": [{"family": "Jambagi", "given": "Shridhar", "initials": "S", "orcid": "0000-0003-4119-2750", "researcher": {"href": "https://publications.scilifelab.se/researcher/231e180fbd154372ae51411274d9ea00.json"}}, {"family": "Hod\u00e9n", "given": "Kristian Persson", "initials": "KP", "orcid": "0000-0003-0354-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b41e8e41574ee6bcb55df3b0d145d9.json"}}, {"family": "\u00d6hlund", "given": "Linda", "initials": "L"}, {"family": "Dixelius", "given": "Christina", "initials": "C", "orcid": "0000-0003-0150-0608", "researcher": {"href": "https://publications.scilifelab.se/researcher/197905a68ba24d429fc14a598dc22132.json"}}], "type": "journal article", "published": "2023-04-03", "journal": {"title": "J Appl Microbiol", "issn": "1365-2672", "issn-l": "1364-5072", "volume": "134", "issue": "4", "pages": null}, "abstract": "This study evaluated the red clover (Trifolium pratense) root-associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites.\r\n\r\n16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence were analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium, and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys, and Tetracladium fungal genera known for endophytic, saprotrophic, and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms.\r\n\r\nWe showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the Rhizobiumleguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.", "doi": "10.1093/jambio/lxad067", "pmid": "37012225", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7100963"}], "notes": [], "created": "2023-05-22T19:56:22.157Z", "modified": "2024-01-16T13:48:33.706Z"}, {"entity": "publication", "iuid": "e822b0cf18d14125ae78bd5afbac5e2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e822b0cf18d14125ae78bd5afbac5e2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e822b0cf18d14125ae78bd5afbac5e2c"}}, "title": "The human bone marrow plasma cell compartment in rheumatoid arthritis - Clonal relationships and anti-citrulline autoantibody producing cells.", "authors": [{"family": "Hensvold", "given": "Aase", "initials": "A"}, {"family": "Horuluoglu", "given": "Begum", "initials": "B"}, {"family": "Sahlstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Thyagarajan", "given": "Radha", "initials": "R"}, {"family": "Diaz Boada", "given": "Juan Sebastian", "initials": "JS"}, {"family": "Hansson", "given": "Monika", "initials": "M"}, {"family": "Mathsson-Alm", "given": "Linda", "initials": "L"}, {"family": "Gerstner", "given": "Christina", "initials": "C"}, {"family": "Sippl", "given": "Natalie", "initials": "N"}, {"family": "Israelsson", "given": "Lena", "initials": "L"}, {"family": "Wedin", "given": "Rikard", "initials": "R"}, {"family": "Steen", "given": "Johanna", "initials": "J"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "R\u00e9thi", "given": "Bence", "initials": "B"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Diaz-Gallo", "given": "Lina-Marcela", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Gr\u00f6nwall", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "136", "issue": null, "pages": "103022"}, "abstract": "A majority of circulating IgG is produced by plasma cells residing in the bone marrow (BM). Long-lived BM plasma cells constitute our humoral immune memory and are essential for infection-specific immunity. They may also provide a reservoir of potentially pathogenic autoantibodies, including rheumatoid arthritis (RA)-associated anti-citrullinated protein autoantibodies (ACPA). Here we investigated paired human BM plasma cell and peripheral blood (PB) B-cell repertoires in seropositive RA, four ACPA+ RA patients and one ACPA- using two different single-cell approaches, flow cytometry sorting, and transcriptomics, followed by recombinant antibody generation. Immunoglobulin (Ig) analysis of >900 paired heavy-light chains from BM plasma cells identified by either surface CD138 expression or transcriptome profiles (including gene expression of MZB1, JCHAIN and XBP1) demonstrated differences in IgG/A repertoires and N-linked glycosylation between patients. For three patients, we identified clonotypes shared between BM plasma cells and PB memory B cells. Notably, four individuals displayed plasma cells with identical heavy chains but different light chains, which may indicate receptor revision or clonal convergence. ACPA-producing BM plasma cells were identified in two ACPA+ patients. Three of 44 recombinantly expressed monoclonal antibodies from ACPA+ RA BM plasma cells were CCP2+, specifically binding to citrullinated peptides. Out of these, two clones reacted with citrullinated histone-4 and activated neutrophils. In conclusion, single-cell investigation of B-cell repertoires in RA bone marrow provided new understanding of human plasma cells clonal relationships and demonstrated pathogenically relevant disease-associated autoantibody expression in long-lived plasma cells.", "doi": "10.1016/j.jaut.2023.103022", "pmid": "37001434", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-8411(23)00031-8"}], "notes": [], "created": "2023-10-04T12:49:42.030Z", "modified": "2024-03-14T12:03:34.639Z"}, {"entity": "publication", "iuid": "dc02fe22100e4a48a4b665ca4b2da117", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc02fe22100e4a48a4b665ca4b2da117.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc02fe22100e4a48a4b665ca4b2da117"}}, "title": "Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.", "authors": [{"family": "Morez", "given": "Adeline", "initials": "A", "orcid": "0000-0003-2393-7931", "researcher": {"href": "https://publications.scilifelab.se/researcher/5de5e14fff424a5cb665c58b38746f03.json"}}, {"family": "Britton", "given": "Kate", "initials": "K"}, {"family": "Noble", "given": "Gordon", "initials": "G"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Martiniano", "given": "Rui", "initials": "R", "orcid": "0000-0003-0216-778X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d685bffed97b435fa9b577a96af5ffc2.json"}}, {"family": "Talamo", "given": "Sahra", "initials": "S"}, {"family": "Evans", "given": "Nicholas J", "initials": "NJ"}, {"family": "Irish", "given": "Joel D", "initials": "JD", "orcid": "0000-0001-7857-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2c6cef2a7a14ccea6067cdfcb24efac.json"}}, {"family": "Donald", "given": "Christina", "initials": "C"}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L", "orcid": "0000-0001-6499-8728", "researcher": {"href": "https://publications.scilifelab.se/researcher/74574daaa4e340bca662b3e3bf4899e9.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "19", "issue": "4", "pages": "e1010360", "issn-l": "1553-7390"}, "abstract": "There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. 300-900 CE), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century CE resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland-where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.", "doi": "10.1371/journal.pgen.1010360", "pmid": "37104250", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10138790"}, {"db": "pii", "key": "PGENETICS-D-22-00892"}], "notes": [], "created": "2023-10-04T12:46:45.288Z", "modified": "2023-10-19T12:00:04.258Z"}, {"entity": "publication", "iuid": "0b0bab0101784ed0ae46809471072bae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b0bab0101784ed0ae46809471072bae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b0bab0101784ed0ae46809471072bae"}}, "title": "Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Forsman", "given": "Anders", "initials": "A"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2023-03-29", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "14", "pages": "1099445", "issn-l": "1664-302X"}, "abstract": "Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (\u223c0.5 cm) to deeper sediments (\u223c 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.", "doi": "10.3389/fmicb.2023.1099445", "pmid": "37065140", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10090409"}], "notes": [], "created": "2023-10-04T12:39:33.084Z", "modified": "2024-01-16T13:48:33.794Z"}, {"entity": "publication", "iuid": "ee01bdbaa4114eec92a4d6c0407a11d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee01bdbaa4114eec92a4d6c0407a11d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee01bdbaa4114eec92a4d6c0407a11d8"}}, "title": "Linking prokaryotic genome size variation to metabolic potential and environment.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1649-6894", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25dfecc53e94af0b79799621f131631.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M", "orcid": "0000-0001-6632-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba68bf651630488dab4d146b11cf612a.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "researcher": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}], "type": "journal article", "published": "2023-03-27", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "3", "issue": "1", "pages": "25", "issn-l": null}, "abstract": "While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.", "doi": "10.1038/s43705-023-00231-x", "pmid": "36973336", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10042847"}, {"db": "pii", "key": "10.1038/s43705-023-00231-x"}], "notes": [], "created": "2023-10-04T12:20:23.424Z", "modified": "2024-01-16T13:48:33.810Z"}, {"entity": "publication", "iuid": "af9a01b34c72458bbe743a8bcd52ca91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af9a01b34c72458bbe743a8bcd52ca91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af9a01b34c72458bbe743a8bcd52ca91"}}, "title": "A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration.", "authors": [{"family": "Subramanian", "given": "Elaiyaraja", "initials": "E"}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Brito", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Kumar", "given": "Anoop", "initials": "A"}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Karampelias", "given": "Christos", "initials": "C"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "Echeverri", "given": "Karen", "initials": "K"}, {"family": "Lui", "given": "Weng-Onn", "initials": "WO"}, {"family": "Andersson", "given": "Olov", "initials": "O"}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A"}], "type": "journal article", "published": "2023-03-27", "journal": {"title": "Dev. Cell", "issn": "1878-1551", "issn-l": "1534-5807", "volume": "58", "issue": "6", "pages": "450-460.e6"}, "abstract": "Building a blastema from the stump is a key step of salamander limb regeneration. Stump-derived cells temporarily suspend their identity as they contribute to the blastema by a process generally referred to as dedifferentiation. Here, we provide evidence for a mechanism that involves an active inhibition of protein synthesis during blastema formation and growth. Relieving this inhibition results in a higher number of cycling cells and enhances the pace of limb regeneration. By small RNA profiling and fate mapping of skeletal muscle progeny as a cellular model for dedifferentiation, we find that the downregulation of miR-10b-5p is critical for rebooting the translation machinery. miR-10b-5p targets ribosomal mRNAs, and its artificial upregulation causes decreased blastema cell proliferation, reduction in transcripts that encode ribosomal subunits, diminished nascent protein synthesis, and retardation of limb regeneration. Taken together, our data identify a link between miRNA regulation, ribosome biogenesis, and protein synthesis during newt limb regeneration.", "doi": "10.1016/j.devcel.2023.02.007", "pmid": "36893754", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1534-5807(23)00049-7"}], "notes": [], "created": "2023-11-02T09:09:33.054Z", "modified": "2024-10-15T11:06:38.554Z"}, {"entity": "publication", "iuid": "4dd2b13839254556b96d58d9c1342df8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4dd2b13839254556b96d58d9c1342df8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4dd2b13839254556b96d58d9c1342df8"}}, "title": "RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents.", "authors": [{"family": "Piombo", "given": "Edoardo", "initials": "E"}, {"family": "Kelbessa", "given": "Bekele Gelena", "initials": "BG"}, {"family": "Sundararajan", "given": "Poorva", "initials": "P"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Vetukuri", "given": "Ramesh Raju", "initials": "RR"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}], "type": "journal article", "published": "2023-03-24", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "14", "pages": "1076522", "issn-l": "1664-302X"}, "abstract": "Oomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors.\n\nTo gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species.\n\nEach of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5' base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.", "doi": "10.3389/fmicb.2023.1076522", "pmid": "37032886", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10080066"}], "notes": [], "created": "2023-10-04T13:02:42.185Z", "modified": "2023-10-19T12:22:56.220Z"}, {"entity": "publication", "iuid": "e7f6c7b32a7744319eae28a8250ba884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7f6c7b32a7744319eae28a8250ba884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7f6c7b32a7744319eae28a8250ba884"}}, "title": "Evidence for a single, ancient origin of a genus-wide alternative life history strategy.", "authors": [{"family": "Tunstr\u00f6m", "given": "Kalle", "initials": "K", "orcid": "0000-0002-5285-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd0ddb97d724542b6e7c46f782f3bbd.json"}}, {"family": "Woronik", "given": "Alyssa", "initials": "A", "orcid": "0000-0003-3017-6069", "researcher": {"href": "https://publications.scilifelab.se/researcher/841b99e196ed4fe7ad25f76200c98ec6.json"}}, {"family": "Hanly", "given": "Joseph J", "initials": "JJ", "orcid": "0000-0002-9459-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/92b6972ffe974d0d95f7350a62ec209e.json"}}, {"family": "Rastas", "given": "Pasi", "initials": "P", "orcid": "0000-0003-2768-1339", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a8f5f2160154bdfa0b21dfc132d4871.json"}}, {"family": "Chichvarkhin", "given": "Anton", "initials": "A"}, {"family": "Warren", "given": "Andrew D", "initials": "AD"}, {"family": "Kawahara", "given": "Akito Y", "initials": "AY", "orcid": "0000-0002-3724-4610", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe112868785c4b8187cdc164e25ef9ae.json"}}, {"family": "Schoville", "given": "Sean D", "initials": "SD", "orcid": "0000-0001-7364-434X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3a4dc2fb0c8434994e065eb9ffad9f5.json"}}, {"family": "Ficarrotta", "given": "Vincent", "initials": "V", "orcid": "0000-0002-4021-4906", "researcher": {"href": "https://publications.scilifelab.se/researcher/3535033454414fc8be454e9880f7dcee.json"}}, {"family": "Porter", "given": "Adam H", "initials": "AH", "orcid": "0000-0002-8154-4207", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49a80fbd4d441e1bf2281a57751b79b.json"}}, {"family": "Watt", "given": "Ward B", "initials": "WB"}, {"family": "Martin", "given": "Arnaud", "initials": "A", "orcid": "0000-0002-5980-2249", "researcher": {"href": "https://publications.scilifelab.se/researcher/d248adda76964813a0fe5de5a84de2cd.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}], "type": "journal article", "published": "2023-03-22", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "12", "pages": "eabq3713", "issn-l": "2375-2548"}, "abstract": "Understanding the evolutionary origins and factors maintaining alternative life history strategies (ALHS) within species is a major goal of evolutionary research. While alternative alleles causing discrete ALHS are expected to purge or fix over time, one-third of the ~90 species of Colias butterflies are polymorphic for a female-limited ALHS called Alba. Whether Alba arose once, evolved in parallel, or has been exchanged among taxa is currently unknown. Using comparative genome-wide association study (GWAS) and population genomic analyses, we placed the genetic basis of Alba in time-calibrated phylogenomic framework, revealing that Alba evolved once near the base of the genus and has been subsequently maintained via introgression and balancing selection. CRISPR-Cas9 mutagenesis was then used to verify a putative cis-regulatory region of Alba, which we identified using phylogenetic foot printing. We hypothesize that this cis-regulatory region acts as a modular enhancer for the induction of the Alba ALHS, which has likely facilitated its long evolutionary persistence.", "doi": "10.1126/sciadv.abq3713", "pmid": "36947619", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10032607"}], "notes": [], "created": "2023-10-04T12:34:51.747Z", "modified": "2023-10-19T11:53:35.081Z"}, {"entity": "publication", "iuid": "146c0055084542878ac0e9cb73932a95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/146c0055084542878ac0e9cb73932a95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/146c0055084542878ac0e9cb73932a95"}}, "title": "An integrated single cell and spatial transcriptomic map of human white adipose tissue.", "authors": [{"family": "Massier", "given": "Lucas", "initials": "L"}, {"family": "Jalkanen", "given": "Jutta", "initials": "J", "orcid": "0000-0002-0219-1096", "researcher": {"href": "https://publications.scilifelab.se/researcher/96620636aff142c484d07894c573f3d2.json"}}, {"family": "Elmastas", "given": "Merve", "initials": "M", "orcid": "0000-0002-1346-5080", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4055754f8cb4035ac1e160cc3cad356.json"}}, {"family": "Zhong", "given": "Jiawei", "initials": "J", "orcid": "0000-0002-2802-0770", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d30cbe9680a42c1b6478921e4b63287.json"}}, {"family": "Wang", "given": "Tongtong", "initials": "T"}, {"family": "Nono Nankam", "given": "Pamela A", "initials": "PA", "orcid": "0000-0001-9301-4556", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff19be55f9dd48f6becb1a0c47000d68.json"}}, {"family": "Frendo-Cumbo", "given": "Scott", "initials": "S", "orcid": "0000-0002-9047-4650", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bfa1b27416e47fd90a77657fcb0a34e.json"}}, {"family": "B\u00e4ckdahl", "given": "Jesper", "initials": "J"}, {"family": "Subramanian", "given": "Narmadha", "initials": "N"}, {"family": "Sekine", "given": "Takuya", "initials": "T"}, {"family": "Kerr", "given": "Alastair G", "initials": "AG", "orcid": "0000-0003-2085-1542", "researcher": {"href": "https://publications.scilifelab.se/researcher/076ba1b03b78451ba1ddb95b04e74b27.json"}}, {"family": "Tseng", "given": "Ben T P", "initials": "BTP"}, {"family": "Laurencikiene", "given": "Jurga", "initials": "J"}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Lourda", "given": "Magda", "initials": "M", "orcid": "0000-0003-3155-1123", "researcher": {"href": "https://publications.scilifelab.se/researcher/64d9a0bc6b5d4039af5bc308a97eaad6.json"}}, {"family": "Kublickiene", "given": "Karolina", "initials": "K", "orcid": "0000-0002-4841-6836", "researcher": {"href": "https://publications.scilifelab.se/researcher/42acd99d04974333989f148a1f960207.json"}}, {"family": "Bhalla", "given": "Nayanika", "initials": "N", "orcid": "0000-0002-6800-0432", "researcher": {"href": "https://publications.scilifelab.se/researcher/add89d1454ce490ab138768993411d70.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Valsesia", "given": "Armand", "initials": "A", "orcid": "0000-0003-0746-9664", "researcher": {"href": "https://publications.scilifelab.se/researcher/b480c6022f2f43bdb95e7a37e11d5235.json"}}, {"family": "Astrup", "given": "Arne", "initials": "A", "orcid": "0000-0001-8968-8996", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa3d74e15326474282c62b26c4c1507b.json"}}, {"family": "Blaak", "given": "Ellen E", "initials": "EE", "orcid": "0000-0002-2496-3464", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fa433d6fe8d4b6b811c20a88378e4eb.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}, {"family": "Viguerie", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-1730-9915", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1b76daf0c9e478b974d0fa9fb4aa5a1.json"}}, {"family": "Langin", "given": "Dominique", "initials": "D", "orcid": "0000-0002-2669-7825", "researcher": {"href": "https://publications.scilifelab.se/researcher/689d03a8a3614168bc04d897a7cfd0c2.json"}}, {"family": "Wolfrum", "given": "Christian", "initials": "C", "orcid": "0000-0002-3862-6805", "researcher": {"href": "https://publications.scilifelab.se/researcher/43777b7ae29b470793e30b6d32d2674f.json"}}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M", "orcid": "0000-0003-4785-1876", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab61ac66c36749019ce5066fb1a5061e.json"}}, {"family": "Mejhert", "given": "Niklas", "initials": "N", "orcid": "0000-0003-1785-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/81eb60b84ea14ad9ba7e4d3433c37a3e.json"}}], "type": "meta-analysis", "published": "2023-03-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1438", "issn-l": "2041-1723"}, "abstract": "To date, single-cell studies of human white adipose tissue (WAT) have been based on small cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a comprehensive meta-analysis of publicly available and newly generated single-cell, single-nucleus, and spatial transcriptomic results from human subcutaneous, omental, and perivascular WAT. Our high-resolution map is built on data from ten studies and allowed us to robustly identify >60 subpopulations of adipocytes, fibroblast and adipogenic progenitors, vascular, and immune cells. Using these results, we deconvolved spatial and bulk transcriptomic data from nine additional cohorts to provide spatial and clinical dimensions to the map. This identified cell-cell interactions as well as relationships between specific cell subtypes and insulin resistance, dyslipidemia, adipocyte volume, and lipolysis upon long-term weight changes. Altogether, our meta-map provides a rich resource defining the cellular and microarchitectural landscape of human WAT and describes the associations between specific cell types and metabolic states.", "doi": "10.1038/s41467-023-36983-2", "pmid": "36922516", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10017705"}, {"db": "pii", "key": "10.1038/s41467-023-36983-2"}], "notes": [], "created": "2023-10-04T12:19:09.279Z", "modified": "2023-10-19T10:08:08.367Z"}, {"entity": "publication", "iuid": "aaccded4ce2948dfb2ccdfcaecffc66b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aaccded4ce2948dfb2ccdfcaecffc66b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aaccded4ce2948dfb2ccdfcaecffc66b"}}, "title": "Comprehensive transcriptome analysis of different potato cultivars provides insight into early blight disease caused by Alternaria solani.", "authors": [{"family": "Sajeevan", "given": "Radha Sivarajan", "initials": "RS", "orcid": "0000-0002-8671-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d0cdc56cd144c628d3c90000b782581.json"}}, {"family": "Abdelmeguid", "given": "Ingi", "initials": "I"}, {"family": "Saripella", "given": "Ganapathi Varma", "initials": "GV"}, {"family": "Lenman", "given": "Marit", "initials": "M"}, {"family": "Alexandersson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6320-2492", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae8dc98de79429495f0a1727a342e9f.json"}}], "type": "journal article", "published": "2023-03-08", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "23", "issue": "1", "pages": "130", "issn-l": "1471-2229"}, "abstract": "Early blight, caused by the necrotrophic fungal pathogen Alternaria solani, is an economically important disease affecting the tuber yield worldwide. The disease is mainly controlled by chemical plant protection agents. However, over-using these chemicals can lead to the evolution of resistant A. solani strains and is environmentally hazardous. Identifying genetic disease resistance factors is crucial for the sustainable management of early blight but little effort has been diverted in this direction. Therefore, we carried out transcriptome sequencing of the A. solani interaction with different potato cultivars with varying levels of early blight resistance to identify key host genes and pathways in a cultivar-specific manner.\n\nIn this study, we have captured transcriptomes from three different potato cultivars with varying susceptibility to A. solani, namely Magnum Bonum, D\u00e9sir\u00e9e, and Kuras, at 18 and 36 h post-infection. We identified many differentially expressed genes (DEGs) between these cultivars, and the number of DEGs increased with susceptibility and infection time. There were 649 transcripts commonly expressed between the potato cultivars and time points, of which 627 and 22 were up- and down-regulated, respectively. Interestingly, overall the up-regulated DEGs were twice in number as compared to down-regulated ones in all the potato cultivars and time points, except Kuras at 36 h post-inoculation. In general, transcription factor families WRKY, ERF, bHLH, MYB, and C2H2 were highly enriched DEGs, of which a significant number were up-regulated. The majority of the key transcripts involved in the jasmonic acid and ethylene biosynthesis pathways were highly up-regulated. Many transcripts involved in the mevalonate (MVA) pathway, isoprenyl-PP, and terpene biosynthesis were also up-regulated across the potato cultivars and time points. Compared to Magnum Bonum and D\u00e9sir\u00e9e, multiple components of the photosynthesis machinery, starch biosynthesis and degradation pathway were down-regulated in the most susceptible potato cultivar, Kuras.\n\nTranscriptome sequencing identified many differentially expressed genes and pathways, thereby contributing to the improved understanding of the interaction between the potato host and A. solani. The transcription factors identified are attractive targets for genetic modification to improve potato resistance against early blight. The results provide important insights into the molecular events at the early stages of disease development, help to shorten the knowledge gap, and support potato breeding programs for improved early blight disease resistance.", "doi": "10.1186/s12870-023-04135-9", "pmid": "36882678", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9993742"}, {"db": "pii", "key": "10.1186/s12870-023-04135-9"}], "notes": [], "created": "2023-10-04T13:03:55.205Z", "modified": "2024-01-16T13:48:33.854Z"}, {"entity": "publication", "iuid": "5b3508419d454b42ad2e8e5537ee4608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b3508419d454b42ad2e8e5537ee4608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b3508419d454b42ad2e8e5537ee4608"}}, "title": "Rapid adaptations of Legionella pneumophila to the human host.", "authors": [{"family": "Leenheer", "given": "Dani\u00ebl", "initials": "D"}, {"family": "Moreno", "given": "Ana\u00edsa B", "initials": "AB"}, {"family": "Paranjape", "given": "Kiran", "initials": "K"}, {"family": "Murray", "given": "Susan", "initials": "S"}, {"family": "Jarraud", "given": "Sophie", "initials": "S"}, {"family": "Ginevra", "given": "Christophe", "initials": "C"}, {"family": "Guy", "given": "Lionel", "initials": "L"}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "9", "issue": "3", "issn-l": null}, "abstract": "Legionella pneumophila are host-adapted bacteria that infect and reproduce primarily in amoeboid protists. Using similar infection mechanisms, they infect human macrophages, and cause Legionnaires' disease, an atypical pneumonia, and the milder Pontiac fever. We hypothesized that, despite the similarities in infection mechanisms, the hosts are different enough that there exist high-selective value mutations that would dramatically increase the fitness of Legionella inside the human host. By comparing a large number of isolates from independent infections, we identified two genes, mutated in three unrelated patients, despite the short duration of the incubation period (2-14 days). One is a gene coding for an outer membrane protein (OMP) belonging to the OmpP1/FadL family. The other is a gene coding for an EAL-domain-containing protein involved in cyclic-di-GMP regulation, which in turn modulates flagellar activity. The clinical strain, carrying the mutated EAL-domain-containing homologue, grows faster in macrophages than the wild-type strain, and thus appears to be better adapted to the human host. As human-to-human transmission is very rare, fixation of these mutations into the population and spread into the environment is unlikely. Therefore, parallel evolution - here mutations in the same genes observed in independent human infections - could point to adaptations to the accidental human host. These results suggest that despite the ability of L. pneumophila to infect, replicate in and exit from macrophages, its human-specific adaptations are unlikely to be fixed in the population.", "doi": "10.1099/mgen.0.000958", "pmid": "36947445", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10132064"}], "notes": [], "created": "2023-10-04T12:58:47.617Z", "modified": "2024-01-16T13:48:33.890Z"}, {"entity": "publication", "iuid": "d62091617279400ebe9fd264e641f6bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d62091617279400ebe9fd264e641f6bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d62091617279400ebe9fd264e641f6bc"}}, "title": "Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.", "authors": [{"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Dziedziech", "given": "Alexis", "initials": "A"}, {"family": "Sekar", "given": "Vaishnovi", "initials": "V"}, {"family": "Ernest", "given": "Medard", "initials": "M"}, {"family": "Alves E Silva", "given": "Thiago Luiz", "initials": "TL"}, {"family": "Balan", "given": "Balu", "initials": "B"}, {"family": "Emami", "given": "S Noushin", "initials": "SN"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Jex", "given": "Aaron", "initials": "A", "orcid": "0000-0002-1285-7947", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd00075176a841c1ad916a094a182f6c.json"}}, {"family": "Jacobs-Lorena", "given": "Marcelo", "initials": "M"}, {"family": "Henriksson", "given": "Johan", "initials": "J"}, {"family": "Vega-Rodriguez", "given": "Joel", "initials": "J"}, {"family": "Ankarklev", "given": "Johan", "initials": "J", "orcid": "0000-0003-3170-8493", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf5386930e34157bf76970b16bffc02.json"}}], "type": "journal article", "published": "2023-02-27", "journal": {"title": "Microbiol Spectr", "issn": "2165-0497", "volume": "11", "issue": "2", "pages": "e0367122", "issn-l": null}, "abstract": "Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 h after blood feeding, including the zygote and ookinete stages. This study revealed the temporal gene expression of the ApiAP2 family of transcription factors and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structural protein prediction analyses, we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation, and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody- or peptide-based transmission suppression strategies. In total, this study uncovers the P. falciparum transcriptome from early to late parasite development in the mosquito midgut, inside its natural vector, which provides an important resource for future malaria transmission-blocking initiatives. IMPORTANCE The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host. However, recent incentives in the field call for novel interventions to block parasite transmission from humans to the mosquito vector. Therefore, we need to better understand the parasite biology during its development inside the mosquito, including a deeper understanding of the expression of genes controlling parasite progression during these stages. Here, we have generated single-cell transcriptome data, covering P. falciparum's development, from gamete to ookinete inside the mosquito midgut, uncovering previously untapped parasite biology, including a repertoire of novel biomarkers to be explored in future transmission-blocking efforts. We anticipate that our study provides an important resource, which can be further explored to improve our understanding of the parasite biology as well as aid in guiding future malaria intervention strategies.", "doi": "10.1128/spectrum.03671-22", "pmid": "36847501", "labels": {"Microbial Single Cell Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10100735"}], "notes": [], "created": "2023-10-06T12:15:41.309Z", "modified": "2024-10-16T07:05:39.782Z"}, {"entity": "publication", "iuid": "972a9d48ef104e73a8766b8630ade5af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/972a9d48ef104e73a8766b8630ade5af"}}, "title": "Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.", "authors": [{"family": "Jun", "given": "Seong-Hwan", "initials": "S"}, {"family": "Toosi", "given": "Hosein", "initials": "H"}, {"family": "Mold", "given": "Jeff", "initials": "J"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "O'Flanagan", "given": "Ciara", "initials": "C"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Aparicio", "given": "Samuel", "initials": "S", "orcid": "0000-0002-0487-9599", "researcher": {"href": "https://publications.scilifelab.se/researcher/8665401549d749ea8c1ab814dbfe5061.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Roth", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3422-8823", "researcher": {"href": "https://publications.scilifelab.se/researcher/55d6b9360321440ca1bc9199a42b624a.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications.scilifelab.se/researcher/b956941833b843f6ace483bf4c21e643.json"}}], "type": "journal article", "published": "2023-02-22", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "982"}, "abstract": "Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer.", "doi": "10.1038/s41467-023-36202-y", "pmid": "36813776", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9946941"}, {"db": "pii", "key": "10.1038/s41467-023-36202-y"}], "notes": [], "created": "2023-03-06T13:47:42.947Z", "modified": "2023-11-29T11:39:09.375Z"}, {"entity": "publication", "iuid": "5ac9844505f448bab02167d3d467c4a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ac9844505f448bab02167d3d467c4a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ac9844505f448bab02167d3d467c4a4"}}, "title": "Genomic architecture of migration timing in a long-distance migratory songbird.", "authors": [{"family": "de Greef", "given": "Evelien", "initials": "E"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Thorstensen", "given": "Matt J", "initials": "MJ"}, {"family": "Delmore", "given": "Kira E", "initials": "KE"}, {"family": "Fraser", "given": "Kevin C", "initials": "KC"}], "type": "journal article", "published": "2023-02-10", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "2437"}, "abstract": "The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks. A moderate to large amount of variance in spring migration arrival timing was explained by genomics (proportion of phenotypic variation explained by genomics = 0.74; polygenic score R2 = 0.24). On chromosome 1, a region that was differentiated between migration timing phenotypes contained genes that could facilitate nocturnal flights and act as epigenetic modifiers. Overall, these results advance our understanding of the genomic underpinnings of migration timing.", "doi": "10.1038/s41598-023-29470-7", "pmid": "36765096", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9918537"}, {"db": "pii", "key": "10.1038/s41598-023-29470-7"}], "notes": [], "created": "2023-03-06T13:47:41.654Z", "modified": "2024-11-25T10:20:21.866Z"}, {"entity": "publication", "iuid": "402524da476a4884a9495be39fc7f50c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/402524da476a4884a9495be39fc7f50c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/402524da476a4884a9495be39fc7f50c"}}, "title": "Larval transcriptomes reflect the evolutionary history of plant-insect associations.", "authors": [{"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Pires Braga", "given": "Mariana", "initials": "M", "orcid": "0000-0002-1253-2536", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab296645778b4d97959314bf28c8209a.json"}}, {"family": "Janz", "given": "Niklas", "initials": "N"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2023-02-04", "journal": {"title": "Evolution", "issn": "1558-5646", "volume": "77", "issue": "2", "pages": "519-533", "issn-l": "0014-3820"}, "abstract": "In this study, we investigated whether patterns of gene expression in larvae feeding on different plants can explain important aspects of the evolution of insect-plant associations, such as phylogenetic conservatism of host use and re-colonization of ancestral hosts that have been lost from the host repertoire. To this end, we performed a phylogenetically informed study comparing the transcriptomes of 4 nymphalid butterfly species in Polygonia and the closely related genus Nymphalis. Larvae were reared on Urtica dioica, Salix spp., and Ribes spp. Plant-specific gene expression was found to be similar across butterfly species, even in the case of host plants that are no longer used by two of the butterfly species. These results suggest that plant-specific transcriptomes can be robust over evolutionary time. We propose that adaptations to particular larval food plants can profitably be understood as an evolved set of modules of co-expressed genes, promoting conservatism in host use and facilitating re-colonization. Moreover, we speculate that the degree of overlap between plant-specific transcriptomes may correlate with the strength of trade-offs between plants as resources and hence to the probability of colonizing hosts and complete host shifts.", "doi": "10.1093/evolut/qpac049", "pmid": "36625474", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6881564"}], "notes": [], "created": "2023-05-17T08:45:56.948Z", "modified": "2024-01-16T13:48:33.977Z"}, {"entity": "publication", "iuid": "f7f0a2b696f74c7c97f50e51dcbc32d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7f0a2b696f74c7c97f50e51dcbc32d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7f0a2b696f74c7c97f50e51dcbc32d8"}}, "title": "Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.", "authors": [{"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Gower", "given": "Graham", "initials": "G", "orcid": "0000-0002-6197-3872", "researcher": {"href": "https://publications.scilifelab.se/researcher/6734ceea85184d94bf6f35eaf593f05e.json"}}, {"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Smith", "given": "Brian Tilston", "initials": "BT"}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Olsson", "given": "Urban", "initials": "U", "orcid": "0000-0003-1435-5411", "researcher": {"href": "https://publications.scilifelab.se/researcher/f16c5531607c4f5190f68a35b15cbd0e.json"}}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Racimo", "given": "Fernando", "initials": "F", "orcid": "0000-0002-5025-2607", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd12137b4184a72a81c48d2926c5280.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2023-02-01", "journal": {"title": "Evolution Letters", "issn": "2056-3744", "volume": "7", "issue": "1", "pages": "24-36", "issn-l": "2056-3744"}, "abstract": "Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.", "doi": "10.1093/evlett/qrac006", "pmid": "37065434", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10091502"}, {"db": "pii", "key": "qrac006"}], "notes": [], "created": "2023-10-04T12:42:09.643Z", "modified": "2023-10-19T11:58:02.781Z"}, {"entity": "publication", "iuid": "2909595198df4c9abdf042b88b8acb93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2909595198df4c9abdf042b88b8acb93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2909595198df4c9abdf042b88b8acb93"}}, "title": "Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative.", "authors": [{"family": "Johannesson", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-0176-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/a376951d80cd405183f4ff8606df8bbc.json"}}, {"family": "Leder", "given": "Erica H", "initials": "EH"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Dupont", "given": "Sam", "initials": "S", "orcid": "0000-0002-9148-6565", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a083981f504ce3ac1d0629d663238b.json"}}, {"family": "Eriksson", "given": "Susanne P", "initials": "SP"}, {"family": "Harding", "given": "Karin", "initials": "K"}, {"family": "Havenhand", "given": "Jonathan N", "initials": "JN"}, {"family": "Jahnke", "given": "Marlene", "initials": "M"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Kvarnemo", "given": "Charlotta", "initials": "C", "orcid": "0000-0001-8983-2900", "researcher": {"href": "https://publications.scilifelab.se/researcher/914d1337967942d8a3790e47e5b5d86b.json"}}, {"family": "Pavia", "given": "Henrik", "initials": "H"}, {"family": "Rafajlovi\u0107", "given": "Marina", "initials": "M", "orcid": "0000-0003-2177-4622", "researcher": {"href": "https://publications.scilifelab.se/researcher/c19ea9bb89f644e897e85f38a6341684.json"}}, {"family": "R\u00f6dstr\u00f6m", "given": "Eva Marie", "initials": "EM"}, {"family": "Thorndyke", "given": "Michael", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "issn-l": "1752-4571", "volume": "16", "issue": "2", "pages": "530-541"}, "abstract": "The Centre for Marine Evolutionary Biology (CeMEB) at the University of Gothenburg, Sweden, was established in 2008 through a 10-year research grant of 8.7 m\u20ac to a team of senior researchers. Today, CeMEB members have contributed >500 scientific publications, 30 PhD theses and have organised 75 meetings and courses, including 18 three-day meetings and four conferences. What are the footprints of CeMEB, and how will the centre continue to play a national and international role as an important node of marine evolutionary research? In this perspective article, we first look back over the 10 years of CeMEB activities and briefly survey some of the many achievements of CeMEB. We furthermore compare the initial goals, as formulated in the grant application, with what has been achieved, and discuss challenges and milestones along the way. Finally, we bring forward some general lessons that can be learnt from a research funding of this type, and we also look ahead, discussing how CeMEB's achievements and lessons can be used as a springboard to the future of marine evolutionary biology.", "doi": "10.1111/eva.13389", "pmid": "36793681", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9923476"}, {"db": "pii", "key": "EVA13389"}], "notes": [], "created": "2023-03-06T13:47:40.061Z", "modified": "2023-03-06T14:14:21.192Z"}, {"entity": "publication", "iuid": "9257ffe92beb4896a039c75856d3f506", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9257ffe92beb4896a039c75856d3f506.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9257ffe92beb4896a039c75856d3f506"}}, "title": "Migratory behaviour is positively associated with genetic diversity in butterflies.", "authors": [{"family": "Garc\u00eda-Berro", "given": "Aurora", "initials": "A", "orcid": "0000-0002-2419-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fdb6dd337074a89bf36e3b06458f042.json"}}, {"family": "Talla", "given": "Venkat", "initials": "V", "orcid": "0000-0003-2653-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/703518ce5a1f4e5ea04719016173a867.json"}}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Wai", "given": "Hong Kar", "initials": "HK", "orcid": "0000-0002-3489-9056", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ed472ef61e94c6b819a009dae03d975.json"}}, {"family": "Shipilina", "given": "Daria", "initials": "D", "orcid": "0000-0002-1145-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/758a7bdbc6654826ab7f06cf3938b5c3.json"}}, {"family": "Chan", "given": "Kok Gan", "initials": "KG", "orcid": "0000-0002-1883-1115", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bb4e116b64d4fa5bb617a53d1bca336.json"}}, {"family": "Pierce", "given": "Naomi E", "initials": "NE", "orcid": "0000-0003-3366-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1e6c94b58244ada2442e0541168252.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Talavera", "given": "Gerard", "initials": "G", "orcid": "0000-0003-1112-1345", "researcher": {"href": "https://publications.scilifelab.se/researcher/1081486b2353478b8dba3388e819822b.json"}}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "3", "pages": "560-574"}, "abstract": "Migration is typically associated with risk and uncertainty at the population level, but little is known about its cost-benefit trade-offs at the species level. Migratory insects in particular often exhibit strong demographic fluctuations due to local bottlenecks and outbreaks. Here, we use genomic data to investigate levels of heterozygosity and long-term population size dynamics in migratory insects, as an alternative to classical local and short-term approaches such as regional field monitoring. We analyse whole-genome sequences from 97 Lepidoptera species and show that individuals of migratory species have significantly higher levels of genome-wide heterozygosity, a proxy for effective population size, than do nonmigratory species. Also, we contribute whole-genome data for one of the most emblematic insect migratory species, the painted lady butterfly (Vanessa cardui), sampled across its worldwide distributional range. This species exhibits one of the highest levels of genomic heterozygosity described in Lepidoptera (2.95 \u00b1 0.15%). Coalescent modelling (PSMC) shows historical demographic stability in V. cardui, and high effective population size estimates of 2-20 million individuals 10,000 years ago. The study reveals that the high risks associated with migration and local environmental fluctuations do not seem to decrease overall genetic diversity and demographic stability in migratory Lepidoptera. We propose a \"compensatory\" demographic model for migratory r-strategist organisms in which local bottlenecks are counterbalanced by reproductive success elsewhere within their typically large distributional ranges. Our findings highlight that the boundaries of populations are substantially different for sedentary and migratory insects, and that, in the latter, local and even regional field monitoring results may not reflect whole population dynamics. Genomic diversity patterns may elucidate key aspects of an insect's migratory nature and population dynamics at large spatiotemporal scales.", "doi": "10.1111/mec.16770", "pmid": "36336800", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10100375"}], "notes": [], "created": "2022-12-19T10:42:50.812Z", "modified": "2024-01-16T13:48:34.019Z"}, {"entity": "publication", "iuid": "2ee8b678c1cc4b938cd6947cc5231c97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ee8b678c1cc4b938cd6947cc5231c97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ee8b678c1cc4b938cd6947cc5231c97"}}, "title": "An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis.", "authors": [{"family": "Le Moan", "given": "Alan", "initials": "A", "orcid": "0000-0002-9124-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/609a745ce1fb42fea85cc8d55db25acf.json"}}, {"family": "Panova", "given": "Marina", "initials": "M", "orcid": "0000-0002-4147-6473", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2398a3ba7fb4cd2b25968f7760b267b.json"}}, {"family": "De Jode", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0003-0428-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1ff392d2a03435795aa8a8a1ee8dd65.json"}}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Duvetorp", "given": "M\u00e5rten", "initials": "M"}, {"family": "Faria", "given": "Rui", "initials": "R", "orcid": "0000-0001-6635-685X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dbdd2fff57949148124073f004f74c2.json"}}, {"family": "Butlin", "given": "Roger", "initials": "R", "orcid": "0000-0003-4736-0954", "researcher": {"href": "https://publications.scilifelab.se/researcher/e510a963ebeb4e8c8af68b10a001a326.json"}}, {"family": "Johannesson", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-0176-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/a376951d80cd405183f4ff8606df8bbc.json"}}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "2", "pages": "279-292", "issn-l": "1752-4571"}, "abstract": "Understanding the genetic targets of natural selection is one of the most challenging goals of population genetics. Some of the earliest candidate genes were identified from associations between allozyme allele frequencies and environmental variation. One such example is the clinal polymorphism in the arginine kinase (Ak) gene in the marine snail Littorina fabalis. While other enzyme loci do not show differences in allozyme frequencies among populations, the Ak alleles are near differential fixation across repeated wave exposure gradients in Europe. Here, we use this case to illustrate how a new sequencing toolbox can be employed to characterize the genomic architecture associated with historical candidate genes. We found that the Ak alleles differ by nine nonsynonymous substitutions, which perfectly explain the different migration patterns of the allozymes during electrophoresis. Moreover, by exploring the genomic context of the Ak gene, we found that the three main Ak alleles are located on different arrangements of a putative chromosomal inversion that reaches near fixation at the opposing ends of two transects covering a wave exposure gradient. This shows Ak is part of a large (3/4 of the chromosome) genomic block of differentiation, in which Ak is unlikely to be the only target of divergent selection. Nevertheless, the nonsynonymous substitutions among Ak alleles and the complete association of one allele with one inversion arrangement suggest that the Ak gene is a strong candidate to contribute to the adaptive significance of the inversion.", "doi": "10.1111/eva.13427", "pmid": "36793696", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9923470"}, {"db": "pii", "key": "EVA13427"}], "notes": [], "created": "2023-10-04T12:04:49.853Z", "modified": "2024-01-16T13:48:34.062Z"}, {"entity": "publication", "iuid": "544b98439adf410680a670acbe0660a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/544b98439adf410680a670acbe0660a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/544b98439adf410680a670acbe0660a5"}}, "title": "A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.", "authors": [{"family": "Sountoulidis", "given": "Alexandros", "initials": "A", "orcid": "0000-0002-8837-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/f49f693f406b4ba28faf373fa67ee683.json"}}, {"family": "Marco Salas", "given": "Sergio", "initials": "S"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Avenel", "given": "Christophe", "initials": "C"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Theelke", "given": "Jonas", "initials": "J", "orcid": "0000-0002-5074-1793", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bfd9c1f49b24c9e8dc5c22bc4288543.json"}}, {"family": "Vicari", "given": "Marco", "initials": "M", "orcid": "0000-0002-3042-6278", "researcher": {"href": "https://publications.scilifelab.se/researcher/6348d0901b3e44cd80bde25cecd0205b.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Liontos", "given": "Andreas", "initials": "A"}, {"family": "Abalo", "given": "Xesus", "initials": "X", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications.scilifelab.se/researcher/944b78e930df40ee8cd5d590638cd4d9.json"}}, {"family": "Andrusivov\u00e1", "given": "\u017daneta", "initials": "\u017d"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Asp", "given": "Michaela", "initials": "M"}, {"family": "Li", "given": "Xiaofei", "initials": "X"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Sariyar", "given": "Sanem", "initials": "S"}, {"family": "Martinez Casals", "given": "Anna", "initials": "A"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Firsova", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-7345-7429", "researcher": {"href": "https://publications.scilifelab.se/researcher/32fc885aa10d48cebd772ad1470def0c.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C", "orcid": "0000-0002-9153-6040", "researcher": {"href": "https://publications.scilifelab.se/researcher/004a4a166cb34d59ba054055658425f6.json"}}], "type": "journal article", "published": "2023-02-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "issn-l": null, "volume": "25", "issue": "2", "pages": "351-365"}, "abstract": "The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.", "doi": "10.1038/s41556-022-01064-x", "pmid": "36646791", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9928586"}, {"db": "pii", "key": "10.1038/s41556-022-01064-x"}], "notes": [], "created": "2023-03-06T13:47:35.567Z", "modified": "2025-10-17T13:02:17.126Z"}, {"entity": "publication", "iuid": "6679c4b418fa47b3a6bf6e9d7539b0f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6679c4b418fa47b3a6bf6e9d7539b0f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6679c4b418fa47b3a6bf6e9d7539b0f1"}}, "title": "Inversions maintain differences between migratory phenotypes of a songbird.", "authors": [{"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Mackintosh", "given": "Alexander", "initials": "A"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Bensch", "given": "Staffan", "initials": "S", "orcid": "0000-0002-0082-0899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b925a620a68049928c3dc0cbc87948ba.json"}}], "type": "journal article", "published": "2023-01-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "452"}, "abstract": "Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.", "doi": "10.1038/s41467-023-36167-y", "pmid": "36707538", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9883250"}, {"db": "pii", "key": "10.1038/s41467-023-36167-y"}], "notes": [], "created": "2023-03-06T13:47:37.052Z", "modified": "2024-01-16T13:48:34.085Z"}, {"entity": "publication", "iuid": "de64a88aa7a04cb6a4e3809354a7c66c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de64a88aa7a04cb6a4e3809354a7c66c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de64a88aa7a04cb6a4e3809354a7c66c"}}, "title": "High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).", "authors": [{"family": "H\u00f6\u00f6k", "given": "L", "initials": "L"}, {"family": "N\u00e4svall", "given": "K", "initials": "K"}, {"family": "Vila", "given": "R", "initials": "R"}, {"family": "Wiklund", "given": "C", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "N", "initials": "N"}], "type": "journal article", "published": "2023-01-20", "journal": {"title": "Chromosome Res.", "issn": "1573-6849", "issn-l": "0967-3849", "volume": "31", "issue": "1", "pages": "2"}, "abstract": "Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.", "doi": "10.1007/s10577-023-09713-z", "pmid": "36662301", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9859909"}, {"db": "pii", "key": "10.1007/s10577-023-09713-z"}], "notes": [], "created": "2023-03-06T13:47:38.756Z", "modified": "2024-01-16T13:48:34.100Z"}, {"entity": "publication", "iuid": "f63e36a5ea3a42329893558a0caec322", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f63e36a5ea3a42329893558a0caec322.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f63e36a5ea3a42329893558a0caec322"}}, "title": "Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.", "authors": [{"family": "Nishimura", "given": "Kaneyasu", "initials": "K"}, {"family": "Yang", "given": "Shanzheng", "initials": "S"}, {"family": "Lee", "given": "Ka Wai", "initials": "KW"}, {"family": "\u00c1sgr\u00edmsd\u00f3ttir", "given": "Emil\u00eda Sif", "initials": "ES"}, {"family": "Nikouei", "given": "Kasra", "initials": "K"}, {"family": "Paslawski", "given": "Wojciech", "initials": "W"}, {"family": "Gnodde", "given": "Sabine", "initials": "S"}, {"family": "Lyu", "given": "Guochang", "initials": "G"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Salt\u00f3", "given": "Carmen", "initials": "C"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}], "type": "journal article", "published": "2023-01-10", "journal": {"title": "Stem Cell Reports", "issn": "2213-6711", "issn-l": "2213-6711", "volume": "18", "issue": "1", "pages": "337-353"}, "abstract": "Stem cell technologies provide new opportunities for modeling cells in health and disease and for regenerative medicine. In both cases, developmental knowledge and defining the molecular properties and quality of the cell types is essential. In this study, we identify developmental factors important for the differentiation of human embryonic stem cells (hESCs) into functional midbrain dopaminergic (mDA) neurons. We found that laminin-511, and dual canonical and non-canonical WNT activation followed by GSK3\u03b2 inhibition plus FGF8b, improved midbrain patterning. In addition, neurogenesis and differentiation were enhanced by activation of liver X receptors and inhibition of fibroblast growth factor signaling. Moreover, single-cell RNA-sequencing analysis revealed a developmental dynamics similar to that of the endogenous human ventral midbrain and the emergence of high-quality molecularly defined midbrain cell types, including mDA neurons. Our study identifies novel factors important for human midbrain development and opens the door for a future application of molecularly defined hESC-derived cell types in Parkinson disease.", "doi": "10.1016/j.stemcr.2022.10.016", "pmid": "36400027", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9860082"}, {"db": "pii", "key": "S2213-6711(22)00512-4"}], "notes": [], "created": "2022-12-19T10:39:26.922Z", "modified": "2023-10-16T15:10:56.300Z"}, {"entity": "publication", "iuid": "3b813ce2f23c44c7a56643ab3b79475e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b813ce2f23c44c7a56643ab3b79475e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b813ce2f23c44c7a56643ab3b79475e"}}, "title": "Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.", "authors": [{"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE"}, {"family": "Psonis", "given": "Nikolaos", "initials": "N"}, {"family": "Kashuba", "given": "Natalia", "initials": "N"}, {"family": "Yorulmaz", "given": "Sevgi", "initials": "S"}, {"family": "George", "given": "Robert", "initials": "R"}, {"family": "Kazanc\u0131", "given": "Duygu Deniz", "initials": "DD"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "G\u00fcr\u00fcn", "given": "Kanat", "initials": "K"}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB"}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC"}, {"family": "Vassou", "given": "Despoina", "initials": "D"}, {"family": "Daskalaki", "given": "Evangelia", "initials": "E"}, {"family": "Karamurat", "given": "Cansu", "initials": "C"}, {"family": "Lagerholm", "given": "Vendela K", "initials": "VK"}, {"family": "Erdal", "given": "\u00d6m\u00fcr Dilek", "initials": "\u00d6D"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Marangoni", "given": "Aurelio", "initials": "A"}, {"family": "Schachner", "given": "Andreas", "initials": "A"}, {"family": "\u00dcst\u00fcnda\u011f", "given": "Handan", "initials": "H"}, {"family": "Shengelia", "given": "Ramaz", "initials": "R"}, {"family": "Bitadze", "given": "Liana", "initials": "L"}, {"family": "Elashvili", "given": "Mikheil", "initials": "M"}, {"family": "Stravopodi", "given": "Eleni", "initials": "E"}, {"family": "\u00d6zba\u015faran", "given": "Mihriban", "initials": "M"}, {"family": "Duru", "given": "G\u00fcne\u015f", "initials": "G"}, {"family": "Nafplioti", "given": "Argyro", "initials": "A"}, {"family": "Rose", "given": "C Brian", "initials": "CB"}, {"family": "Gencer", "given": "Tu\u011fba", "initials": "T"}, {"family": "Darbyshire", "given": "Gareth", "initials": "G"}, {"family": "Gavashelishvili", "given": "Alexander", "initials": "A"}, {"family": "Pitskhelauri", "given": "Konstantine", "initials": "K"}, {"family": "\u00c7evik", "given": "\u00d6zlem", "initials": "\u00d6"}, {"family": "Vuru\u015fkan", "given": "Osman", "initials": "O"}, {"family": "Kyparissi-Apostolika", "given": "Nina", "initials": "N"}, {"family": "B\u00fcy\u00fckkarakaya", "given": "Ali Metin", "initials": "AM"}, {"family": "O\u011fuzhano\u011flu", "given": "Umay", "initials": "U"}, {"family": "G\u00fcnel", "given": "Sevin\u00e7", "initials": "S"}, {"family": "Tabakaki", "given": "Eugenia", "initials": "E"}, {"family": "Aliev", "given": "Akper", "initials": "A"}, {"family": "Ibrahimov", "given": "Anar", "initials": "A"}, {"family": "Shadlinski", "given": "Vaqif", "initials": "V"}, {"family": "Sampson", "given": "Adamantios", "initials": "A"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM"}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7"}, {"family": "Stamatakis", "given": "Alexandros", "initials": "A"}, {"family": "Poulakakis", "given": "Nikos", "initials": "N"}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS"}, {"family": "Pavlidis", "given": "Pavlos", "initials": "P"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}], "type": "historical article", "published": "2023-01-09", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "33", "issue": "1", "pages": "41-57.e15"}, "abstract": "We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term \"the expanding mobility model.\" Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.", "doi": "10.1016/j.cub.2022.11.034", "pmid": "36493775", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9839366"}, {"db": "pii", "key": "S0960-9822(22)01824-3"}], "notes": [], "created": "2022-12-19T10:42:52.482Z", "modified": "2024-01-16T13:48:34.166Z"}, {"entity": "publication", "iuid": "391c840c74b743c3a178c3733764fb08", "links": {"self": {"href": "https://publications.scilifelab.se/publication/391c840c74b743c3a178c3733764fb08.json"}, "display": {"href": "https://publications.scilifelab.se/publication/391c840c74b743c3a178c3733764fb08"}}, "title": "The genetic history of Scandinavia from the Roman Iron Age to the present.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Moore", "given": "Kristjan H S", "initials": "KHS"}, {"family": "Ebenesersd\u00f3ttir", "given": "S Sunna", "initials": "SS"}, {"family": "Kilinc", "given": "Gulsah Merve", "initials": "GM"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Papmehl-Dufay", "given": "Ludvig", "initials": "L"}, {"family": "Alfsdotter", "given": "Clara", "initials": "C"}, {"family": "Berglund", "given": "Birgitta", "initials": "B"}, {"family": "Alrawi", "given": "Loey", "initials": "L"}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Sobrado", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Gilbert", "given": "Edmund", "initials": "E"}, {"family": "Cavalleri", "given": "Gianpiero L", "initials": "GL"}, {"family": "Hovig", "given": "Eivind", "initials": "E"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Hansen", "given": "Thomas F", "initials": "TF"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Christophersen", "given": "Axel", "initials": "A"}, {"family": "Turner-Walker", "given": "Gordon", "initials": "G"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Daskalaki", "given": "Eva", "initials": "E"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "P\u00e9rez-Ramallo", "given": "Patxi", "initials": "P"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}, {"family": "Gunnarsson", "given": "Fredrik", "initials": "F"}, {"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M"}, {"family": "Einarsson", "given": "Lars", "initials": "L"}, {"family": "Victor", "given": "Helena", "initials": "H"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Zachrisson", "given": "Torun", "initials": "T"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Stef\u00e1nsson", "given": "K\u00e1ri", "initials": "K"}, {"family": "Helgason", "given": "Agnar", "initials": "A"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2023-01-05", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "186", "issue": "1", "pages": "32-46.e19"}, "abstract": "We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.", "doi": "10.1016/j.cell.2022.11.024", "pmid": "36608656", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(22)01468-4"}], "notes": [], "created": "2023-01-13T13:02:52.491Z", "modified": "2024-01-16T13:48:34.189Z"}, {"entity": "publication", "iuid": "5fbcb25764184d7bb218c6ee81a45712", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5fbcb25764184d7bb218c6ee81a45712.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5fbcb25764184d7bb218c6ee81a45712"}}, "title": "A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.", "authors": [{"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Lutgen", "given": "Dave", "initials": "D"}, {"family": "Bowie", "given": "Rauri C K", "initials": "RCK"}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "1", "pages": null}, "abstract": "Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.", "doi": "10.1093/molbev/msac278", "pmid": "36578177", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10161543"}, {"db": "pii", "key": "6964684"}], "notes": [], "created": "2023-01-13T13:02:53.719Z", "modified": "2023-10-16T15:41:07.444Z"}, {"entity": "publication", "iuid": "5eb9ce6d678b47a8a7e86b5fe0b1e75c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eb9ce6d678b47a8a7e86b5fe0b1e75c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eb9ce6d678b47a8a7e86b5fe0b1e75c"}}, "title": "Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.", "authors": [{"family": "Wen", "given": "Jia", "initials": "J"}, {"family": "Trost", "given": "Brett", "initials": "B", "orcid": "0000-0003-4863-7273", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5d8ce778d624eef846a7b72bdf00f52.json"}}, {"family": "Engchuan", "given": "Worrawat", "initials": "W"}, {"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Pallotto", "given": "Linda M", "initials": "LM"}, {"family": "Mitina", "given": "Aleksandra", "initials": "A"}, {"family": "Ancalade", "given": "NaEshia", "initials": "N"}, {"family": "Farrell", "given": "Martilias", "initials": "M", "orcid": "0000-0002-9520-6209", "researcher": {"href": "https://publications.scilifelab.se/researcher/20be04f56c474537ad8fa07cb17241cf.json"}}, {"family": "Backstrom", "given": "Ian", "initials": "I", "orcid": "0000-0003-2203-540X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8473bd9fd724354a100af414ad1126e.json"}}, {"family": "Guo", "given": "Keyi", "initials": "K"}, {"family": "Pellecchia", "given": "Giovanna", "initials": "G", "orcid": "0000-0003-4747-3473", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f06138fd254a6fa35e81614a9d9ae9.json"}}, {"family": "Thiruvahindrapuram", "given": "Bhooma", "initials": "B", "orcid": "0000-0003-1128-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f13d26ba0fac47d4a966f4189af223ec.json"}}, {"family": "Giusti-Rodriguez", "given": "Paola", "initials": "P"}, {"family": "Rosen", "given": "Jonathan David", "initials": "JD"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Won", "given": "Hyejung", "initials": "H", "orcid": "0000-0003-3651-0566", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec02856f79674901b278a7c04b7ed8d8.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE", "orcid": "0000-0002-7315-7899", "researcher": {"href": "https://publications.scilifelab.se/researcher/b277b6387de142bbab91fad82d9eff09.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Bassett", "given": "Anne S", "initials": "AS", "orcid": "0000-0002-0681-7279", "researcher": {"href": "https://publications.scilifelab.se/researcher/4884004ffeb34bcfbe80536ae35ba668.json"}}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Yuen", "given": "Ryan K C", "initials": "RKC", "orcid": "0000-0001-7273-4968", "researcher": {"href": "https://publications.scilifelab.se/researcher/a867c10748aa4c6ab8191fbfbe5757c9.json"}}, {"family": "Szatkiewicz", "given": "Jin P", "initials": "JP", "orcid": "0000-0002-4898-7401", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb39edd3c6c14938a47f1e22ecfea080.json"}}], "type": "journal article", "published": "2023-01-00", "journal": {"title": "Mol. Psychiatry", "issn": "1476-5578", "issn-l": "1359-4184", "volume": "28", "issue": "1", "pages": "475-482"}, "abstract": "Tandem repeat expansions (TREs) are associated with over 60 monogenic disorders and have recently been implicated in complex disorders such as cancer and autism spectrum disorder. The role of TREs in schizophrenia is now emerging. In this study, we have performed a genome-wide investigation of TREs in schizophrenia. Using genome sequence data from 1154 Swedish schizophrenia cases and 934 ancestry-matched population controls, we have detected genome-wide rare (<0.1% population frequency) TREs that have motifs with a length of 2-20 base pairs. We find that the proportion of individuals carrying rare TREs is significantly higher in the schizophrenia group. There is a significantly higher burden of rare TREs in schizophrenia cases than in controls in genic regions, particularly in postsynaptic genes, in genes overlapping brain expression quantitative trait loci, and in brain-expressed genes that are differentially expressed between schizophrenia cases and controls. We demonstrate that TRE-associated genes are more constrained and primarily impact synaptic and neuronal signaling functions. These results have been replicated in an independent Canadian sample that consisted of 252 schizophrenia cases of European ancestry and 222 ancestry-matched controls. Our results support the involvement of rare TREs in schizophrenia etiology.", "doi": "10.1038/s41380-022-01857-4", "pmid": "36380236", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9812781"}, {"db": "pii", "key": "10.1038/s41380-022-01857-4"}], "notes": [], "created": "2022-11-29T12:28:58.891Z", "modified": "2023-10-16T12:47:55.341Z"}, {"entity": "publication", "iuid": "a16d73f3d11243b781d82b0c4cd80dd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a16d73f3d11243b781d82b0c4cd80dd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a16d73f3d11243b781d82b0c4cd80dd2"}}, "title": "Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.", "authors": [{"family": "Peng", "given": "Guotao", "initials": "G", "orcid": "0000-0001-7169-9961", "researcher": {"href": "https://publications.scilifelab.se/researcher/db378a8a935d4389bbc8d8742a3e965d.json"}}, {"family": "Sinkko", "given": "Hanna M", "initials": "HM"}, {"family": "Alenius", "given": "Harri", "initials": "H", "orcid": "0000-0003-0106-8923", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f88b2c54fe044a1b76ed7107677c11a.json"}}, {"family": "Lozano", "given": "Neus", "initials": "N", "orcid": "0000-0002-9026-1743", "researcher": {"href": "https://publications.scilifelab.se/researcher/888bbbf4a6064ed39fb6f60f27c40e42.json"}}, {"family": "Kostarelos", "given": "Kostas", "initials": "K", "orcid": "0000-0002-2224-6672", "researcher": {"href": "https://publications.scilifelab.se/researcher/fca5748332c84d198ca3a4bb615b3a0d.json"}}, {"family": "Br\u00e4utigam", "given": "Lars", "initials": "L"}, {"family": "Fadeel", "given": "Bengt", "initials": "B", "orcid": "0000-0001-5559-8482", "researcher": {"href": "https://publications.scilifelab.se/researcher/959b4accdbfe49158353b8cb12260d1b.json"}}], "type": "journal article", "published": "2023-01-00", "journal": {"title": "Nat Nanotechnol", "issn": "1748-3395", "issn-l": null, "volume": "18", "issue": "1", "pages": "42-48"}, "abstract": "The gut microbiome produces metabolites that interact with the aryl hydrocarbon receptor (AhR), a key regulator of immune homoeostasis in the gut1,2. Here we show that oral exposure to graphene oxide (GO) modulates the composition of the gut microbiome in adult zebrafish, with significant differences in wild-type versus ahr2-deficient animals. Furthermore, GO was found to elicit AhR-dependent induction of cyp1a and homing of lck+ cells to the gut in germ-free zebrafish larvae when combined with the short-chain fatty acid butyrate. To obtain further insights into the immune responses to GO, we used single-cell RNA sequencing to profile cells from whole germ-free embryos as well as cells enriched for lck. These studies provided evidence for the existence of innate lymphoid cell (ILC)-like cells3 in germ-free zebrafish. Moreover, GO endowed with a 'corona' of microbial butyrate triggered the induction of ILC2-like cells with attributes of regulatory cells. Taken together, this study shows that a nanomaterial can influence the crosstalk between the microbiome and immune system in an AhR-dependent manner.", "doi": "10.1038/s41565-022-01260-8", "pmid": "36509925", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9879769"}, {"db": "pii", "key": "10.1038/s41565-022-01260-8"}], "notes": [], "created": "2023-01-13T13:02:12.339Z", "modified": "2024-01-16T13:48:34.263Z"}, {"entity": "publication", "iuid": "50a02fa12ac04985a5c99c48a5130c1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50a02fa12ac04985a5c99c48a5130c1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50a02fa12ac04985a5c99c48a5130c1a"}}, "title": "Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).", "authors": [{"family": "Hempel", "given": "Elisabeth", "initials": "E", "orcid": "0000-0002-0089-8741", "researcher": {"href": "https://publications.scilifelab.se/researcher/57de484e593048109df40f4590cbad5a.json"}}, {"family": "Bibi", "given": "Faysal", "initials": "F", "orcid": "0000-0002-9414-5547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac6a6d03a0c440328ca1a58fd70cf0f3.json"}}, {"family": "Faith", "given": "J Tyler", "initials": "JT", "orcid": "0000-0002-1101-7161", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ca9eaaad9a4b0ba2bb9b586a51965e.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP", "orcid": "0000-0001-7281-0676", "researcher": {"href": "https://publications.scilifelab.se/researcher/178cb44eedd74528a956ad645fe3aa16.json"}}, {"family": "Klittich", "given": "Achim M", "initials": "AM"}, {"family": "Duch\u00eane", "given": "David A", "initials": "DA", "orcid": "0000-0002-5479-1974", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c838bf8e40a42e79fe4847c5fd22e3c.json"}}, {"family": "Brink", "given": "James S", "initials": "JS"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC", "orcid": "0000-0003-2439-5484", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c18227dc17f428daca466f6fc7d3888.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}], "type": "journal article", "published": "2022-12-05", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "12", "pages": null}, "abstract": "The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4\u00d7 mean coverage from a historical specimen (\u223c200 years old) and one at 2.1\u00d7 mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.", "doi": "10.1093/molbev/msac241", "pmid": "36322483", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9750129"}, {"db": "pii", "key": "6794086"}], "notes": [], "created": "2022-12-19T10:42:47.834Z", "modified": "2023-10-16T15:14:22.657Z"}, {"entity": "publication", "iuid": "96ef84e02ca044b0b3df8e2e4becd74e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96ef84e02ca044b0b3df8e2e4becd74e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96ef84e02ca044b0b3df8e2e4becd74e"}}, "title": "Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.", "authors": [{"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Farnelid", "given": "Hanna", "initials": "H"}, {"family": "Garc\u00eda", "given": "Sandra Mart\u00ednez", "initials": "SM"}, {"family": "Teira", "given": "Eva", "initials": "E"}, {"family": "Galand", "given": "Pierre E", "initials": "PE"}, {"family": "Obernosterer", "given": "Ingrid", "initials": "I"}, {"family": "Quince", "given": "Christopher", "initials": "C"}, {"family": "Vila-Costa", "given": "Maria", "initials": "M"}, {"family": "Gasol", "given": "Josep M", "initials": "JM"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}], "type": "journal article", "published": "2022-12-01", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "13", "pages": "869093", "issn-l": "1664-302X"}, "abstract": "Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations - \"key\" in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.", "doi": "10.3389/fmicb.2022.869093", "pmid": "36532459", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9751014"}], "notes": [], "created": "2023-10-23T09:41:30.096Z", "modified": "2023-10-23T09:41:30.100Z"}, {"entity": "publication", "iuid": "90b62e312a974e36bc3ecd5d37537c5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90b62e312a974e36bc3ecd5d37537c5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90b62e312a974e36bc3ecd5d37537c5e"}}, "title": "Species composition of shoreline wolf spider communities vary with salinity, but their diets vary with wrack inflow.", "authors": [{"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA", "orcid": "0000-0001-6362-6199", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddfc67c7c774583861a5ea3774eaa1a.json"}}, {"family": "Cirtwill", "given": "Alyssa R", "initials": "AR"}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Hoffmann", "given": "Alexander", "initials": "A"}, {"family": "Langbak", "given": "Marie", "initials": "M"}, {"family": "\u00c5hl\u00e9n", "given": "David", "initials": "D"}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "12", "pages": "e9701", "issn-l": "2045-7758"}, "abstract": "Wolf spiders are typically the most common group of arthropod predators on both lake and marine shorelines because of the high prey availability in these habitats. However, shores are also harsh environments due to flooding and, in proximity to marine waters, to toxic salinity levels. Here, we describe the spider community, prey availabilities, and spider diets between shoreline sites with different salinities, albeit with comparatively small differences (5\u2030 vs. 7\u2030). Despite the small environmental differences, spider communities between lower and higher saline sites showed an almost complete species turnover. At the same time, differences in prey availability or spider gut contents did not match changes in spider species composition but rather changed with habitat characteristics within a region, where spiders collected at sites with thick wrack beds had a different diet than sites with little wrack. These data suggest that shifts in spider communities are due to habitat characteristics other than prey availabilities, and the most likely candidate restricting species in high salinity would be saline sensitivity. At the same time, species absence from low-saline habitats remains unresolved.", "doi": "10.1002/ece3.9701", "pmid": "36590338", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9797640"}, {"db": "pii", "key": "ECE39701"}, {"db": "Dryad", "key": "10.5061/dryad.gxd2547qk"}], "notes": [], "created": "2023-10-04T11:56:08.364Z", "modified": "2024-01-16T13:48:34.358Z"}, {"entity": "publication", "iuid": "d5152c9076804763be932ac33683daa3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d5152c9076804763be932ac33683daa3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d5152c9076804763be932ac33683daa3"}}, "title": "Screening patients with autoimmune endocrine disorders for cytokine autoantibodies reveals monogenic immune deficiencies.", "authors": [{"family": "Sj\u00f8gren", "given": "Thea", "initials": "T"}, {"family": "Bratland", "given": "Eirik", "initials": "E"}, {"family": "R\u00f8yrvik", "given": "Ellen C", "initials": "EC"}, {"family": "Grytaas", "given": "Marianne Aa", "initials": "MA"}, {"family": "Benneche", "given": "Andreas", "initials": "A"}, {"family": "Knappskog", "given": "Per M", "initials": "PM"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Oftedal", "given": "Bergithe E", "initials": "BE"}, {"family": "Husebye", "given": "Eystein S", "initials": "ES"}, {"family": "Wolff", "given": "Anette S B", "initials": "ASB"}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "133", "issue": null, "pages": "102917"}, "abstract": "Autoantibodies against type I interferons (IFN) alpha (\u03b1) and omega (\u03c9), and interleukins (IL) 17 and 22 are a hallmark of autoimmune polyendocrine syndrome type 1 (APS-1), caused by mutations in the autoimmune regulator (AIRE) gene. Such antibodies are also seen in a number of monogenic immunodeficiencies.\n\nTo determine whether screening for cytokine autoantibodies (anti-IFN-\u03c9 and anti-IL22) can be used to identify patients with monogenic immune disorders.\n\nA novel ELISA assay was employed to measure IL22 autoantibodies in 675 patients with autoimmune primary adrenal insufficiency (PAI) and a radio immune assay (RIA) was used to measure autoantibodies against IFN-\u03c9 in 1778 patients with a variety of endocrine diseases, mostly of autoimmune aetiology. Positive cases were sequenced for all coding exons of the AIRE gene. If no AIRE mutations were found, we applied next generation sequencing (NGS) to search for mutations in immune related genes.\n\nWe identified 29 patients with autoantibodies against IFN-\u03c9 and/or IL22. Of these, four new APS-1 cases with disease-causing variants in AIRE were found. In addition, we identified two patients with pathogenic heterozygous variants in CTLA4 and NFKB2, respectively. Nine rare variants in other immune genes were identified in six patients, although further studies are needed to determine their disease-causing potential.\n\nScreening of cytokine autoantibodies can efficiently identify patients with previously unknown monogenic and possible oligogenic causes of autoimmune and immune deficiency diseases. This information is crucial for providing personalised treatment and follow-up of patients and their relatives.", "doi": "10.1016/j.jaut.2022.102917", "pmid": "36191466", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-8411(22)00125-1"}], "notes": [], "created": "2022-11-09T15:48:20.727Z", "modified": "2024-01-16T13:48:34.369Z"}, {"entity": "publication", "iuid": "244765187cff4949831aab7eacfe9384", "links": {"self": {"href": "https://publications.scilifelab.se/publication/244765187cff4949831aab7eacfe9384.json"}, "display": {"href": "https://publications.scilifelab.se/publication/244765187cff4949831aab7eacfe9384"}}, "title": "An overlooked subset of Cx3cr1wt/wt microglia in the Cx3cr1CreER-Eyfp/wt mouse has a repopulation advantage over Cx3cr1CreER-Eyfp/wt microglia following microglial depletion", "authors": [{"family": "Zhou", "given": "Kai", "initials": "K", "orcid": "0000-0003-1026-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/435dbc44e7fd468a9f2284cbe8810d52.json"}}, {"family": "Han", "given": "Jinming", "initials": "J"}, {"family": "Lund", "given": "Harald", "initials": "H"}, {"family": "Boggavarapu", "given": "Nageswara Rao", "initials": "NR"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM"}, {"family": "Goto", "given": "Shinobu", "initials": "S"}, {"family": "Cheng", "given": "Huaitao", "initials": "H"}, {"family": "Wang", "given": "Yuyu", "initials": "Y"}, {"family": "Tachi", "given": "Asuka", "initials": "A"}, {"family": "Xie", "given": "Cuicui", "initials": "C"}, {"family": "Zhu", "given": "Keying", "initials": "K"}, {"family": "Sun", "given": "Ying", "initials": "Y"}, {"family": "Osman", "given": "Ahmed M", "initials": "AM"}, {"family": "Liang", "given": "Dong", "initials": "D"}, {"family": "Han", "given": "Wei", "initials": "W"}, {"family": "Gemzell-Danielsson", "given": "Kristina", "initials": "K"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Zhang", "given": "Xing Mei", "initials": "XM"}, {"family": "Zhu", "given": "Changlian", "initials": "C"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Joseph", "given": "Bertrand", "initials": "B"}, {"family": "Harris", "given": "Robert A", "initials": "RA"}, {"family": "Blomgren", "given": "Klas", "initials": "K", "orcid": "0000-0002-0476-7271", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fb3b554177d481ebc9d4aa0f3b1fbc4.json"}}], "type": "journal-article", "published": "2022-12-00", "journal": {"title": "J Neuroinflammation", "issn": "1742-2094", "issn-l": "1742-2094", "volume": "19", "issue": "1", "pages": "20"}, "abstract": "Fluorescent reporter labeling and promoter-driven Cre-recombinant technologies have facilitated cellular investigations of physiological and pathological processes, including the widespread use of the Cx3cr1CreER-Eyfp/wt mouse strain for studies of microglia.\r\n\r\nImmunohistochemistry, Flow Cytometry, RNA sequencing and whole-genome sequencing were used to identify the subpopulation of microglia in Cx3cr1CreER-Eyfp/wt mouse brains. Genetically mediated microglia depletion using Cx3cr1CreER-Eyfp/wtRosa26DTA/wt mice and CSF1 receptor inhibitor PLX3397 were used to deplete microglia. Primary microglia proliferation and migration assay were used for in vitro studies.\r\n\r\nWe unexpectedly identified a subpopulation of microglia devoid of genetic modification, exhibiting higher Cx3cr1 and CX3CR1 expression than Cx3cr1CreER-Eyfp/wtCre+Eyfp+ microglia in Cx3cr1CreER-Eyfp/wt mouse brains, thus termed Cx3cr1highCre-Eyfp- microglia. This subpopulation constituted less than 1% of all microglia under homeostatic conditions, but after Cre-driven DTA-mediated microglial depletion, Cx3cr1highCre-Eyfp- microglia escaped depletion and proliferated extensively, eventually occupying one-third of the total microglial pool. We further demonstrated that the Cx3cr1highCre-Eyfp- microglia had lost their genetic heterozygosity and become homozygous for wild-type Cx3cr1. Therefore, Cx3cr1highCre-Eyfp- microglia are Cx3cr1wt/wtCre-Eyfp-. Finally, we demonstrated that CX3CL1-CX3CR1 signaling regulates microglial repopulation both in vivo and in vitro.\r\n\r\nOur results raise a cautionary note regarding the use of Cx3cr1CreER-Eyfp/wt mouse strains, particularly when interpreting the results of fate mapping, and microglial depletion and repopulation studies.", "doi": "10.1186/s12974-022-02381-6", "pmid": "35062962", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8783445"}, {"db": "pii", "key": "10.1186/s12974-022-02381-6"}], "notes": [], "created": "2022-12-01T13:48:40.480Z", "modified": "2024-02-12T08:44:32.493Z"}, {"entity": "publication", "iuid": "f28cf32f387f44e79298f119437d9707", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f28cf32f387f44e79298f119437d9707.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f28cf32f387f44e79298f119437d9707"}}, "title": "Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.", "authors": [{"family": "Osbeck", "given": "Christofer M G", "initials": "CMG", "orcid": "0000-0001-6866-8881", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcf66a1877984850bba6e683b9b3ea29.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Teikari", "given": "Jonna E", "initials": "JE"}, {"family": "Moran", "given": "Mary Ann", "initials": "MA"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2022-11-17", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "17", "issue": "11", "pages": "e0243406"}, "abstract": "Phytoplankton release massive amounts of dissolved organic matter (DOM) into the water column during recurring blooms in coastal waters and inland seas. The released DOM encompasses a complex mixture of both known and unknown compounds, and is a rich nutrient source for heterotrophic bacteria. The metabolic activity of bacteria during and after phytoplankton blooms can hence be expected to reflect the characteristics of the released DOM. We therefore investigated if bacterioplankton could be used as \"living sensors\" of phytoplankton DOM quantity and/or quality, by applying gene expression analyses to identify bacterial metabolisms induced by DOM. We used transcriptional analysis of two Baltic Sea bacterial isolates (Polaribacter sp. BAL334 [Flavobacteriia] and Brevundimonas sp. BAL450 [Alphaproteobacteria]) growing with DOM from axenic cultures of the dinoflagellate Prorocentrum minimum. We observed pronounced differences between the two bacteria both in growth and the expressed metabolic pathways in cultures exposed to dinoflagellate DOM compared with controls. Differences in metabolic responses between the two isolates were caused both by differences in gene repertoire between them (e.g. in the SEED categories for membrane transport, motility and photoheterotrophy) and the regulation of expression (e.g. fatty acid metabolism), emphasizing the importance of separating the responses of different taxa in analyses of community sequence data. Similarities between the bacteria included substantially increased expression of genes for Ton and Tol transport systems in both isolates, which are commonly associated with uptake of complex organic molecules. Polaribacter sp. BAL334 showed stronger metabolic responses to DOM harvested from exponential than stationary phase dinoflagellates (128 compared to 26 differentially expressed genes), whereas Brevundimonas sp. BAL450 responded more to the DOM from stationary than exponential phase dinoflagellates (33 compared to 6 differentially expressed genes). These findings suggest that shifts in bacterial metabolisms during different phases of phytoplankton blooms can be detected in individual bacterial species and can provide insights into their involvement in DOM transformations.", "doi": "10.1371/journal.pone.0243406", "pmid": "36395342", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9671461"}, {"db": "pii", "key": "PONE-D-20-36147"}], "notes": [], "created": "2022-12-19T10:39:24.121Z", "modified": "2023-11-25T08:15:01.355Z"}, {"entity": "publication", "iuid": "2e70e86c3aaf497c87f80edf7723f239", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e70e86c3aaf497c87f80edf7723f239.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e70e86c3aaf497c87f80edf7723f239"}}, "title": "Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus).", "authors": [{"family": "Cockerill", "given": "Christopher A", "initials": "CA", "orcid": "0000-0001-9776-3183", "researcher": {"href": "https://publications.scilifelab.se/researcher/43a0788d687045f7b0257996a55327b0.json"}}, {"family": "Hasselgren", "given": "Malin", "initials": "M"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Wall\u00e9n", "given": "Johan F", "initials": "JF", "orcid": "0000-0001-8264-8393", "researcher": {"href": "https://publications.scilifelab.se/researcher/473afb510ef24fa1b48d6f35b0d64a22.json"}}, {"family": "Landa", "given": "Arild", "initials": "A", "orcid": "0000-0002-2533-5179", "researcher": {"href": "https://publications.scilifelab.se/researcher/25a8980130dc4d48add362d535eb217e.json"}}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Ehrich", "given": "Dorothee", "initials": "D", "orcid": "0000-0002-3028-9488", "researcher": {"href": "https://publications.scilifelab.se/researcher/c056bc462f8e433ba76bc65bb308df9b.json"}}, {"family": "Sokolov", "given": "Aleksandr", "initials": "A"}, {"family": "Sokolova", "given": "Natalya", "initials": "N", "orcid": "0000-0002-6692-4375", "researcher": {"href": "https://publications.scilifelab.se/researcher/8af9e1e989134044838373fd27e6f0db.json"}}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2022-11-15", "journal": {"title": "Genes", "issn": "2073-4425", "issn-l": "2073-4425", "volume": "13", "issue": "11", "pages": null}, "abstract": "Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions.", "doi": "10.3390/genes13112124", "pmid": "36421799", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9690288"}, {"db": "pii", "key": "genes13112124"}], "notes": [], "created": "2022-12-19T10:39:28.357Z", "modified": "2023-10-16T15:12:25.538Z"}, {"entity": "publication", "iuid": "f6085b6a093542799cfce5d77056cf6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6085b6a093542799cfce5d77056cf6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6085b6a093542799cfce5d77056cf6d"}}, "title": "Early changes in gene expression profiles in AML patients during induction chemotherapy.", "authors": [{"family": "Jakobsen", "given": "Ingrid", "initials": "I", "orcid": "0000-0003-4450-0333", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf014a7141ae4ebe854146cee082c6b2.json"}}, {"family": "Sundkvist", "given": "Max", "initials": "M"}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}, {"family": "Lotfi", "given": "Kourosh", "initials": "K", "orcid": "0000-0001-5797-7232", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c292ca46bf444fd8b79adc76555e722.json"}}], "type": "journal article", "published": "2022-11-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "752"}, "abstract": "Elucidation of the genetic mechanisms underlying treatment response to standard induction chemotherapy in AML patients is warranted, in order to aid in risk-adapted treatment decisions as novel treatments are emerging. In this pilot study, we explored the treatment-induced expression patterns in a small cohort of AML patients by analyzing differential gene expression (DGE) over the first 2 days of induction chemotherapy.\n\nBlood samples were collected from ten AML patients at baseline (before treatment initiation) and during the first 2 days of treatment (Day 1; approximately 24 h, and Day 2; approximately 48 h after treatment initiation, respectively) and RNA was extracted for subsequent RNA sequencing. DGE between time points were assessed by pairwise analysis using the R package edgeR version 3.18.1 in all patients as well as in relation to treatment response (complete remission, CR, vs non-complete remission, nCR). Ingenuity Pathway Analysis (Qiagen) software was used for pathway analysis and visualization.\n\nAfter initial data quality control, two patients were excluded from further analysis, resulting in a final cohort of eight patients with data from all three timepoints. DGE analysis demonstrated activation of pathways with genes directly or indirectly associated with NF-\u03baB signaling. Significant activation of the NF-\u03baB pathway was seen in 50% of the patients 2 days after treatment start, while iNOS pathway effects could be identified already after 1 day. nCR patients displayed activation of pathways associated with cell cycle progression, oncogenesis and anti-apoptotic behavior, including the STAT3 pathway and Salvage pathways of pyrimidine ribonucleotides. Notably, a significant induction of cytidine deaminase, an enzyme responsible for the deamination of Ara-C, could be observed between baseline and Day 2 in the nCR patients but not in patients achieving CR.\n\nIn conclusion, we show that time-course analysis of gene expression represents a feasible approach to identify relevant pathways affected by standard induction chemotherapy in AML patients. This poses as a potential method for elucidating new drug targets and biomarkers for categorizing disease aggressiveness and evaluating treatment response. However, more studies on larger cohorts are warranted to elucidate the transcriptional basis for drug response.", "doi": "10.1186/s12864-022-08960-4", "pmid": "36376859", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9664790"}, {"db": "pii", "key": "10.1186/s12864-022-08960-4"}], "notes": [], "created": "2022-12-19T10:42:55.959Z", "modified": "2023-10-16T15:31:03.123Z"}, {"entity": "publication", "iuid": "78ffb8b1ccac450ba856236c88120517", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78ffb8b1ccac450ba856236c88120517.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78ffb8b1ccac450ba856236c88120517"}}, "title": "Genomic trajectories of a near-extinction event in the Chatham Island black robin.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Sigeman", "given": "Hanna", "initials": "H"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Kardailsky", "given": "Olga", "initials": "O"}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Hale", "given": "Marie", "initials": "M"}, {"family": "Houston", "given": "Dave", "initials": "D"}, {"family": "Kennedy", "given": "Euan", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Massaro", "given": "Melanie", "initials": "M"}, {"family": "Robertson", "given": "Bruce C", "initials": "BC"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2022-11-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "747"}, "abstract": "Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.\n\nWe found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.\n\nOur results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.", "doi": "10.1186/s12864-022-08963-1", "pmid": "36357860", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9647977"}, {"db": "pii", "key": "10.1186/s12864-022-08963-1"}], "notes": [], "created": "2022-12-19T10:39:30.158Z", "modified": "2023-10-16T15:12:57.954Z"}, {"entity": "publication", "iuid": "15b298c3dbdc466f99868b9b5e5aed52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15b298c3dbdc466f99868b9b5e5aed52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15b298c3dbdc466f99868b9b5e5aed52"}}, "title": "A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition.", "authors": [{"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0ad7b1c36784c0092fd82f6d792c4bb.json"}}, {"family": "Kazanc\u0131", "given": "Duygu Deniz", "initials": "DD", "orcid": "0000-0002-8333-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f28aea0bd7e4bb7b6ac3d8843cae17f.json"}}, {"family": "Aydo\u011fan", "given": "Ay\u00e7a", "initials": "A", "orcid": "0000-0003-0171-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/191b5ce05f6343e4825ef86d5703f8df.json"}}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC", "orcid": "0000-0003-4424-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57ecd0264874105bb04cf9eb0cfce25.json"}}, {"family": "Erdal", "given": "\u00d6m\u00fcr Dilek", "initials": "\u00d6D", "orcid": "0000-0002-1559-4062", "researcher": {"href": "https://publications.scilifelab.se/researcher/43a1b606e9644c3794a02cf3e5c77984.json"}}, {"family": "Sar\u0131altun", "given": "Sava\u015f", "initials": "S", "orcid": "0000-0003-4190-3727", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e2757acc7047bf8e33983e6585be80.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "G\u00fcr\u00fcn", "given": "Kanat", "initials": "K", "orcid": "0000-0002-0433-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc7d8b8f978438e8812dee4049122df.json"}}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b98a6e55a69644cda1e305da05c6838d.json"}}, {"family": "Fernandes", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7434-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9a0a0289d9a46518acfa124747e38bf.json"}}, {"family": "\u00c7akan", "given": "G\u00f6khan", "initials": "G", "orcid": "0000-0002-1840-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef6138f4d74e4270b91f894300b40d3f.json"}}, {"family": "Koruyucu", "given": "Meliha Melis", "initials": "MM", "orcid": "0000-0002-1579-4478", "researcher": {"href": "https://publications.scilifelab.se/researcher/f034fb30cc694e00b12d060be03a7081.json"}}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Karamurat", "given": "Cansu", "initials": "C", "orcid": "0000-0002-3596-9036", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c6c312d10a4d5a8c806b8550709016.json"}}, {"family": "\u00d6zkan", "given": "Mustafa", "initials": "M", "orcid": "0000-0002-7520-4572", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d994334753f4081811a1897ab1a3317.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Sevkar", "given": "Arda", "initials": "A", "orcid": "0000-0003-4573-6778", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c781bd3197040a3a9e4dee03b57dc65.json"}}, {"family": "S\u00fcrer", "given": "Elif", "initials": "E", "orcid": "0000-0002-0738-6669", "researcher": {"href": "https://publications.scilifelab.se/researcher/8061a22cfed349b18cdee6c00e8661c9.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7", "orcid": "0000-0001-8675-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/acefd01d35f04a0b99350ec4828adfcb.json"}}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS", "orcid": "0000-0001-8143-8159", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f77cf0f580409f98004f71cf99c001.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Erim \u00d6zdo\u011fan", "given": "Asl\u0131", "initials": "A"}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}], "type": "journal article", "published": "2022-11-04", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "44", "pages": "eabo3609"}, "abstract": "Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic \u00c7ay\u00f6n\u00fc in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that \u00c7ay\u00f6n\u00fc was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting \u00c7ay\u00f6n\u00fc's cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.", "doi": "10.1126/sciadv.abo3609", "pmid": "36332018", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9635823"}], "notes": [], "created": "2022-12-19T10:42:53.985Z", "modified": "2023-10-16T15:30:26.817Z"}, {"entity": "publication", "iuid": "5a7dbe2f2ad04caab77711a646a48243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a7dbe2f2ad04caab77711a646a48243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a7dbe2f2ad04caab77711a646a48243"}}, "title": "The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Gilchrist", "given": "Ciaran", "initials": "C", "orcid": "0000-0002-7639-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/44917102032e428998899b3e63e5c4df.json"}}, {"family": "R\u00eago", "given": "Alexandre", "initials": "A"}, {"family": "Bendixsen", "given": "Devin P", "initials": "DP", "orcid": "0000-0003-0831-7646", "researcher": {"href": "https://publications.scilifelab.se/researcher/533f0c534a214ee68a037b243a63a028.json"}}, {"family": "Brice", "given": "Claire", "initials": "C"}, {"family": "Grosse-Sommer", "given": "Julie Michelle", "initials": "JM"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Stelkens", "given": "Rike", "initials": "R", "orcid": "0000-0002-8530-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3449c244a4c13b8610e401f4cbef4.json"}}], "type": "journal article", "published": "2022-11-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "11", "pages": null}, "abstract": "Adaptation from standing genetic variation is an important process underlying evolution in natural populations, but we rarely get the opportunity to observe the dynamics of fitness and genomic changes in real time. Here, we used experimental evolution and Pool-Seq to track the phenotypic and genomic changes of genetically diverse asexual populations of the yeast Saccharomyces cerevisiae in four environments with different fitness costs. We found that populations rapidly and in parallel increased in fitness in stressful environments. In contrast, allele frequencies showed a range of trajectories, with some populations fixing all their ancestral variation in <30 generations and others maintaining diversity across hundreds of generations. We detected parallelism at the genomic level (involving genes, pathways, and aneuploidies) within and between environments, with idiosyncratic changes recurring in the environments with higher stress. In particular, we observed a tendency of becoming haploid-like in one environment, whereas the populations of another environment showed low overall parallelism driven by standing genetic variation despite high selective pressure. This work highlights the interplay between standing genetic variation and the influx of de novo mutations in populations adapting to a range of selective pressures with different underlying trait architectures, advancing our understanding of the constraints and drivers of adaptation.", "doi": "10.1093/molbev/msac242", "pmid": "36334099", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9703598"}, {"db": "pii", "key": "6806091"}], "notes": [], "created": "2022-11-25T07:56:20.931Z", "modified": "2024-01-16T13:48:34.514Z"}, {"entity": "publication", "iuid": "aeb500e0ef0b45969b3c981d10c0624f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb500e0ef0b45969b3c981d10c0624f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb500e0ef0b45969b3c981d10c0624f"}}, "title": "Population dynamics and demographic history of Eurasian collared lemmings.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Marangoni", "given": "Aurelio", "initials": "A"}, {"family": "Baca", "given": "Mateusz", "initials": "M"}, {"family": "Popovi\u0107", "given": "Danijela", "initials": "D"}, {"family": "Goropashnaya", "given": "Anna V", "initials": "AV"}, {"family": "Stewart", "given": "John R", "initials": "JR"}, {"family": "Knul", "given": "Monika V", "initials": "MV"}, {"family": "Noiret", "given": "Pierre", "initials": "P"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Jimenez", "given": "Elodie-Laure", "initials": "EL"}, {"family": "Abramson", "given": "Natalia I", "initials": "NI"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Kuzmina", "given": "Elena A", "initials": "EA"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Fedorov", "given": "Vadim B", "initials": "VB"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2022-11-03", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "issn-l": null, "volume": "22", "issue": "1", "pages": "126"}, "abstract": "Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.\n\nHere, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.\n\nThis study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.", "doi": "10.1186/s12862-022-02081-y", "pmid": "36329382", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9632076"}, {"db": "pii", "key": "10.1186/s12862-022-02081-y"}], "notes": [], "created": "2022-12-19T10:39:31.539Z", "modified": "2024-01-16T13:48:34.525Z"}, {"entity": "publication", "iuid": "5eab650a5a5a402b8a354be7de674cb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eab650a5a5a402b8a354be7de674cb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eab650a5a5a402b8a354be7de674cb0"}}, "title": "Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831).", "authors": [{"family": "Michell", "given": "Craig T", "initials": "CT"}, {"family": "Pohjoism\u00e4ki", "given": "Jaakko L O", "initials": "JLO", "orcid": "0000-0002-1185-3610", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3dec32b253440eab477911e81ec3c1f.json"}}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Thulin", "given": "Carl-Gustaf", "initials": "CG"}], "type": "dataset", "published": "2022-11-03", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "667"}, "abstract": "We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (Lepus timidus sylvaticus), along with samples from two mountain hares (Lepus timidus timidus) and two brown hares (Lepus europaeus) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the seven hare specimens were mapped to the Lepus timidus pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. The data presented here could be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies.", "doi": "10.1038/s41597-022-01794-5", "pmid": "36329035", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9633808"}, {"db": "pii", "key": "10.1038/s41597-022-01794-5"}], "notes": [], "created": "2022-12-19T10:39:22.701Z", "modified": "2023-10-16T12:44:10.504Z"}, {"entity": "publication", "iuid": "f31d14aaa42b47d58a36c9a3d82d7097", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f31d14aaa42b47d58a36c9a3d82d7097.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f31d14aaa42b47d58a36c9a3d82d7097"}}, "title": "Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks.", "authors": [{"family": "Murach", "given": "Kevin A", "initials": "KA"}, {"family": "Liu", "given": "Zhengye", "initials": "Z"}, {"family": "Jude", "given": "Baptiste", "initials": "B"}, {"family": "Figueiredo", "given": "Vandre C", "initials": "VC"}, {"family": "Wen", "given": "Yuan", "initials": "Y"}, {"family": "Khadgi", "given": "Sabin", "initials": "S"}, {"family": "Lim", "given": "Seongkyun", "initials": "S"}, {"family": "Morena da Silva", "given": "Francielly", "initials": "F"}, {"family": "Greene", "given": "Nicholas P", "initials": "NP"}, {"family": "Lanner", "given": "Johanna T", "initials": "JT"}, {"family": "McCarthy", "given": "John J", "initials": "JJ"}, {"family": "Vechetti", "given": "Ivan J", "initials": "IJ"}, {"family": "von Walden", "given": "Ferdinand", "initials": "F"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "298", "issue": "11", "pages": "102515"}, "abstract": "Myc is a powerful transcription factor implicated in epigenetic reprogramming, cellular plasticity, and rapid growth as well as tumorigenesis. Cancer in skeletal muscle is extremely rare despite marked and sustained Myc induction during loading-induced hypertrophy. Here, we investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets, we define global and Myc-specific dynamics at the onset of mechanical overload-induced muscle fiber growth. Data collation across analyses reveals an under-appreciated role for the muscle fiber in extracellular matrix remodeling during adaptation, along with the contribution of mRNA stability to epigenetic-related transcript levels in muscle. We also identify Runx1 and Ankrd1 (Marp1) as abundant myonucleus-enriched loading-induced genes. We observed that a strong induction of cell cycle regulators including Myc occurs with mechanical overload in myonuclei. Additionally, in vivo Myc-controlled gene expression in the plantaris was defined using a genetic muscle fiber-specific doxycycline-inducible Myc-overexpression model. We determined Myc is implicated in numerous aspects of gene expression during early-phase muscle fiber growth. Specifically, brief induction of Myc protein in muscle represses Reverb\u03b1, Reverb\u03b2, and Myh2 while increasing Rpl3, recapitulating gene expression in myonuclei during acute overload. Experimental, comparative, and in silico analyses place Myc at the center of a stable and actively transcribed, loading-responsive, muscle fiber-localized regulatory hub. Collectively, our experiments are a roadmap for understanding global and Myc-mediated transcriptional networks that regulate rapid remodeling in postmitotic cells. We provide open webtools for exploring the five RNA-seq datasets as a resource to the field.", "doi": "10.1016/j.jbc.2022.102515", "pmid": "36150502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9583450"}, {"db": "pii", "key": "S0021-9258(22)00958-9"}], "notes": [], "created": "2022-12-19T10:39:21.302Z", "modified": "2023-10-16T12:43:38.308Z"}, {"entity": "publication", "iuid": "3bf2980f77984d3781a222f5e286a2b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bf2980f77984d3781a222f5e286a2b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bf2980f77984d3781a222f5e286a2b2"}}, "title": "Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly.", "authors": [{"family": "Shipilina", "given": "Daria", "initials": "D"}, {"family": "N\u00e4svall", "given": "Karin", "initials": "K"}, {"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Talavera", "given": "Gerard", "initials": "G"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Genomics", "issn": "1089-8646", "issn-l": "0888-7543", "volume": "114", "issue": "6", "pages": "110481"}, "abstract": "Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.", "doi": "10.1016/j.ygeno.2022.110481", "pmid": "36115505", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0888-7543(22)00226-9"}], "notes": [], "created": "2022-12-19T10:36:00.194Z", "modified": "2023-10-16T12:18:32.115Z"}, {"entity": "publication", "iuid": "cc6b33256f5b4fbb8ec0bfe8b1760761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc6b33256f5b4fbb8ec0bfe8b1760761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc6b33256f5b4fbb8ec0bfe8b1760761"}}, "title": "Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.", "authors": [{"family": "Banijamali", "given": "Mahsan", "initials": "M"}, {"family": "H\u00f6jer", "given": "Pontus", "initials": "P"}, {"family": "Nagy", "given": "Abel", "initials": "A"}, {"family": "H\u00e5\u00e5g", "given": "Petra", "initials": "P"}, {"family": "Gomero", "given": "Elizabeth Paz", "initials": "EP"}, {"family": "Stiller", "given": "Christiane", "initials": "C"}, {"family": "Kaminskyy", "given": "Vitaliy O", "initials": "VO"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "Karlstr\u00f6m", "given": "Amelie Eriksson", "initials": "AE"}, {"family": "Viktorsson", "given": "Kristina", "initials": "K"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "J Extracell Vesicles", "issn": "2001-3078", "issn-l": "2001-3078", "volume": "11", "issue": "11", "pages": "e12277"}, "abstract": "Small extracellular vesicles (sEVs) have in recent years evolved as a source of biomarkers for disease diagnosis and therapeutic follow up. sEV samples derived from multicellular organisms exhibit a high heterogeneous repertoire of vesicles which current methods based on ensemble measurements cannot capture. In this work we present droplet barcode sequencing for protein analysis (DBS-Pro) to profile surface proteins on individual sEVs, facilitating identification of sEV-subtypes within and between samples. The method allows for analysis of multiple proteins through use of DNA barcoded affinity reagents and sequencing as readout. High throughput single vesicle profiling is enabled through compartmentalization of individual sEVs in emulsion droplets followed by droplet barcoding through PCR. In this proof-of-concept study we demonstrate that DBS-Pro allows for analysis of single sEVs, with a mixing rate below 2%. A total of over 120,000 individual sEVs obtained from a NSCLC cell line and from malignant pleural effusion (MPE) fluid of NSCLC patients have been analyzed based on their surface proteins. We also show that the method enables single vesicle surface protein profiling and by extension characterization of sEV-subtypes, which is essential to identify the cellular origin of vesicles in heterogenous samples.", "doi": "10.1002/jev2.12277", "pmid": "36329610", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9633998"}], "notes": [], "created": "2022-12-19T10:39:25.541Z", "modified": "2023-10-16T12:48:34.221Z"}, {"entity": "publication", "iuid": "61fa13eeb4e7471fb3fc42d11ed00aeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61fa13eeb4e7471fb3fc42d11ed00aeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61fa13eeb4e7471fb3fc42d11ed00aeb"}}, "title": "Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.", "authors": [{"family": "Lovri\u0107", "given": "Alen", "initials": "A"}, {"family": "Rassolie", "given": "Ali", "initials": "A"}, {"family": "Alam", "given": "Seher", "initials": "S"}, {"family": "Mandi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Saini", "given": "Amarjit", "initials": "A"}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Fernandez-Gonzalo", "given": "Rodrigo", "initials": "R"}, {"family": "Gustafsson", "given": "Thomas", "initials": "T"}, {"family": "Rullman", "given": "Eric", "initials": "E", "orcid": "0000-0003-2854-7262", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf3c60e63af042eba26ce2732374fcdb.json"}}], "type": "journal article", "published": "2022-10-22", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "1121"}, "abstract": "Skeletal muscle adaptations to exercise have been associated with a range of health-related benefits, but cell type-specific adaptations within the muscle are incompletely understood. Here we use single-cell sequencing to determine the effects of exercise on cellular composition and cell type-specific processes in human skeletal muscle before and after intense exercise. Fifteen clusters originating from six different cell populations were identified. Most cell populations remained quantitatively stable after exercise, but a large transcriptional response was observed in mesenchymal, endothelial, and myogenic cells, suggesting that these cells are specifically involved in skeletal muscle remodeling. We found three subpopulations of myogenic cells characterized by different maturation stages based on the expression of markers such as PAX7, MYOD1, TNNI1, and TNNI2. Exercise accelerated the trajectory of myogenic progenitor cells towards maturation by increasing the transcriptional features of fast- and slow-twitch muscle fibers. The transcriptional regulation of these contractile elements upon differentiation was validated in vitro on primary myoblast cells. The cell type-specific adaptive mechanisms induced by exercise presented here contribute to the understanding of the skeletal muscle adaptations triggered by physical activity and may ultimately have implications for physiological and pathological processes affecting skeletal muscle, such as sarcopenia, cachexia, and glucose homeostasis.", "doi": "10.1038/s42003-022-04088-z", "pmid": "36273106", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9588010"}, {"db": "pii", "key": "10.1038/s42003-022-04088-z"}], "notes": [], "created": "2022-12-19T10:36:03.073Z", "modified": "2023-10-16T12:41:05.413Z"}, {"entity": "publication", "iuid": "497d78814e574349803eab61487da580", "links": {"self": {"href": "https://publications.scilifelab.se/publication/497d78814e574349803eab61487da580.json"}, "display": {"href": "https://publications.scilifelab.se/publication/497d78814e574349803eab61487da580"}}, "title": "Soil Microbiome Influences on Seedling Establishment and Growth of Prosopis chilensis and Prosopis tamarugo from Northern Chile.", "authors": [{"family": "Castro", "given": "David", "initials": "D", "orcid": "0000-0003-0836-6624", "researcher": {"href": "https://publications.scilifelab.se/researcher/04be48fb09cc4c868f2dbdb90e461a23.json"}}, {"family": "Concha", "given": "Christopher", "initials": "C"}, {"family": "Jamett", "given": "Fabiola", "initials": "F"}, {"family": "Ib\u00e1\u00f1ez", "given": "Cristian", "initials": "C", "orcid": "0000-0001-7767-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c276a57fcef465996a2ba6c316535eb.json"}}, {"family": "Hurry", "given": "Vaughan", "initials": "V", "orcid": "0000-0001-5151-5184", "researcher": {"href": "https://publications.scilifelab.se/researcher/094945ff08b940579618f5a75fcc98a9.json"}}], "type": "journal article", "published": "2022-10-14", "journal": {"title": "Plants (Basel)", "issn": "2223-7747", "issn-l": null, "volume": "11", "issue": "20", "pages": null}, "abstract": "Prosopis chilensis and Prosopis tamarugo, two woody legumes adapted to the arid regions of Chile, have a declining distribution due to the lack of new seedling establishment. This study investigated the potential of both species to establish in soil collected from four locations in Chile, within and outside the species distribution, and to assess the role of the root-colonizing microbiome in seedling establishment and growth. Seedling survival, height, and water potential were measured to assess establishment success and growth. 16S and ITS2 amplicon sequencing was used to characterize the composition of microbial communities from the different soils and to assess the ability of both Prosopis species to recruit bacteria and fungi from the different soils. Both species were established on three of the four soils. P. tamarugo seedlings showed significantly higher survival in foreign soils and maintained significantly higher water potential in Mediterranean soils. Amplicon sequencing showed that the four soils harbored distinct microbial communities. Root-associated microbial composition indicated that P. chilensis preferentially recruited mycorrhizal fungal partners while P. tamarugo recruited abundant bacteria with known salt-protective functions. Our results suggest that a combination of edaphic properties and microbial soil legacy are potential factors mediating the Prosopis establishment success in different soils.", "doi": "10.3390/plants11202717", "pmid": "36297741", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9610084"}, {"db": "pii", "key": "plants11202717"}], "notes": [], "created": "2022-12-19T10:42:49.397Z", "modified": "2023-10-16T15:14:59.195Z"}, {"entity": "publication", "iuid": "1722fbb67c6f43dd94b26537ac9d0fa3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1722fbb67c6f43dd94b26537ac9d0fa3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1722fbb67c6f43dd94b26537ac9d0fa3"}}, "title": "Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.", "authors": [{"family": "Kahsay", "given": "A", "initials": "A"}, {"family": "Rodriguez-Marquez", "given": "E", "initials": "E"}, {"family": "L\u00f3pez-P\u00e9rez", "given": "A", "initials": "A"}, {"family": "H\u00f6rnblad", "given": "A", "initials": "A"}, {"family": "von Hofsten", "given": "J", "initials": "J"}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "17149"}, "abstract": "Rhabdomyosarcoma is a soft tissue cancer that arises in skeletal muscle due to mutations in myogenic progenitors that lead to ineffective differentiation and malignant transformation. The transcription factors Pax3 and Pax7 and their downstream target genes are tightly linked with the fusion positive alveolar subtype, whereas the RAS pathway is usually involved in the embryonal, fusion negative variant. Here, we analyse the role of Pax3 in a fusion negative context, by linking alterations in gene expression in pax3a/pax3b double mutant zebrafish with tumour progression in kRAS-induced rhabdomyosarcoma tumours. Several genes in the RAS/MAPK signalling pathway were significantly down-regulated in pax3a/pax3b double mutant zebrafish. Progression of rhabdomyosarcoma tumours was also delayed in the pax3a/pax3b double mutant zebrafish indicating that Pax3 transcription factors have an unappreciated role in mediating malignancy in fusion negative rhabdomyosarcoma.", "doi": "10.1038/s41598-022-21525-5", "pmid": "36229514", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9561152"}, {"db": "pii", "key": "10.1038/s41598-022-21525-5"}], "notes": [], "created": "2022-11-09T15:48:52.515Z", "modified": "2024-01-16T13:48:34.762Z"}, {"entity": "publication", "iuid": "a88f4582c71849449a5371c7385f78ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a88f4582c71849449a5371c7385f78ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a88f4582c71849449a5371c7385f78ca"}}, "title": "Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system.", "authors": [{"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S", "orcid": "0000-0002-5476-7499", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc1a03d6cd414b748807788a0c8e11fb.json"}}, {"family": "Joglar", "given": "Vanessa", "initials": "V"}, {"family": "Amnebrink", "given": "Dennis", "initials": "D", "orcid": "0000-0002-2747-6346", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd3d739280a4ce281be628a3b4b217e.json"}}, {"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C", "orcid": "0000-0001-8302-5710", "researcher": {"href": "https://publications.scilifelab.se/researcher/28271fe98d59405b92dc026d1740dd9a.json"}}, {"family": "Gonz\u00e1lez", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-9926-3323", "researcher": {"href": "https://publications.scilifelab.se/researcher/985211e3b6354b6e9fe4be56a9c2b5b2.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Fern\u00e1ndez", "given": "Emilio", "initials": "E", "orcid": "0000-0001-7985-0814", "researcher": {"href": "https://publications.scilifelab.se/researcher/748dd6833e474966b5c7b79ef52dd1c7.json"}}, {"family": "Teira", "given": "Eva", "initials": "E", "orcid": "0000-0002-4333-0101", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed7047ae09241a182466fee66736dbd.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "16", "issue": "10", "pages": "2360-2372"}, "abstract": "Coastal upwelling zones are hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM are not well understood. We therefore carried out comparative time-series metatranscriptome analyses of bacterioplankton in the Northwest Iberian upwelling system, using parallel sampling of seawater and mesocosms with in situ-like conditions. The mesocosm experiment uncovered a taxon-specific progression of transcriptional responses from bloom development (characterized by a diverse set of taxa in the orders Cellvibrionales, Rhodobacterales, and Pelagibacterales), over early decay (mainly taxa in the Alteromonadales and Flavobacteriales), to senescence phases (Flavobacteriales and Saprospirales taxa). Pronounced order-specific differences in the transcription of glycoside hydrolases, peptidases, and transporters were found, supporting that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of mesocosm and field samples revealed a high degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the labile DOM pool. Our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the time scales typical of upwelling-driven phytoplankton blooms.", "doi": "10.1038/s41396-022-01273-0", "pmid": "35804052", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9478159"}, {"db": "pii", "key": "10.1038/s41396-022-01273-0"}], "notes": [], "created": "2022-08-19T08:38:12.799Z", "modified": "2024-01-16T13:48:34.858Z"}, {"entity": "publication", "iuid": "dc75e1039071444c97665eeac886fd6a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc75e1039071444c97665eeac886fd6a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc75e1039071444c97665eeac886fd6a"}}, "title": "Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters.", "authors": [{"family": "Capo", "given": "Eric", "initials": "E", "orcid": "0000-0001-9143-7061", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4017e9c8167487b882ee2d045d96494.json"}}, {"family": "Feng", "given": "Caiyan", "initials": "C"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Soerensen", "given": "Anne L", "initials": "AL", "orcid": "0000-0002-8490-8600", "researcher": {"href": "https://publications.scilifelab.se/researcher/80c5602b03254dd6a9bee71d0429b678.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Hawkes", "given": "Jeffrey", "initials": "J", "orcid": "0000-0003-0664-2242", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1580e588fb405b95b1690038d93914.json"}}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E", "orcid": "0000-0001-9570-8738", "researcher": {"href": "https://publications.scilifelab.se/researcher/d52d4c83dda84cea9e018199a8cfc304.json"}}], "type": "journal article", "published": "2022-09-20", "journal": {"title": "Environ. Sci. Technol.", "issn": "1520-5851", "issn-l": "0013-936X", "volume": "56", "issue": "18", "pages": "13119-13130"}, "abstract": "Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc+ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc+ MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.", "doi": "10.1021/acs.est.2c03784", "pmid": "36069707", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9494745"}], "notes": [], "created": "2022-11-29T09:47:11.811Z", "modified": "2023-10-04T10:56:50.418Z"}, {"entity": "publication", "iuid": "362c451c88124be69c423cc4853c5216", "links": {"self": {"href": "https://publications.scilifelab.se/publication/362c451c88124be69c423cc4853c5216.json"}, "display": {"href": "https://publications.scilifelab.se/publication/362c451c88124be69c423cc4853c5216"}}, "title": "Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.", "authors": [{"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a238f7adbc242398a46fd24190a2811.json"}}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Friedrich", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3889-5589", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e1de4177ae649aba93a633ca451ebdb.json"}}, {"family": "Berglund", "given": "Emelie", "initials": "E", "orcid": "0000-0003-1857-307X", "researcher": {"href": "https://publications.scilifelab.se/researcher/87df6f4e3aed48938e7bee3acf27847e.json"}}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Tanoglidi", "given": "Anna", "initials": "A"}, {"family": "Liu", "given": "Yao", "initials": "Y", "orcid": "0000-0001-5572-723X", "researcher": {"href": "https://publications.scilifelab.se/researcher/08bfef572b6e4c7287380d8a5783bd9c.json"}}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L", "orcid": "0000-0002-5108-4481", "researcher": {"href": "https://publications.scilifelab.se/researcher/98234e5e06c241879f6f986ded3ab6f9.json"}}, {"family": "Erickson", "given": "Andrew", "initials": "A"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Lamb", "given": "Alastair D", "initials": "AD", "orcid": "0000-0002-2968-7155", "researcher": {"href": "https://publications.scilifelab.se/researcher/798d88b3df1e4a7d994e90b5d60372e6.json"}}, {"family": "Sonnhammer", "given": "Erik", "initials": "E", "orcid": "0000-0002-9015-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d7888c298484f958c2c5f7fe0a8a9ba.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2022-09-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "5475"}, "abstract": "The molecular mechanisms underlying lethal castration-resistant prostate cancer remain poorly understood, with intratumoral heterogeneity a likely contributing factor. To examine the temporal aspects of resistance, we analyze tumor heterogeneity in needle biopsies collected before and after treatment with androgen deprivation therapy. By doing so, we are able to couple clinical responsiveness and morphological information such as Gleason score to transcriptome-wide data. Our data-driven analysis of transcriptomes identifies several distinct intratumoral cell populations, characterized by their unique gene expression profiles. Certain cell populations present before treatment exhibit gene expression profiles that match those of resistant tumor cell clusters, present after treatment. We confirm that these clusters are resistant by the localization of active androgen receptors to the nuclei in cancer cells post-treatment. Our data also demonstrates that most stromal cells adjacent to resistant clusters do not express the androgen receptor, and we identify differentially expressed genes for these cells. Altogether, this study shows the potential to increase the power in predicting resistant tumors.", "doi": "10.1038/s41467-022-33069-3", "pmid": "36115838", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Spatial omics": null}, "xrefs": [{"db": "pmc", "key": "PMC9482614"}, {"db": "pii", "key": "10.1038/s41467-022-33069-3"}], "notes": [], "created": "2022-12-19T10:35:54.516Z", "modified": "2023-10-23T09:22:51.156Z"}, {"entity": "publication", "iuid": "8e627a82e39d4c059ca3d5e9ae6a57d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e627a82e39d4c059ca3d5e9ae6a57d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e627a82e39d4c059ca3d5e9ae6a57d8"}}, "title": "Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.", "authors": [{"family": "Pe\u00f1a-P\u00e9rez", "given": "Luc\u00eda", "initials": "L", "orcid": "0000-0002-5044-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/111f8a8c4c6d4d2ea60e5fc76831b7fa.json"}}, {"family": "Frengen", "given": "Nicolai", "initials": "N", "orcid": "0000-0003-1834-7638", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c9b75c9a3ed48dbbd4cc4fae9836623.json"}}, {"family": "Hauenstein", "given": "Julia", "initials": "J", "orcid": "0000-0001-6674-4297", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bda375874844045bd86d62d3b25e071.json"}}, {"family": "Gran", "given": "Charlotte", "initials": "C"}, {"family": "Gustafsson", "given": "Charlotte", "initials": "C"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F", "orcid": "0000-0001-7198-5116", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a3bc9c440024ec994e534c3a6627f55.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Wallblom", "given": "Ann", "initials": "A"}, {"family": "Krstic", "given": "Aleksandra", "initials": "A"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R", "orcid": "0000-0003-0738-0328", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafa5ad22891454298bf31a94d77175f.json"}}], "type": "journal article", "published": "2022-09-13", "journal": {"title": "Blood Adv", "issn": "2473-9537", "issn-l": "2473-9529", "volume": "6", "issue": "17", "pages": "5009-5023"}, "abstract": "Multiple myeloma (MM) is an incurable and aggressive plasma cell malignancy characterized by a complex karyotype with multiple structural variants (SVs) and copy-number variations (CNVs). Linked-read whole-genome sequencing (lrWGS) allows for refined detection and reconstruction of SVs by providing long-range genetic information from standard short-read sequencing. This makes lrWGS an attractive solution for capturing the full genomic complexity of MM. Here we show that high-quality lrWGS data can be generated from low numbers of cells subjected to fluorescence-activated cell sorting (FACS) without DNA purification. Using this protocol, we analyzed MM cells after FACS from 37 patients with MM using lrWGS. We found high concordance between lrWGS and fluorescence in situ hybridization (FISH) for the detection of recurrent translocations and CNVs. Outside of the regions investigated by FISH, we identified >150 additional SVs and CNVs across the cohort. Analysis of the lrWGS data allowed for resolution of the structure of diverse SVs affecting the MYC and t(11;14) loci, causing the duplication of genes and gene regulatory elements. In addition, we identified private SVs causing the dysregulation of genes recurrently involved in translocations with the IGH locus and show that these can alter the molecular classification of MM. Overall, we conclude that lrWGS allows for the detection of aberrations critical for MM prognostics and provides a feasible route for providing comprehensive genetics. Implementing lrWGS could provide more accurate clinical prognostics, facilitate genomic medicine initiatives, and greatly improve the stratification of patients included in clinical trials.", "doi": "10.1182/bloodadvances.2021006720", "pmid": "35675515", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9631623"}, {"db": "pii", "key": "485485"}], "notes": [], "created": "2022-08-19T08:37:59.788Z", "modified": "2024-01-16T13:48:35.011Z"}, {"entity": "publication", "iuid": "12ece6c4901347fab2888fd0883ac4f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12ece6c4901347fab2888fd0883ac4f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12ece6c4901347fab2888fd0883ac4f7"}}, "title": "Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination.", "authors": [{"family": "Gao", "given": "Yu", "initials": "Y"}, {"family": "Cai", "given": "Curtis", "initials": "C"}, {"family": "Wullimann", "given": "David", "initials": "D"}, {"family": "Niessl", "given": "Julia", "initials": "J"}, {"family": "Rivera-Ballesteros", "given": "Olga", "initials": "O"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Lange", "given": "Joshua", "initials": "J"}, {"family": "Cuapio", "given": "Angelica", "initials": "A"}, {"family": "Blennow", "given": "Ola", "initials": "O"}, {"family": "Hansson", "given": "Lotta", "initials": "L"}, {"family": "Mielke", "given": "Stephan", "initials": "S"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Vesterbacka", "given": "Jan", "initials": "J"}, {"family": "Akber", "given": "Mira", "initials": "M"}, {"family": "Perez-Potti", "given": "Andre", "initials": "A"}, {"family": "Sekine", "given": "Takuya", "initials": "T"}, {"family": "M\u00fcller", "given": "Thomas R", "initials": "TR"}, {"family": "Boulouis", "given": "Caroline", "initials": "C"}, {"family": "Kammann", "given": "Tobias", "initials": "T"}, {"family": "Parrot", "given": "Tiphaine", "initials": "T"}, {"family": "Muvva", "given": "Jagadeeswara Rao", "initials": "JR"}, {"family": "Sobkowiak", "given": "Michal", "initials": "M"}, {"family": "Healy", "given": "Katie", "initials": "K"}, {"family": "Bogdanovic", "given": "Gordana", "initials": "G"}, {"family": "Muschiol", "given": "Sandra", "initials": "S"}, {"family": "S\u00f6derdahl", "given": "Gunnar", "initials": "G"}, {"family": "\u00d6sterborg", "given": "Anders", "initials": "A"}, {"family": "Hellgren", "given": "Fredrika", "initials": "F"}, {"family": "Grifoni", "given": "Alba", "initials": "A"}, {"family": "Weiskopf", "given": "Daniela", "initials": "D"}, {"family": "Sette", "given": "Alessandro", "initials": "A"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K"}, {"family": "S\u00e4llberg Chen", "given": "Margaret", "initials": "M"}, {"family": "Ljungman", "given": "Per", "initials": "P"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK"}, {"family": "Smith", "given": "C I Edvard", "initials": "CIE"}, {"family": "Bergman", "given": "Peter", "initials": "P"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Aleman", "given": "Soo", "initials": "S"}, {"family": "Buggert", "given": "Marcus", "initials": "M"}], "type": "journal article", "published": "2022-09-13", "journal": {"title": "Immunity", "issn": "1097-4180", "issn-l": "1074-7613", "volume": "55", "issue": "9", "pages": "1732-1746.e5"}, "abstract": "Many immunocompromised patients mount suboptimal humoral immunity after SARS-CoV-2 mRNA vaccination. Here, we assessed the single-cell profile of SARS-CoV-2-specific T cells post-mRNA vaccination in healthy individuals and patients with various forms of immunodeficiencies. Impaired vaccine-induced cell-mediated immunity was observed in many immunocompromised patients, particularly in solid-organ transplant and chronic lymphocytic leukemia patients. Notably, individuals with an inherited lack of mature B cells, i.e., X-linked agammaglobulinemia (XLA) displayed highly functional spike-specific T cell responses. Single-cell RNA-sequencing further revealed that mRNA vaccination induced a broad functional spectrum of spike-specific CD4+ and CD8+ T cells in healthy individuals and patients with XLA. These responses were founded on polyclonal repertoires of CD4+ T cells and robust expansions of oligoclonal effector-memory CD45RA+ CD8+ T cells with stem-like characteristics. Collectively, our data provide the functional continuum of SARS-CoV-2-specific T cell responses post-mRNA vaccination, highlighting that cell-mediated immunity is of variable functional quality across immunodeficiency syndromes.", "doi": "10.1016/j.immuni.2022.07.005", "pmid": "35961317", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9293955"}, {"db": "pii", "key": "S1074-7613(22)00338-7"}], "notes": [], "created": "2022-08-19T08:38:19.764Z", "modified": "2024-01-16T13:48:35.019Z"}, {"entity": "publication", "iuid": "50214f3ea74a4cd89f24e91e10750c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50214f3ea74a4cd89f24e91e10750c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50214f3ea74a4cd89f24e91e10750c93"}}, "title": "Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae).", "authors": [{"family": "Thureborn", "given": "Olle", "initials": "O"}, {"family": "Razafimandimbison", "given": "Sylvain G", "initials": "SG"}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2022-09-08", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "13", "issue": null, "pages": "967456"}, "abstract": "Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.", "doi": "10.3389/fpls.2022.967456", "pmid": "36160958", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9493367"}, {"db": "Dryad", "key": "10.5061/dryad.d7wm37q44"}], "notes": [], "created": "2022-12-19T10:35:58.954Z", "modified": "2023-10-16T12:18:04.650Z"}, {"entity": "publication", "iuid": "df3618d6438546bdbd1578a94586afc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df3618d6438546bdbd1578a94586afc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df3618d6438546bdbd1578a94586afc8"}}, "title": "Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice.", "authors": [{"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Birgersson", "given": "Madeleine", "initials": "M", "orcid": "0000-0002-5876-0710", "researcher": {"href": "https://publications.scilifelab.se/researcher/68ea3a27e23a4f978e9c4e74ebdfbf11.json"}}, {"family": "Indukuri", "given": "Rajitha", "initials": "R", "orcid": "0000-0001-6570-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94148ec0ffb74f9bb0243c18a1256c22.json"}}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2022-09-08", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "23", "issue": "18", "pages": null}, "abstract": "There are significant sex differences in colorectal cancer (CRC), including in incidence, onset, and molecular characteristics. Further, while inflammatory bowel disease (IBD) is a risk factor for CRC in both sexes, men with IBD have a 60% higher risk of developing CRC compared to women. In this study, we investigated sex differences during colitis-associated CRC (CAC) using a chemically induced CAC mouse model. The mice were treated with azoxymethane (AOM) and dextran sodium sulfate (DSS) and followed for 9 and 15 weeks. We performed RNA-sequencing of colon samples from males (n = 15) and females (n = 15) to study different stages of inflammation and identify corresponding transcriptomic sex differences in non-tumor colon tissue. We found a significant transcriptome response to AOM/DSS treatment in both sexes, including in pathways related to inflammation and cell proliferation. Notably, we found a stronger response in males and that male-specific differentially expressed genes were involved in NF\u03baB signaling and circadian rhythm. Further, an overrepresented proportion of male-specific gene regulations were predicted to be targets of Stat3, whereas for females, targets of the glucocorticoid receptor (Gr/Nr3c1) were overrepresented. At 15 weeks, the most apparent sex difference involved genes with functions in T cell proliferation, followed by the regulation of demethylases. The majority of sex differences were thus related to inflammation and the immune system. Our novel data, profiling the transcriptomic response to chemically induced colitis and CAC, indicate clear sex differences in CRC initiation and progression.", "doi": "10.3390/ijms231810408", "pmid": "36142324", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9499483"}, {"db": "pii", "key": "ijms231810408"}], "notes": [], "created": "2022-12-19T10:36:01.618Z", "modified": "2023-10-16T12:40:09.780Z"}, {"entity": "publication", "iuid": "7c8ceca997cd49d6927b755e583e0da4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c8ceca997cd49d6927b755e583e0da4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c8ceca997cd49d6927b755e583e0da4"}}, "title": "Schwann cell precursors represent a neural crest-like state with biased multipotency.", "authors": [{"family": "Kastriti", "given": "Maria Eleni", "initials": "ME", "orcid": "0000-0002-0563-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e0722d8c5484a13bb37c3a3b084ff8c.json"}}, {"family": "Faure", "given": "Louis", "initials": "L", "orcid": "0000-0003-4621-586X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbf218e53c854d69a1b474a61480c33f.json"}}, {"family": "Von Ahsen", "given": "Dorothea", "initials": "D"}, {"family": "Bouderlique", "given": "Thibault Gerald", "initials": "TG"}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0001-5252-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af59464d2c74c27af7a43fb5d1a670e.json"}}, {"family": "Solovieva", "given": "Tatiana", "initials": "T", "orcid": "0000-0001-6194-2550", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c88055db071476db108cbc014226964.json"}}, {"family": "Jackson", "given": "Cameron", "initials": "C"}, {"family": "Bronner", "given": "Marianne", "initials": "M", "orcid": "0000-0003-4274-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/56516b93bfb047aeab63c9d2fee21d4a.json"}}, {"family": "Meijer", "given": "Dies", "initials": "D", "orcid": "0000-0002-8461-6341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae5c7bfbb900485fb51238882500ab76.json"}}, {"family": "Hadjab", "given": "Saida", "initials": "S"}, {"family": "Lallemend", "given": "Francois", "initials": "F"}, {"family": "Erickson", "given": "Alek", "initials": "A"}, {"family": "Kaucka", "given": "Marketa", "initials": "M", "orcid": "0000-0002-8781-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/933187e42ddc4ab6a29c46d5cca411e6.json"}}, {"family": "Dyachuk", "given": "Viacheslav", "initials": "V"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Lahti", "given": "Laura", "initials": "L"}, {"family": "Krivanek", "given": "Jan", "initials": "J", "orcid": "0000-0002-7590-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e716ca0e1b464dd9850687d8f5aa6758.json"}}, {"family": "Brunet", "given": "Jean-Francois", "initials": "JF"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal article", "published": "2022-09-01", "journal": {"title": "EMBO J.", "issn": "1460-2075", "volume": "41", "issue": "17", "pages": "e108780", "issn-l": "0261-4189"}, "abstract": "Schwann cell precursors (SCPs) are nerve-associated progenitors that can generate myelinating and non-myelinating Schwann cells but also are multipotent like the neural crest cells from which they originate. SCPs are omnipresent along outgrowing peripheral nerves throughout the body of vertebrate embryos. By using single-cell transcriptomics to generate a gene expression atlas of the entire neural crest lineage, we show that early SCPs and late migratory crest cells have similar transcriptional profiles characterised by a multipotent \"hub\" state containing cells biased towards traditional neural crest fates. SCPs keep diverging from the neural crest after being primed towards terminal Schwann cells and other fates, with different subtypes residing in distinct anatomical locations. Functional experiments using CRISPR-Cas9 loss-of-function further show that knockout of the common \"hub\" gene Sox8 causes defects in neural crest-derived cells along peripheral nerves by facilitating differentiation of SCPs towards sympathoadrenal fates. Finally, specific tumour populations found in melanoma, neurofibroma and neuroblastoma map to different stages of SCP/Schwann cell development. Overall, SCPs resemble migrating neural crest cells that maintain multipotency and become transcriptionally primed towards distinct lineages.", "doi": "10.15252/embj.2021108780", "pmid": "35815410", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9434083"}], "notes": [], "created": "2024-10-14T11:53:36.186Z", "modified": "2024-10-14T11:53:37.393Z"}, {"entity": "publication", "iuid": "c3972e12a2a341bebf0a47a42d2b7f76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3972e12a2a341bebf0a47a42d2b7f76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3972e12a2a341bebf0a47a42d2b7f76"}}, "title": "Uncovering the genomic basis of an extraordinary plant invasion.", "authors": [{"family": "Bieker", "given": "Vanessa C", "initials": "VC", "orcid": "0000-0002-2061-9041", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4a4bac15f0242b49d53423af4b9d420.json"}}, {"family": "Battlay", "given": "Paul", "initials": "P", "orcid": "0000-0001-6050-1868", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c813a6c4db44888bee6aa989cefd2c.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Sun", "given": "Xin", "initials": "X"}, {"family": "Wilson", "given": "Jonathan", "initials": "J"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC", "orcid": "0000-0001-7068-2017", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb2930d582f4483afc1f5bd52e37818.json"}}, {"family": "Bretagnolle", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0003-0164-840X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f773658a75ab40388df09f0b80378ba0.json"}}, {"family": "Nurkowski", "given": "Kristin", "initials": "K", "orcid": "0000-0003-0441-0026", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18bf81e0b244df09bd39b8269319d1f.json"}}, {"family": "Lee", "given": "Chris", "initials": "C", "orcid": "0000-0003-1108-8514", "researcher": {"href": "https://publications.scilifelab.se/researcher/42b9b738df714f89a1890c0be4347146.json"}}, {"family": "Barreiro", "given": "F\u00e1tima S\u00e1nchez", "initials": "FS", "orcid": "0000-0002-5902-0052", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c84c6755fbf476bba3d19b2782dadea.json"}}, {"family": "Owens", "given": "Gregory L", "initials": "GL", "orcid": "0000-0002-4019-5215", "researcher": {"href": "https://publications.scilifelab.se/researcher/59c73f36ad5f46a0961e238c2a112eef.json"}}, {"family": "Lee", "given": "Jacqueline Y", "initials": "JY"}, {"family": "Kellner", "given": "Fabian L", "initials": "FL", "orcid": "0000-0002-9057-3018", "researcher": {"href": "https://publications.scilifelab.se/researcher/155192b37bb44a38828c8153d0367986.json"}}, {"family": "van Boheeman", "given": "Lotte", "initials": "L"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S", "orcid": "0000-0002-2004-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/637bc46cf8094999aad02a3d646e82fd.json"}}, {"family": "Gaudeul", "given": "Myriam", "initials": "M"}, {"family": "Mueller-Schaerer", "given": "Heinz", "initials": "H", "orcid": "0000-0003-0936-1470", "researcher": {"href": "https://publications.scilifelab.se/researcher/169aa99153034932a8f0ebfc672625ca.json"}}, {"family": "Lommen", "given": "Suzanne", "initials": "S", "orcid": "0000-0003-2457-9849", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d4f5b016df34f5e84ed26bcce3ff19c.json"}}, {"family": "Karrer", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-5172-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3dcc8fd40f34eeca34142841befc2b1.json"}}, {"family": "Chauvel", "given": "Bruno", "initials": "B"}, {"family": "Sun", "given": "Yan", "initials": "Y", "orcid": "0000-0002-6439-266X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e20068fe5222436aaabdb511df958de1.json"}}, {"family": "Kostantinovic", "given": "Bojan", "initials": "B", "orcid": "0000-0001-5071-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/deaf9ddd367343d8bb7ab4469a3aa47b.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Poczai", "given": "P\u00e9ter", "initials": "P", "orcid": "0000-0002-0107-1068", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3a91af46eeb4b8b91eb6f9efe2182a8.json"}}, {"family": "Rieseberg", "given": "Loren H", "initials": "LH", "orcid": "0000-0002-2712-2417", "researcher": {"href": "https://publications.scilifelab.se/researcher/58f1bbbb7e2d43808507f11c2f2dcf97.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Hodgins", "given": "Kathryn A", "initials": "KA", "orcid": "0000-0003-2795-5213", "researcher": {"href": "https://publications.scilifelab.se/researcher/b521c30f4b1d495d9b5e8a7d28a90e30.json"}}, {"family": "Martin", "given": "Michael D", "initials": "MD", "orcid": "0000-0002-2010-5139", "researcher": {"href": "https://publications.scilifelab.se/researcher/2498075af1374bafbeefec3b208f86ff.json"}}], "type": "journal article", "published": "2022-08-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "34", "pages": "eabo5115"}, "abstract": "Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.", "doi": "10.1126/sciadv.abo5115", "pmid": "36001672", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9401624"}], "notes": [], "created": "2022-12-19T10:29:59.209Z", "modified": "2023-10-16T11:47:51.223Z"}, {"entity": "publication", "iuid": "ae4ff1411a31429f8d1c53a6fc16ed11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae4ff1411a31429f8d1c53a6fc16ed11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae4ff1411a31429f8d1c53a6fc16ed11"}}, "title": "PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.", "authors": [{"family": "Toskas", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-5897-9501", "researcher": {"href": "https://publications.scilifelab.se/researcher/687adc14acf7400eaa552f41eb39807e.json"}}, {"family": "Yaghmaeian-Salmani", "given": "Behzad", "initials": "B", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Skiteva", "given": "Olga", "initials": "O"}, {"family": "Paslawski", "given": "Wojciech", "initials": "W", "orcid": "0000-0003-2141-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce039c7e5e774d66a8c0331a3c990ccc.json"}}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Skara", "given": "Vasiliki", "initials": "V", "orcid": "0000-0002-0017-6116", "researcher": {"href": "https://publications.scilifelab.se/researcher/e412dda73e2e40a380e10775f45fbd66.json"}}, {"family": "Antoniou", "given": "Irene", "initials": "I", "orcid": "0000-0002-3616-9049", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a00a046dece4cae9afa12a5c7caa723.json"}}, {"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Chergui", "given": "Karima", "initials": "K", "orcid": "0000-0001-5702-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/be439b7cafce4d919881a7b0ef7d6340.json"}}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Holmberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-3018-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f84bece88a264d228d3770ca634b4a19.json"}}], "type": "journal article", "published": "2022-08-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "34", "pages": "eabo1543"}, "abstract": "How neurons can maintain cellular identity over an entire life span remains largely unknown. Here, we show that maintenance of identity in differentiated dopaminergic and serotonergic neurons is critically reliant on the Polycomb repressive complex 2 (PRC2). Deletion of the obligate PRC2 component, Eed, in these neurons resulted in global loss of H3K27me3, followed by a gradual activation of genes harboring both H3K27me3 and H3K9me3 modifications. Notably, H3K9me3 was lost at these PRC2 targets before gene activation. Neuronal survival was not compromised; instead, there was a reduction in subtype-specific gene expression and a progressive impairment of dopaminergic and serotonergic neuronal function, leading to behavioral deficits characteristic of Parkinson's disease and anxiety. Single-cell analysis revealed subtype-specific vulnerability to loss of PRC2 repression in dopamine neurons of the substantia nigra. Our study reveals that a PRC2-dependent nonpermissive chromatin state is essential to maintain the subtype identity and function of dopaminergic and serotonergic neurons.", "doi": "10.1126/sciadv.abo1543", "pmid": "36026451", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9417181"}], "notes": [], "created": "2022-08-30T11:39:49.253Z", "modified": "2024-10-14T11:50:28.807Z"}, {"entity": "publication", "iuid": "301efd49a74e490ea103f7210d81aa56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/301efd49a74e490ea103f7210d81aa56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/301efd49a74e490ea103f7210d81aa56"}}, "title": "A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Zuccon", "given": "Dario", "initials": "D"}, {"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "Tison", "given": "Jean-Luc", "initials": "JL"}, {"family": "Emslie", "given": "Steven D", "initials": "SD"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Hume", "given": "Julian P", "initials": "JP"}, {"family": "Werdelin", "given": "Lars", "initials": "L"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2022-08-23", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "857"}, "abstract": "The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.", "doi": "10.1038/s42003-022-03811-0", "pmid": "35999361", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9399080"}, {"db": "pii", "key": "10.1038/s42003-022-03811-0"}, {"db": "Dryad", "key": "10.5061/dryad.qz612jmjm"}], "notes": [], "created": "2022-11-09T15:56:49.491Z", "modified": "2024-01-16T13:48:35.118Z"}, {"entity": "publication", "iuid": "84870ae38812488595d58a590c3f912d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84870ae38812488595d58a590c3f912d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84870ae38812488595d58a590c3f912d"}}, "title": "Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.", "authors": [{"family": "Zufia", "given": "Javier Alegria", "initials": "JA"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Farnelid", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2022-08-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "14330"}, "abstract": "Picocyanobacteria (< 2 \u00b5m in diameter) are significant contributors to total phytoplankton biomass. Due to the high diversity within this group, their seasonal dynamics and relationship with environmental parameters, especially in brackish waters, are largely unknown. In this study, the abundance and community composition of phycoerythrin rich picocyanobacteria (PE-SYN) and phycocyanin rich picocyanobacteria (PC-SYN) were monitored at a coastal (K-station) and at an offshore station (LMO; ~ 10 km from land) in the Baltic Sea over three years (2018-2020). Cell abundances of picocyanobacteria correlated positively to temperature and negatively to nitrate (NO3) concentration. While PE-SYN abundance correlated to the presence of nitrogen fixers, PC-SYN abundance was linked to stratification/shallow waters. The picocyanobacterial targeted amplicon sequencing revealed an unprecedented diversity of 2169 picocyanobacterial amplicons sequence variants (ASVs). A unique assemblage of distinct picocyanobacterial clades across seasons was identified. Clade A/B dominated the picocyanobacterial community, except during summer when low NO3, high phosphate (PO4) concentrations and warm temperatures promoted S5.2 dominance. This study, providing multiyear data, links picocyanobacterial populations to environmental parameters. The difference in the response of the two functional groups and clades underscore the need for further high-resolution studies to understand their role in the ecosystem.", "doi": "10.1038/s41598-022-18454-8", "pmid": "35995823", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9395346"}, {"db": "pii", "key": "10.1038/s41598-022-18454-8"}], "notes": [], "created": "2022-11-29T09:33:46.926Z", "modified": "2024-01-16T13:48:35.127Z"}, {"entity": "publication", "iuid": "6acd41f51fcb4036b0c0e0ac6f968aa8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6acd41f51fcb4036b0c0e0ac6f968aa8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6acd41f51fcb4036b0c0e0ac6f968aa8"}}, "title": "Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Chac\u00f3n-Duque", "given": "J Camilo", "initials": "JC"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2022-08-19", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "8", "pages": "104826"}, "abstract": "Woolly mammoths had a set of adaptations that enabled them to thrive in the Arctic environment. Many mammoth-specific single nucleotide polymorphisms (SNPs) responsible for unique mammoth traits have been previously identified from ancient genomes. However, a multitude of other genetic variants likely contributed to woolly mammoth evolution. In this study, we sequenced two woolly mammoth genomes and combined these with previously sequenced mammoth and elephant genomes to conduct a survey of mammoth-specific deletions and indels. We find that deletions are highly enriched in non-coding regions, suggesting selection against structural variants that affect protein sequences. Nonetheless, at least 87 woolly mammoth genes contain deletions or indels that modify the coding sequence, including genes involved in skeletal morphology and hair growth. These results suggest that deletions and indels contributed to the unique phenotypic adaptations of the woolly mammoth, and were potentially critical to surviving in its natural environment.", "doi": "10.1016/j.isci.2022.104826", "pmid": "35992080", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9382235"}, {"db": "pii", "key": "S2589-0042(22)01098-7"}], "notes": [], "created": "2022-11-10T16:02:19.204Z", "modified": "2024-01-16T13:48:35.153Z"}, {"entity": "publication", "iuid": "998efaa46c9942f3a499d5dba6686f2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/998efaa46c9942f3a499d5dba6686f2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/998efaa46c9942f3a499d5dba6686f2e"}}, "title": "Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield.", "authors": [{"family": "Osterholz", "given": "Helena", "initials": "H", "orcid": "0000-0002-2858-9799", "researcher": {"href": "https://publications.scilifelab.se/researcher/2049c163450b4ad48ab5efc5b11cd50e.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Alakangas", "given": "Linda J", "initials": "LJ"}, {"family": "Tullborg", "given": "Eva-Lena", "initials": "EL"}, {"family": "Dittmar", "given": "Thorsten", "initials": "T"}, {"family": "Kalinowski", "given": "Birgitta E", "initials": "BE"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "4837"}, "abstract": "The deep terrestrial biosphere encompasses the life below the photosynthesis-fueled surface that perseveres in typically nutrient and energy depleted anoxic groundwaters. The composition and cycling of this vast dissolved organic matter (DOM) reservoir relevant to the global carbon cycle remains to be deciphered. Here we show that recent Baltic Sea-influenced to ancient pre-Holocene saline Fennoscandian Shield deep bedrock fracture waters carried DOM with a strong terrigenous signature and varying contributions from abiotic and biotic processes. Removal of easily degraded carbon at the surface-to-groundwater transition and corresponding microbial community assembly processes likely resulted in the highly similar DOM signatures across the notably different water types that selected for a core microbiome. In combination with the aliphatic character, depleted \u03b413C signatures in DOM indicated recent microbial production in the oldest, saline groundwater. Our study revealed the persistence of terrestrially-sourced carbon in severely energy limited deep continental groundwaters supporting deep microbial life.", "doi": "10.1038/s41467-022-32457-z", "pmid": "35977924", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9385861"}, {"db": "pii", "key": "10.1038/s41467-022-32457-z"}], "notes": [], "created": "2022-12-19T10:30:02.867Z", "modified": "2024-01-16T13:48:35.176Z"}, {"entity": "publication", "iuid": "58588cae7b6442fe9c8f7dc7d96e0976", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58588cae7b6442fe9c8f7dc7d96e0976.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58588cae7b6442fe9c8f7dc7d96e0976"}}, "title": "Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.", "authors": [{"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Yang", "given": "Hong", "initials": "H"}, {"family": "Krishnan", "given": "Shuba", "initials": "S"}, {"family": "Svensson Akusj\u00e4rvi", "given": "Sara", "initials": "S"}, {"family": "Gupta", "given": "Soham", "initials": "S"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Nordqvist", "given": "Hampus", "initials": "H"}, {"family": "Ponnan", "given": "Sivasankaran Munusamy", "initials": "SM"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Treutiger", "given": "Carl Johan", "initials": "CJ"}, {"family": "O'Mahony", "given": "Liam", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U"}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Cell Syst", "issn": "2639-5460", "issn-l": "2405-4712", "volume": "13", "issue": "8", "pages": "665-681.e4"}, "abstract": "The clinical outcome and disease severity in coronavirus disease 2019 (COVID-19) are heterogeneous, and the progression or fatality of the disease cannot be explained by a single factor like age or comorbidities. In this study, we used system-wide network-based system biology analysis using whole blood RNA sequencing, immunophenotyping by flow cytometry, plasma metabolomics, and single-cell-type metabolomics of monocytes to identify the potential determinants of COVID-19 severity at personalized and group levels. Digital cell quantification and immunophenotyping of the mononuclear phagocytes indicated a substantial role in coordinating the immune cells that mediate COVID-19 severity. Stratum-specific and personalized genome-scale metabolic modeling indicated monocarboxylate transporter family genes (e.g., SLC16A6), nucleoside transporter genes (e.g., SLC29A1), and metabolites such as \u03b1-ketoglutarate, succinate, malate, and butyrate could play a crucial role in COVID-19 severity. Metabolic perturbations targeting the central metabolic pathway (TCA cycle) can be an alternate treatment strategy in severe COVID-19.", "doi": "10.1016/j.cels.2022.06.006", "pmid": "35933992", "labels": {"Affinity Proteomics Uppsala": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9263811"}, {"db": "pii", "key": "S2405-4712(22)00276-9"}], "notes": [], "created": "2022-08-19T08:38:32.732Z", "modified": "2025-10-17T13:03:14.718Z"}, {"entity": "publication", "iuid": "8e39a8eda2624cc2bcf0078f26f26f14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e39a8eda2624cc2bcf0078f26f26f14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e39a8eda2624cc2bcf0078f26f26f14"}}, "title": "Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Izabel-Shen", "given": "Dandan", "initials": "D"}, {"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2022-08-15", "journal": {"title": "Microbiome", "issn": "2049-2618", "issn-l": "2049-2618", "volume": "10", "issue": "1", "pages": "126"}, "abstract": "Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea.\n\nThe composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments.\n\nThis study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.", "doi": "10.1186/s40168-022-01321-z", "pmid": "35965333", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9377124"}, {"db": "pii", "key": "10.1186/s40168-022-01321-z"}], "notes": [], "created": "2022-08-19T08:38:28.503Z", "modified": "2024-01-16T13:48:35.232Z"}, {"entity": "publication", "iuid": "0ac98776ee8e49bba2d81056caff401f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ac98776ee8e49bba2d81056caff401f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ac98776ee8e49bba2d81056caff401f"}}, "title": "Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation.", "authors": [{"family": "Liu", "given": "Ruishan", "initials": "R"}, {"family": "Pisco", "given": "Angela Oliveira", "initials": "AO"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Zou", "given": "James", "initials": "J"}], "type": "journal article", "published": "2022-08-15", "journal": {"title": "J. Mol. Biol.", "issn": "1089-8638", "issn-l": "0022-2836", "volume": "434", "issue": "15", "pages": "167606"}, "abstract": "Recent development in inferring RNA velocity from single-cell RNA-seq opens up exciting new vista into developmental lineage and cellular dynamics. However, the estimated velocity only gives a snapshot of how the transcriptome instantaneously changes in individual cells, and it does not provide quantitative predictions and insights about the whole system. In this work, we develop RNA-ODE, a principled computational framework that extends RNA velocity to quantify systems level dynamics and improve single-cell data analysis. We model the gene expression dynamics by an ordinary differential equation (ODE) based formalism. Given a snapshot of gene expression at one time, RNA-ODE is able to predict and extrapolate the expression trajectory of each cell by solving the dynamic equations. Systematic experiments on simulations and on new data from developing brain demonstrate that RNA-ODE substantially improves many aspects of standard single-cell analysis. By leveraging temporal dynamics, RNA-ODE more accurately estimates cell state lineage and pseudo-time compared to previous state-of-the-art methods. It also infers gene regulatory networks and identifies influential genes whose expression changes can decide cell fate. We expect RNA-ODE to be a Swiss army knife that aids many facets of single-cell RNA-seq analysis.", "doi": "10.1016/j.jmb.2022.167606", "pmid": "35489382", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-2836(22)00186-3"}], "notes": [], "created": "2022-08-19T08:37:17.668Z", "modified": "2023-03-06T14:10:33.833Z"}, {"entity": "publication", "iuid": "f5d32b355e2d404eb507d8116fa5b82c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5d32b355e2d404eb507d8116fa5b82c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5d32b355e2d404eb507d8116fa5b82c"}}, "title": "Ageing desexualizes the Drosophila brain transcriptome.", "authors": [{"family": "Malacrin\u00f2", "given": "Antonino", "initials": "A", "orcid": "0000-0002-0811-1229", "researcher": {"href": "https://publications.scilifelab.se/researcher/87bd49ad478444cab6499c1a21842b04.json"}}, {"family": "Brengdahl", "given": "Martin I", "initials": "MI", "orcid": "0000-0002-1052-7274", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e3bb8001b67490ea32b07376f5805cb.json"}}, {"family": "Kimber", "given": "Christopher M", "initials": "CM", "orcid": "0000-0003-4620-0166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f28663cb3a346399397c35b10b2dbf1.json"}}, {"family": "Mital", "given": "Avani", "initials": "A", "orcid": "0000-0003-1443-5737", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1c90b815054825b7f5d6597fe51fa8.json"}}, {"family": "Shenoi", "given": "Vinesh N", "initials": "VN", "orcid": "0000-0003-4318-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/97ad7fddc1894a53876f37218c481ae9.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Friberg", "given": "Urban", "initials": "U", "orcid": "0000-0001-6112-9586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd49b16c2cc641e4b14ef1a14bcad59d.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "issn-l": "0962-8452", "volume": "289", "issue": "1980", "pages": "20221115"}, "abstract": "General evolutionary theory predicts that individuals in low condition should invest less in sexual traits compared to individuals in high condition. Whether this positive association between condition and investment also holds between young (high condition) and senesced (low condition) individuals is however less clear, since elevated investment into reproduction may be beneficial when individuals approach the end of their life. To address how investment into sexual traits changes with age, we study genes with sex-biased expression in the brain, the tissue from which sexual behaviours are directed. Across two distinct populations of Drosophila melanogaster, we find that old brains display fewer sex-biased genes, and that expression of both male-biased and female-biased genes converges towards a sexually intermediate phenotype owing to changes in both sexes with age. We further find that sex-biased genes in general show heightened age-dependent expression in comparison to unbiased genes and that age-related changes in the sexual brain transcriptome are commonly larger in males than females. Our results hence show that ageing causes a desexualization of the fruit fly brain transcriptome and that this change mirrors the general prediction that low condition individuals should invest less in sexual phenotypes.", "doi": "10.1098/rspb.2022.1115", "pmid": "35946149", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9364003"}], "notes": [], "created": "2022-08-23T20:40:19.341Z", "modified": "2024-01-16T13:48:35.419Z"}, {"entity": "publication", "iuid": "9d6ef0ad3fbc4458add397850c87d9d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d6ef0ad3fbc4458add397850c87d9d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d6ef0ad3fbc4458add397850c87d9d8"}}, "title": "A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes.", "authors": [{"family": "Tunstrom", "given": "Kalle", "initials": "K", "orcid": "0000-0002-5285-1531", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd0ddb97d724542b6e7c46f782f3bbd.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}, {"family": "Parmesan", "given": "Camille", "initials": "C"}, {"family": "Singer", "given": "Michael C", "initials": "MC"}, {"family": "Mikheyev", "given": "Alexander S", "initials": "AS"}], "type": "journal article", "published": "2022-08-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "14", "issue": "8", "pages": null}, "abstract": "Insects have been key players in the assessments of biodiversity impacts of anthropogenically driven environmental change, including the evolutionary and ecological impacts of climate change. Populations of Edith's Checkerspot Butterfly (Euphydryas editha) adapt rapidly to diverse environmental conditions, with numerous high-impact studies documenting these dynamics over several decades. However, studies of the underlying genetic bases of these responses have been hampered by missing genomic resources, limiting the ability to connect genomic responses to environmental change. Using a combination of Oxford Nanopore long reads, haplotype merging, HiC scaffolding followed by Illumina polishing, we generated a highly contiguous and complete assembly (contigs n = 142, N50 = 21.2 Mb, total length = 607.8 Mb; BUSCOs n = 5,286, single copy complete = 97.8%, duplicated = 0.9%, fragmented = 0.3%, missing = 1.0%). A total of 98% of the assembled genome was placed into 31 chromosomes, which displayed large-scale synteny with other well-characterized lepidopteran genomes. The E. editha genome, annotation, and functional descriptions now fill a missing gap for one of the leading field-based ecological model systems in North America.", "doi": "10.1093/gbe/evac113", "pmid": "35876165", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9348621"}, {"db": "pii", "key": "6649524"}], "notes": [], "created": "2022-08-19T08:38:20.953Z", "modified": "2024-01-16T13:48:35.474Z"}, {"entity": "publication", "iuid": "6b272f66ea784595a9d1db9edde67b67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6b272f66ea784595a9d1db9edde67b67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6b272f66ea784595a9d1db9edde67b67"}}, "title": "Spatially resolved clonal copy number alterations in benign and malignant tissue.", "authors": [{"family": "Erickson", "given": "Andrew", "initials": "A"}, {"family": "He", "given": "Mengxiao", "initials": "M", "orcid": "0000-0001-5905-8467", "researcher": {"href": "https://publications.scilifelab.se/researcher/79045a6ac62b4f8ea64233619eb6bfc9.json"}}, {"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Marklund", "given": "Maja", "initials": "M", "orcid": "0000-0003-2627-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a238f7adbc242398a46fd24190a2811.json"}}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Kvastad", "given": "Linda", "initials": "L"}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J", "orcid": "0000-0002-1136-7719", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cec49beb1cb4ee09871ef7cfe323396.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Alonso Galicia", "given": "Leire", "initials": "L", "orcid": "0000-0001-8437-1332", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a941bba10fa44d4a5ac841ed50f060f.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Basmaci", "given": "Elisa", "initials": "E"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Rajakumar", "given": "Timothy", "initials": "T"}, {"family": "Doultsinos", "given": "Dimitrios", "initials": "D", "orcid": "0000-0003-0873-9873", "researcher": {"href": "https://publications.scilifelab.se/researcher/91375a3b6b634771ada73458e9f2f2b1.json"}}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Ji", "given": "Andrew L", "initials": "AL", "orcid": "0000-0001-9688-5680", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba3c3c39f53a471cbd699bf4a8d64b23.json"}}, {"family": "Khavari", "given": "Paul A", "initials": "PA", "orcid": "0000-0003-0098-4989", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2aea38b6ba9430cbcfdc23b3190a2ec.json"}}, {"family": "Tarish", "given": "Firaz", "initials": "F"}, {"family": "Tanoglidi", "given": "Anna", "initials": "A"}, {"family": "Maaskola", "given": "Jonas", "initials": "J", "orcid": "0000-0002-6665-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/a615b8e0928f45b083b4d4c8692af424.json"}}, {"family": "Colling", "given": "Richard", "initials": "R", "orcid": "0000-0001-6344-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/e817042b24944db1b2fcf74aee34f4e3.json"}}, {"family": "Mirtti", "given": "Tuomas", "initials": "T"}, {"family": "Hamdy", "given": "Freddie C", "initials": "FC"}, {"family": "Woodcock", "given": "Dan J", "initials": "DJ", "orcid": "0000-0003-0576-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e7fdc16acf4d3c98337e934a1f3433.json"}}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Mills", "given": "Ian G", "initials": "IG", "orcid": "0000-0001-5347-5083", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f24c9f52d047e4bf5c697768bd568e.json"}}, {"family": "Lamb", "given": "Alastair D", "initials": "AD"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "608", "issue": "7922", "pages": "360-367"}, "abstract": "Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics2 to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.", "doi": "10.1038/s41586-022-05023-2", "pmid": "35948708", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Spatial omics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9365699"}, {"db": "pii", "key": "10.1038/s41586-022-05023-2"}], "notes": [], "created": "2022-08-19T08:38:11.036Z", "modified": "2023-10-16T11:27:00.695Z"}, {"entity": "publication", "iuid": "c3b67c44bad84085803c8a248a084eca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3b67c44bad84085803c8a248a084eca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3b67c44bad84085803c8a248a084eca"}}, "title": "Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.", "authors": [{"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Grujcic", "given": "Vesna", "initials": "V", "orcid": "0000-0002-3322-599X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd1ed7a2d7e477d8f8c5a340152b36c.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "John", "given": "Uwe", "initials": "U", "orcid": "0000-0002-1297-4086", "researcher": {"href": "https://publications.scilifelab.se/researcher/76918fd58a374cdcacfe02298e7d29a3.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-7819-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/812b8d6654af4482a308367f052f64c7.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "22", "issue": "6", "pages": "2304-2318"}, "abstract": "High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.", "doi": "10.1111/1755-0998.13623", "pmid": "35437888", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-08-19T08:37:10.426Z", "modified": "2024-01-16T13:48:35.514Z"}, {"entity": "publication", "iuid": "8a917b160092465fb49d2ecc4a7ad428", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a917b160092465fb49d2ecc4a7ad428.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a917b160092465fb49d2ecc4a7ad428"}}, "title": "Mosaic Deletions of Known Genes Explain Skeletal Dysplasias With High and Low Bone Mass.", "authors": [{"family": "Muurinen", "given": "Mari", "initials": "M"}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Tournis", "given": "Symeon", "initials": "S", "orcid": "0000-0002-8301-324X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c929a6b8fcda403db768010385f47629.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Balanika", "given": "Alexia", "initials": "A"}, {"family": "Vastardis", "given": "Heleni", "initials": "H"}, {"family": "Ala-Mello", "given": "Sirpa", "initials": "S"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O", "orcid": "0000-0002-4547-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0614bdc717455b9af64a05ab4aa4aa.json"}}, {"family": "Costantini", "given": "Alice", "initials": "A", "orcid": "0000-0003-1408-9272", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d1ec6874e0c41b8a22cb4c0f3275bec.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "JBMR Plus", "issn": "2473-4039", "issn-l": null, "volume": "6", "issue": "8", "pages": "e10660"}, "abstract": "Mosaicism, a state in which an individual has two or more genetically distinct populations of cells in the body, can be difficult to detect because of either mild or atypical clinical presentation and limitations in the commonly used detection methods. Knowledge of the role of mosaicism is limited in many skeletal disorders, including osteopathia striata with cranial sclerosis (OSCS) and cleidocranial dysplasia (CCD). We used whole-genome sequencing (WGS) with coverage >40\u00d7 to identify the genetic causes of disease in two clinically diagnosed patients. In a female patient with OSCS, we identified a mosaic 7-nucleotide frameshift deletion in exon 2 of AMER1, NM_152424.4:c.855_861del:p.(His285Glnfs*7), affecting 8.3% of the WGS reads. In a male patient with CCD, approximately 34% of the WGS reads harbored a 3710-basepair mosaic deletion, NC_000006.11:g.45514471_45518181del, starting in intron 8 of RUNX2 and terminating in the 3' untranslated region. Droplet digital polymerase chain reaction was used to validate these deletions and quantify the absolute level of mosaicism in each patient. Although constitutional variants in AMER1 and RUNX2 are a known cause of OSCS and CCD, respectively, the mosaic changes here reported have not been described previously. Our study indicates that mosaicism should be considered in unsolved cases of skeletal dysplasia and should be investigated with comprehensive and sensitive detection methods. \u00a9 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.", "doi": "10.1002/jbm4.10660", "pmid": "35991531", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9382864"}, {"db": "pii", "key": "JBM410660"}], "notes": [], "created": "2022-12-19T10:29:57.640Z", "modified": "2023-10-16T11:46:03.533Z"}, {"entity": "publication", "iuid": "d45d0bb1d1394334810204ba11c91173", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d45d0bb1d1394334810204ba11c91173.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d45d0bb1d1394334810204ba11c91173"}}, "title": "Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.", "authors": [{"family": "Rodr\u00edguez", "given": "Juanjo", "initials": "J"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Timonen", "given": "Sari", "initials": "S"}, {"family": "Brugel", "given": "Sonia", "initials": "S"}, {"family": "Skrobonja", "given": "Aleksandra", "initials": "A"}, {"family": "Rowe", "given": "Owen", "initials": "O"}], "type": "journal article", "published": "2022-07-27", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "issn-l": "1664-302X", "volume": "13", "issue": null, "pages": "809166"}, "abstract": "Methylmercury (MeHg) is a potent neurotoxin commonly found in aquatic environments and primarily formed by microbial methylation of inorganic divalent mercury (Hg(II)) under anoxic conditions. Recent evidence, however, points to the production of MeHg also in oxic pelagic waters, but the magnitude and the drivers for this process remain unclear. Here, we performed a controlled experiment testing the hypothesis that inputs of terrestrial dissolved organic matter (tDOM) to coastal waters enhance MeHg formation via increased bacterial activity. Natural brackish seawater from a coastal area of the Baltic Sea was exposed to environmentally relevant levels of Hg(II) and additions of tDOM according to climate change scenarios. MeHg formation was observed to be coupled to elevated bacterial production rates, which, in turn, was linked to input levels of tDOM. The increased MeHg formation was, however, not coupled to any specific change in bacterial taxonomic composition nor to an increased abundance of known Hg(II) methylation genes. Instead, we found that the abundance of genes for the overall bacterial carbon metabolism was higher under increased tDOM additions. The findings of this study may have important ecological implications in a changing global climate by pointing to the risk of increased exposure of MeHg to pelagic biota.", "doi": "10.3389/fmicb.2022.809166", "pmid": "35966696", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9363918"}], "notes": [], "created": "2022-08-19T08:38:24.195Z", "modified": "2023-10-16T11:35:15.857Z"}, {"entity": "publication", "iuid": "6bff612fe3ec481fac4d9121712adcf7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6bff612fe3ec481fac4d9121712adcf7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6bff612fe3ec481fac4d9121712adcf7"}}, "title": "Targeted Chromosome Conformation Capture (HiCap).", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A"}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}], "type": "journal article", "published": "2022-07-23", "journal": {"title": "Methods Mol. Biol.", "issn": "1940-6029", "volume": "2532", "pages": "75-94", "issn-l": "1064-3745"}, "abstract": "Targeted chromosome conformation capture (HiCap) is an experimental method for detecting spatial interactions of genomic features such as promoters and/or enhancers. The protocol first describes the design of sequence capture probes. After that, it provides details on the chromosome conformation capture adapted for next-generation sequencing (Hi-C). Finally, the methodology for coupling Hi-C with sequence capture technology is described.", "doi": "10.1007/978-1-0716-2497-5_5", "pmid": "35867246", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-18T09:46:10.209Z", "modified": "2024-03-18T09:46:10.214Z"}, {"entity": "publication", "iuid": "2d6d346c818547ab92955961b9b6ec68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d6d346c818547ab92955961b9b6ec68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d6d346c818547ab92955961b9b6ec68"}}, "title": "Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.", "authors": [{"family": "Richards", "given": "Mark", "initials": "M", "orcid": "0000-0002-2266-3329", "researcher": {"href": "https://publications.scilifelab.se/researcher/78aeb57529d4440d95ce52bd92470e71.json"}}, {"family": "Nwadozi", "given": "Emmanuel", "initials": "E"}, {"family": "Pal", "given": "Sagnik", "initials": "S", "orcid": "0000-0002-5562-1555", "researcher": {"href": "https://publications.scilifelab.se/researcher/7508e78421d641b2974bf705b6851bc8.json"}}, {"family": "Martinsson", "given": "Pernilla", "initials": "P"}, {"family": "Kaakinen", "given": "Mika", "initials": "M"}, {"family": "Gloger", "given": "Marleen", "initials": "M", "orcid": "0000-0002-3319-7642", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3e99b33a5f04f238d33ddc34398382c.json"}}, {"family": "Sj\u00f6berg", "given": "Elin", "initials": "E", "orcid": "0000-0002-8799-4874", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd51131ccec248aea0bcf013a7da3296.json"}}, {"family": "Koltowska", "given": "Katarzyna", "initials": "K", "orcid": "0000-0002-6841-8900", "researcher": {"href": "https://publications.scilifelab.se/researcher/06a8aeda504340c1af3ab893fd413a65.json"}}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Eklund", "given": "Lauri", "initials": "L", "orcid": "0000-0002-3177-7504", "researcher": {"href": "https://publications.scilifelab.se/researcher/45e9730513144d3384dd2749dc2d3882.json"}}, {"family": "Nordling", "given": "Sofia", "initials": "S"}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L", "orcid": "0000-0003-4275-2000", "researcher": {"href": "https://publications.scilifelab.se/researcher/647e2a349efd4e11827209883e86079b.json"}}], "type": "journal article", "published": "2022-07-21", "journal": {"title": "Elife", "issn": "2050-084X", "issn-l": "2050-084X", "volume": "11", "issue": null, "pages": null}, "abstract": "Dysfunctional and leaky blood vessels resulting from disruption of the endothelial cell (EC) barrier accompanies numerous diseases. The EC barrier is established through endothelial cell tight and adherens junctions. However, the expression pattern and precise contribution of different junctional proteins to the EC barrier is poorly understood. Here, we focus on organs with continuous endothelium to identify structural and functional in vivo characteristics of the EC barrier. Assembly of multiple single-cell RNAseq datasets into a single integrated database revealed the variability and commonalities of EC barrier patterning. Across tissues, Claudin5 exhibited diminishing expression along the arteriovenous axis, correlating with EC barrier integrity. Functional analysis identified tissue-specific differences in leakage properties and response to the leakage agonist histamine. Loss of Claudin5 enhanced histamine-induced leakage in an organotypic and vessel type-specific manner in an inducible, EC-specific, knock-out mouse. Mechanistically, Claudin5 loss left junction ultrastructure unaffected but altered its composition, with concomitant loss of zonula occludens-1 and upregulation of VE-Cadherin expression. These findings uncover the organ-specific organisation of the EC barrier and distinct importance of Claudin5 in different vascular beds, providing insights to modify EC barrier stability in a targeted, organ-specific manner.", "doi": "10.7554/eLife.78517", "pmid": "35861713", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9348850"}, {"db": "pii", "key": "78517"}, {"db": "GEO", "key": "GSE202290"}, {"db": "GEO", "key": "GSE132042"}], "notes": [], "created": "2022-08-19T08:38:34.050Z", "modified": "2024-01-16T13:48:35.673Z"}, {"entity": "publication", "iuid": "c2eb6231b5e54b648bdaf3fb9a000dba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2eb6231b5e54b648bdaf3fb9a000dba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2eb6231b5e54b648bdaf3fb9a000dba"}}, "title": "Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.", "authors": [{"family": "Kuhl", "given": "Heiner", "initials": "H", "orcid": "0000-0001-7623-9227", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3326add41974413be16c8a2bed157f8.json"}}, {"family": "Du", "given": "Kang", "initials": "K", "orcid": "0000-0002-1497-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eda8755c14042289ac7196edeffca01.json"}}, {"family": "Schartl", "given": "Manfred", "initials": "M", "orcid": "0000-0001-9882-5948", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f97783b5013409ebc1a6bd2df5ca92c.json"}}, {"family": "Kalous", "given": "Luk\u00e1\u0161", "initials": "L", "orcid": "0000-0001-5518-1505", "researcher": {"href": "https://publications.scilifelab.se/researcher/c086140440e54f3793c444182f695216.json"}}, {"family": "St\u00f6ck", "given": "Matthias", "initials": "M", "orcid": "0000-0003-4888-8371", "researcher": {"href": "https://publications.scilifelab.se/researcher/83a4dc450751436d9b552ce68da65fd9.json"}}, {"family": "Lamatsch", "given": "Dunja K", "initials": "DK", "orcid": "0000-0002-6023-4381", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f2363dc6d8417b88455ec1aadec818.json"}}], "type": "journal article", "published": "2022-07-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "4092"}, "abstract": "Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.", "doi": "10.1038/s41467-022-31515-w", "pmid": "35835759", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Other": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9283417"}, {"db": "pii", "key": "10.1038/s41467-022-31515-w"}], "notes": [], "created": "2022-08-19T08:38:44.948Z", "modified": "2024-01-16T13:48:35.681Z"}, {"entity": "publication", "iuid": "b476824c8ec54e5687ef3cd3b02390fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b476824c8ec54e5687ef3cd3b02390fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b476824c8ec54e5687ef3cd3b02390fb"}}, "title": "Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.", "authors": [{"family": "Hardt", "given": "Uta", "initials": "U"}, {"family": "Carlberg", "given": "Konstantin", "initials": "K"}, {"family": "Af Klint", "given": "Erik", "initials": "E"}, {"family": "Sahlstr\u00f6m", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "van Vollenhoven", "given": "Annika", "initials": "A"}, {"family": "Hernandez Machado", "given": "Susana", "initials": "S"}, {"family": "Israelsson", "given": "Lena", "initials": "L"}, {"family": "Amara", "given": "Khaled", "initials": "K"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Korotkova", "given": "Marina", "initials": "M"}, {"family": "Karlsson Hedestam", "given": "Gunilla B", "initials": "GB"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Teichmann", "given": "Sarah A", "initials": "SA"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "11876"}, "abstract": "B cells play a significant role in established Rheumatoid Arthritis (RA). However, it is unclear to what extent differentiated B cells are present in joint tissue already at the onset of disease. Here, we studied synovial biopsies (n = 8) captured from untreated patients at time of diagnosis. 3414 index-sorted B cells underwent RNA sequencing and paired tissue pieces were subjected to spatial transcriptomics (n = 4). We performed extensive bioinformatics analyses to dissect the local B cell composition. Select plasma cell immunoglobulin sequences were expressed as monoclonal antibodies and tested by ELISA. Memory and plasma cells were found irrespective of autoantibody status of the patients. Double negative memory B cells were prominent, but did not display a distinct transcriptional profile. The tissue architecture implicate both local B cell maturation via T cell help and plasma cell survival niches with a strong CXCL12-CXCR4 axis. The immunoglobulin sequence analyses revealed clonality between the memory B and plasma cell pools further supporting local maturation. One of the plasma cell-derived antibodies displayed citrulline autoreactivity, demonstrating local autoreactive plasma cell differentiation in joint biopsies captured from untreated early RA. Hence, plasma cell niches are not a consequence of chronic inflammation, but are already present at the time of diagnosis.", "doi": "10.1038/s41598-022-15293-5", "pmid": "35831338", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9279471"}, {"db": "pii", "key": "10.1038/s41598-022-15293-5"}], "notes": [], "created": "2022-08-19T08:38:18.413Z", "modified": "2024-01-16T13:48:35.776Z"}, {"entity": "publication", "iuid": "26b36e84d7ee4479848b114b7c51ba21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26b36e84d7ee4479848b114b7c51ba21"}}, "title": "An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.", "authors": [{"family": "Ballarino", "given": "Roberto", "initials": "R", "orcid": "0000-0001-7812-0940", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb720f25876d45c39b9dad1b4b48a6fa.json"}}, {"family": "Bouwman", "given": "Britta A M", "initials": "BAM", "orcid": "0000-0002-9827-9497", "researcher": {"href": "https://publications.scilifelab.se/researcher/7933c49c5e6448408159ddb654286127.json"}}, {"family": "Agostini", "given": "Federico", "initials": "F", "orcid": "0000-0002-5453-2737", "researcher": {"href": "https://publications.scilifelab.se/researcher/a21ea8b7e9a5427eb0e48a822c840b8b.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Diekmann", "given": "Constantin", "initials": "C", "orcid": "0000-0002-4779-3541", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc495c18087429f81dd51007ffe1582.json"}}, {"family": "Wernersson", "given": "Erik", "initials": "E", "orcid": "0000-0003-4778-1660", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0de6d4af244cec84bbe8c1240d89ae.json"}}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "dataset", "published": "2022-07-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "9", "issue": "1", "pages": "400"}, "abstract": "Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.", "doi": "10.1038/s41597-022-01508-x", "pmid": "35821502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9276747"}, {"db": "pii", "key": "10.1038/s41597-022-01508-x"}], "notes": [], "created": "2022-08-19T08:38:43.514Z", "modified": "2023-10-16T11:44:09.152Z"}, {"entity": "publication", "iuid": "295946d0d80a471e994050ec989a80e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/295946d0d80a471e994050ec989a80e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/295946d0d80a471e994050ec989a80e9"}}, "title": "FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees.", "authors": [{"family": "Andr\u00e9", "given": "Domenique", "initials": "D"}, {"family": "Marcon", "given": "Alice", "initials": "A"}, {"family": "Lee", "given": "Keh Chien", "initials": "KC"}, {"family": "Goretti", "given": "Daniela", "initials": "D"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Schmid", "given": "Markus", "initials": "M"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}], "type": "journal article", "published": "2022-07-11", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "13", "pages": "2988-2996.e4"}, "abstract": "In temperate and boreal regions, perennials adapt their annual growth cycle to the change of seasons. These adaptations ensure survival in harsh environmental conditions, allowing growth at different latitudes and altitudes, and are therefore tightly regulated. Populus tree species cease growth and form terminal buds in autumn when photoperiod falls below a certain threshold.1 This is followed by establishment of dormancy and cold hardiness over the winter. At the center of the photoperiodic pathway in Populus is the gene FLOWERING LOCUS T2 (FT2), which is expressed during summer and harbors significant SNPs in its locus associated with timing of bud set.1-4 The paralogous gene FT1, on the other hand, is hyper-induced in chilling buds during winter.3,5 Even though its function is so far unknown, it has been suggested to be involved in the regulation of flowering and the release of winter dormancy.3,5 In this study, we employ CRISPR-Cas9-mediated gene editing to individually study the function of the FT-like genes in Populus trees. We show that while FT2 is required for vegetative growth during spring and summer and regulates the entry into dormancy, expression of FT1 is absolutely required for bud flush in spring. Gene expression profiling suggests that this function of FT1 is linked to the release of winter dormancy rather than to the regulation of bud flush per se. These data show how FT duplication and sub-functionalization have allowed Populus trees to regulate two completely different and major developmental control points during the yearly growth cycle.", "doi": "10.1016/j.cub.2022.05.023", "pmid": "35660141", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(22)00782-5"}], "notes": [], "created": "2022-08-19T08:38:06.251Z", "modified": "2024-01-16T13:48:35.826Z"}, {"entity": "publication", "iuid": "3e65ed75308b49efab3cff693834b734", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e65ed75308b49efab3cff693834b734.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e65ed75308b49efab3cff693834b734"}}, "title": "Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.", "authors": [{"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Faure", "given": "Louis", "initials": "L", "orcid": "0000-0003-4621-586X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbf218e53c854d69a1b474a61480c33f.json"}}, {"family": "Uhl", "given": "Phoebe", "initials": "P", "orcid": "0000-0002-5521-7261", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed69ade5f1bc491385c66f6e9df66adf.json"}}, {"family": "Fontanet", "given": "Paula", "initials": "P", "orcid": "0000-0002-5324-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe102480cb7458a941fc70fe7f5cb9b.json"}}, {"family": "Filova", "given": "Iva", "initials": "I"}, {"family": "Pavlinkova", "given": "Gabriela", "initials": "G"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}, {"family": "Lallemend", "given": "Francois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}], "type": "journal article", "published": "2022-07-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3878"}, "abstract": "Different types of spiral ganglion neurons (SGNs) are essential for auditory perception by transmitting complex auditory information from hair cells (HCs) to the brain. Here, we use deep, single cell transcriptomics to study the molecular mechanisms that govern their identity and organization in mice. We identify a core set of temporally patterned genes and gene regulatory networks that may contribute to the diversification of SGNs through sequential binary decisions and demonstrate a role for NEUROD1 in driving specification of a Ic-SGN phenotype. We also find that each trajectory of the decision tree is defined by initial co-expression of alternative subtype molecular controls followed by gradual shifts toward cell fate resolution. Finally, analysis of both developing SGN and HC types reveals cell-cell signaling potentially playing a role in the differentiation of SGNs. Our results indicate that SGN identities are drafted prior to birth and reveal molecular principles that shape their differentiation and will facilitate studies of their development, physiology, and dysfunction.", "doi": "10.1038/s41467-022-31580-1", "pmid": "35790771", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9256748"}, {"db": "pii", "key": "10.1038/s41467-022-31580-1"}], "notes": [], "created": "2022-08-19T08:38:31.468Z", "modified": "2023-10-16T11:38:03.441Z"}, {"entity": "publication", "iuid": "e654709c79ea4b1aae048dc238ff4283", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e654709c79ea4b1aae048dc238ff4283.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e654709c79ea4b1aae048dc238ff4283"}}, "title": "Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.", "authors": [{"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Baltar", "given": "Federico", "initials": "F"}, {"family": "Israelsson", "given": "Stina", "initials": "S"}, {"family": "Fridolfsson", "given": "Emil", "initials": "E"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2022-07-05", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "issn-l": "1664-302X", "volume": "13", "issue": null, "pages": "834675"}, "abstract": "Although free-living (FL) and particle-attached (PA) bacteria are recognized as ecologically distinct compartments of marine microbial food-webs, few, if any, studies have determined their dynamics in abundance, function (production, respiration and substrate utilization) and taxonomy over a yearly cycle. In the Baltic Sea, abundance and production of PA bacteria (defined as the size-fraction >3.0 \u03bcm) peaked over 3 months in summer (6 months for FL bacteria), largely coinciding with blooms of Chitinophagales (Bacteroidetes). Pronounced changes in the growth efficiency (range 0.05-0.27) of FL bacteria (defined as the size-fraction <3.0 \u03bcm) indicated the magnitude of seasonal variability of ecological settings bacteria experience. Accordingly, 16S rRNA gene analyses of bacterial community composition uncovered distinct correlations between taxa, environmental variables and metabolisms, including Firmicutes associated with elevated hydrolytic enzyme activity in winter and Verrucomicrobia with utilization of algal-derived substrates during summer. Further, our results suggested a substrate-controlled succession in the PA fraction, from Bacteroidetes using polymers to Actinobacteria and Betaproteobacteria using monomers across the spring to autumn phytoplankton bloom transition. Collectively, our findings emphasize pronounced seasonal changes in both the composition of the bacterial community in the PA and FL size-fractions and their contribution to organic matter utilization and carbon cycling. This is important for interpreting microbial ecosystem function-responses to natural and human-induced environmental changes.", "doi": "10.3389/fmicb.2022.834675", "pmid": "36212867", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9533715"}], "notes": [], "created": "2022-12-19T10:35:56.143Z", "modified": "2023-10-16T12:12:53.982Z"}, {"entity": "publication", "iuid": "8d94f67c6d20452f85a77b9b0d1ab4e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d94f67c6d20452f85a77b9b0d1ab4e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d94f67c6d20452f85a77b9b0d1ab4e6"}}, "title": "High-throughput muscle fiber typing from RNA sequencing data.", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Santel", "given": "Malgorzata", "initials": "M"}, {"family": "Parikh", "given": "Hemang M", "initials": "HM"}, {"family": "Ekstr\u00f6m", "given": "Ola", "initials": "O"}, {"family": "Camp", "given": "Gray J", "initials": "GJ"}, {"family": "Miyamoto-Mikami", "given": "Eri", "initials": "E"}, {"family": "Str\u00f6m", "given": "Kristoffer", "initials": "K"}, {"family": "Mir", "given": "Bilal Ahmad", "initials": "BA"}, {"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D"}, {"family": "Lehtovirta", "given": "Mikko", "initials": "M"}, {"family": "Kobayashi", "given": "Hiroyuki", "initials": "H"}, {"family": "Kakigi", "given": "Ryo", "initials": "R"}, {"family": "Naito", "given": "Hisashi", "initials": "H"}, {"family": "Eriksson", "given": "Karl-Fredrik", "initials": "KF"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Fuku", "given": "Noriyuki", "initials": "N"}, {"family": "Treutlein", "given": "Barbara", "initials": "B"}, {"family": "P\u00e4\u00e4bo", "given": "Svante", "initials": "S"}, {"family": "Hansson", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2022-07-02", "journal": {"title": "Skelet Muscle", "issn": "2044-5040", "issn-l": null, "volume": "12", "issue": "1", "pages": "16"}, "abstract": "Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. Here, we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for a larger number of individuals to be tested.\n\nBy using single-nuclei RNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPase staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22).\n\nThe correlation between the sequencing-based method and the other two were rATPas = 0.44 [0.13-0.67], [95% CI], and rmyosin = 0.83 [0.61-0.93], with p = 5.70 \u00d7 10-3 and 2.00 \u00d7 10-6, respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of ~ 10,000 paired-end reads.\n\nThis new method ( https://github.com/OlaHanssonLab/PredictFiberType ) consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor-efficient way. It is now feasible to study the association between fiber type distribution and e.g. health outcomes in large well-powered studies.", "doi": "10.1186/s13395-022-00299-4", "pmid": "35780170", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9250227"}, {"db": "pii", "key": "10.1186/s13395-022-00299-4"}], "notes": [], "created": "2022-08-08T11:24:18.233Z", "modified": "2023-10-16T11:37:02.132Z"}, {"entity": "publication", "iuid": "a72cb32990a74c7e89f0d8c5a229cf56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a72cb32990a74c7e89f0d8c5a229cf56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a72cb32990a74c7e89f0d8c5a229cf56"}}, "title": "Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden.", "authors": [{"family": "Ellerstrand", "given": "Simon Jacobsen", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Choudhury", "given": "Shruti", "initials": "S"}, {"family": "Svensson", "given": "Kajsa", "initials": "K"}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}, {"family": "Kirkeby", "given": "Carsten", "initials": "C", "orcid": "0000-0001-9292-5526", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5e9edff945441609746525fdfc2d275.json"}}, {"family": "Powell", "given": "Daniel", "initials": "D"}, {"family": "Schlyter", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-1244-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/38df140cdd0e4a1693da808131833114.json"}}, {"family": "J\u00f6nsson", "given": "Anna Maria", "initials": "AM", "orcid": "0000-0003-2938-4725", "researcher": {"href": "https://publications.scilifelab.se/researcher/680836380a394bcdb00036fa3a6632da.json"}}, {"family": "Brydegaard", "given": "Mikkel", "initials": "M", "orcid": "0000-0003-0586-664X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b87150cf4c574f10acb2265d508dba8b.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Runemark", "given": "Anna", "initials": "A", "orcid": "0000-0002-8976-5530", "researcher": {"href": "https://publications.scilifelab.se/researcher/e914e2d1ccbd4d35ae574187762ae01f.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "12", "issue": "7", "pages": "e9078"}, "abstract": "The Eurasian spruce bark beetle, Ips typographus, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few kilometers. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in I. typographus typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of I. typographus in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Str\u00f6msund (63\u00b0 46' 8\u2033 N) in the north to Nyteboda (56\u00b0 8' 50\u2033 N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (F ST) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of I. typographus in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.", "doi": "10.1002/ece3.9078", "pmid": "35822111", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9260063"}, {"db": "pii", "key": "ECE39078"}], "notes": [], "created": "2022-08-19T08:38:39.655Z", "modified": "2024-01-16T13:48:35.960Z"}, {"entity": "publication", "iuid": "56262ad49b494fa8b107ecbb3ebdfbdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56262ad49b494fa8b107ecbb3ebdfbdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56262ad49b494fa8b107ecbb3ebdfbdf"}}, "title": "Grey wolf genomic history reveals a dual ancestry of dogs.", "authors": [{"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0002-4096-9268", "researcher": {"href": "https://publications.scilifelab.se/researcher/77429e0da9574e9ab3d1a14ae5dbb803.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Taron", "given": "Ulrike H", "initials": "UH"}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Pfrengle", "given": "Saskia", "initials": "S"}, {"family": "Cassatt-Johnstone", "given": "Molly", "initials": "M"}, {"family": "Lebrasseur", "given": "Oph\u00e9lie", "initials": "O", "orcid": "0000-0003-0687-8538", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f100bd635446739f54bcabbf1840bc.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}, {"family": "Fernandes", "given": "Daniel M", "initials": "DM", "orcid": "0000-0002-7434-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9a0a0289d9a46518acfa124747e38bf.json"}}, {"family": "Ollivier", "given": "Morgane", "initials": "M", "orcid": "0000-0002-8361-4221", "researcher": {"href": "https://publications.scilifelab.se/researcher/0190489b1648467889a31b4cb6c61b15.json"}}, {"family": "Speidel", "given": "Leo", "initials": "L"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Ramos-Madrigal", "given": "Jazmin", "initials": "J", "orcid": "0000-0002-1661-7991", "researcher": {"href": "https://publications.scilifelab.se/researcher/31e1ca5ba0dc44fbbb8106beab9e4e44.json"}}, {"family": "Feuerborn", "given": "Tatiana R", "initials": "TR", "orcid": "0000-0003-1610-3402", "researcher": {"href": "https://publications.scilifelab.se/researcher/13118af643b44e6a9a8ecb0bbc6f4613.json"}}, {"family": "Reiter", "given": "Ella", "initials": "E"}, {"family": "Gretzinger", "given": "Joscha", "initials": "J"}, {"family": "M\u00fcnzel", "given": "Susanne C", "initials": "SC"}, {"family": "Swali", "given": "Pooja", "initials": "P"}, {"family": "Conard", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0002-4633-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/07e1c44c0d3043e7a728e597638227d6.json"}}, {"family": "Car\u00f8e", "given": "Christian", "initials": "C"}, {"family": "Haile", "given": "James", "initials": "J", "orcid": "0000-0002-8521-8337", "researcher": {"href": "https://publications.scilifelab.se/researcher/253913f4bc03438fb7e5c075014d2f6e.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Baumann", "given": "Chris", "initials": "C", "orcid": "0000-0002-1001-8621", "researcher": {"href": "https://publications.scilifelab.se/researcher/24d6abbf7c5e49e8b2174f9524d78a34.json"}}, {"family": "Benecke", "given": "Norbert", "initials": "N"}, {"family": "Bocherens", "given": "Herv\u00e9", "initials": "H", "orcid": "0000-0002-0494-0126", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d9c075dbc01496eb0d6aa417d7d4f77.json"}}, {"family": "Brace", "given": "Selina", "initials": "S", "orcid": "0000-0003-2126-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/476fbd04aaaf453f943f5eea976c3cff.json"}}, {"family": "Carden", "given": "Ruth F", "initials": "RF"}, {"family": "Drucker", "given": "Doroth\u00e9e G", "initials": "DG", "orcid": "0000-0003-0854-4371", "researcher": {"href": "https://publications.scilifelab.se/researcher/1812d1c5ae4e469ca33dd7011ff71d6c.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Gasparik", "given": "Mih\u00e1ly", "initials": "M"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Grigoriev", "given": "Semyon", "initials": "S"}, {"family": "Groves", "given": "Pam", "initials": "P"}, {"family": "Hertwig", "given": "Stefan T", "initials": "ST"}, {"family": "Ivanova", "given": "Varvara V", "initials": "VV"}, {"family": "Janssens", "given": "Luc", "initials": "L"}, {"family": "Jennings", "given": "Richard P", "initials": "RP", "orcid": "0000-0001-9996-7518", "researcher": {"href": "https://publications.scilifelab.se/researcher/155126141b5a42f7ae00b1cb94869cc6.json"}}, {"family": "Kasparov", "given": "Aleksei K", "initials": "AK"}, {"family": "Kirillova", "given": "Irina V", "initials": "IV"}, {"family": "Kurmaniyazov", "given": "Islam", "initials": "I"}, {"family": "Kuzmin", "given": "Yaroslav V", "initials": "YV", "orcid": "0000-0002-4512-2269", "researcher": {"href": "https://publications.scilifelab.se/researcher/1326bb181c944b00a73d940f87ddf298.json"}}, {"family": "Kosintsev", "given": "Pavel A", "initials": "PA"}, {"family": "L\u00e1zni\u010dkov\u00e1-Galetov\u00e1", "given": "Martina", "initials": "M"}, {"family": "Leduc", "given": "Charlotte", "initials": "C"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Nussbaumer", "given": "Marc", "initials": "M"}, {"family": "O'Drisceoil", "given": "C\u00f3il\u00edn", "initials": "C"}, {"family": "Orlando", "given": "Ludovic", "initials": "L", "orcid": "0000-0003-3936-1850", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca463500fb034711b6200d5b611e4c1d.json"}}, {"family": "Outram", "given": "Alan", "initials": "A", "orcid": "0000-0003-3360-089X", "researcher": {"href": "https://publications.scilifelab.se/researcher/72994df1ee5b4b8495743cb6e0c7d7c8.json"}}, {"family": "Pavlova", "given": "Elena Y", "initials": "EY"}, {"family": "Perri", "given": "Angela R", "initials": "AR", "orcid": "0000-0002-4349-1060", "researcher": {"href": "https://publications.scilifelab.se/researcher/377cc5152a114643a10e7a649782786e.json"}}, {"family": "Pilot", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Pitulko", "given": "Vladimir V", "initials": "VV"}, {"family": "Plotnikov", "given": "Valerii V", "initials": "VV", "orcid": "0000-0002-4870-3499", "researcher": {"href": "https://publications.scilifelab.se/researcher/378b10136be74923bff019375f5d6c91.json"}}, {"family": "Protopopov", "given": "Albert V", "initials": "AV"}, {"family": "Rehazek", "given": "Andr\u00e9", "initials": "A"}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Seguin-Orlando", "given": "Andaine", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Verjux", "given": "Christian", "initials": "C"}, {"family": "Zaibert", "given": "Victor F", "initials": "VF"}, {"family": "Zazula", "given": "Grant", "initials": "G"}, {"family": "Cromb\u00e9", "given": "Philippe", "initials": "P", "orcid": "0000-0002-4198-8057", "researcher": {"href": "https://publications.scilifelab.se/researcher/2891aed57f0a41ad9e4e567a991bda89.json"}}, {"family": "Hansen", "given": "Anders J", "initials": "AJ", "orcid": "0000-0002-1890-2702", "researcher": {"href": "https://publications.scilifelab.se/researcher/559502adc31544c68eeb97e52c51ff81.json"}}, {"family": "Willerslev", "given": "Eske", "initials": "E"}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA", "orcid": "0000-0003-0291-7819", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7aebc9371db4bbcb03eaef58473fc3e.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Pinhasi", "given": "Ron", "initials": "R", "orcid": "0000-0003-1629-8131", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8eedf480ae494d9e6249ec58dd1867.json"}}, {"family": "Schuenemann", "given": "Verena J", "initials": "VJ"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Krause", "given": "Johannes", "initials": "J", "orcid": "0000-0001-9144-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2416e8bd2bfb4aa3988f4a37fca2de2e.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}], "type": "historical article", "published": "2022-07-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "607", "issue": "7918", "pages": "313-320"}, "abstract": "The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.", "doi": "10.1038/s41586-022-04824-9", "pmid": "35768506", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9279150"}, {"db": "pii", "key": "10.1038/s41586-022-04824-9"}], "notes": [], "created": "2022-08-19T08:38:22.331Z", "modified": "2024-01-16T13:48:35.979Z"}, {"entity": "publication", "iuid": "52d17bcd67b34305a5fe00573dccf416", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52d17bcd67b34305a5fe00573dccf416.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52d17bcd67b34305a5fe00573dccf416"}}, "title": "Genomic dynamics of brown trout populations released to a novel environment.", "authors": [{"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "issn-l": "2045-7758", "volume": "12", "issue": "7", "pages": "e9050"}, "abstract": "Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.", "doi": "10.1002/ece3.9050", "pmid": "35813906", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9251865"}, {"db": "pii", "key": "ECE39050"}], "notes": [], "created": "2022-08-01T12:29:56.905Z", "modified": "2024-01-16T13:48:36.012Z"}, {"entity": "publication", "iuid": "8b30b2a0bc7d4450858a511d977b85f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b30b2a0bc7d4450858a511d977b85f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b30b2a0bc7d4450858a511d977b85f6"}}, "title": "Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy.", "authors": [{"family": "Novotny", "given": "Andreas", "initials": "A"}, {"family": "Jan", "given": "Kinlan Mehdi Goulwen", "initials": "KMG"}, {"family": "Dierking", "given": "Jan", "initials": "J"}, {"family": "Winder", "given": "Monika", "initials": "M"}], "type": "journal article", "published": "2022-06-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "10952"}, "abstract": "Marine communities undergo rapid changes related to human-induced ecosystem pressures. The Baltic Sea pelagic food web has experienced several regime shifts during the past century, resulting in a system where competition between the dominant planktivorous mesopredatory clupeid fish species herring (Clupea harengus) and sprat (Sprattus sprattus) and the rapidly increasing stickleback (Gasterosteus aculeatus) population is assumed to be high. Here, we investigate diet overlap between these three planktivorous fishes in the Baltic Sea, utilizing DNA metabarcoding on the 18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results show niche differentiation between clupeids and stickleback, and highlight that rotifers play an important role in this pattern, as a resource that is not being used by the clupeids nor by other zooplankton in spring. We further show that all the diet assessment methods used in this study are consistent, but also that DNA metabarcoding describes the plankton-fish link at the highest taxonomic resolution. This study suggests that rotifers and other understudied soft-bodied prey may have an important function in the pelagic food web and that the growing population of pelagic stickleback may be supported by the open feeding niche offered by the rotifers.", "doi": "10.1038/s41598-022-15116-7", "pmid": "35768563", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9242992"}, {"db": "pii", "key": "10.1038/s41598-022-15116-7"}, {"db": "Dryad", "key": "10.5061/dryad.vq83bk3vk"}], "notes": [], "created": "2022-08-19T08:38:41.032Z", "modified": "2024-01-16T13:48:36.049Z"}, {"entity": "publication", "iuid": "ed2e8e4e4607450599075cb68f775f98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed2e8e4e4607450599075cb68f775f98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed2e8e4e4607450599075cb68f775f98"}}, "title": "Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation.", "authors": [{"family": "Petrus-Reurer", "given": "Sandra", "initials": "S"}, {"family": "Lederer", "given": "Alex R", "initials": "AR"}, {"family": "Baqu\u00e9-Vidal", "given": "Laura", "initials": "L"}, {"family": "Douagi", "given": "Iyadh", "initials": "I"}, {"family": "Pannagel", "given": "Belinda", "initials": "B"}, {"family": "Khven", "given": "Irina", "initials": "I"}, {"family": "Aronsson", "given": "Monica", "initials": "M"}, {"family": "Bartuma", "given": "Hammurabi", "initials": "H"}, {"family": "Wagner", "given": "Magdalena", "initials": "M"}, {"family": "Wrona", "given": "Andreas", "initials": "A"}, {"family": "Efstathopoulos", "given": "Paschalis", "initials": "P"}, {"family": "Jaberi", "given": "Elham", "initials": "E"}, {"family": "Willenbrock", "given": "Hanni", "initials": "H"}, {"family": "Shimizu", "given": "Yutaka", "initials": "Y"}, {"family": "Villaescusa", "given": "J Carlos", "initials": "JC"}, {"family": "Andr\u00e9", "given": "Helder", "initials": "H"}, {"family": "Sundstr\u04e7m", "given": "Erik", "initials": "E"}, {"family": "Bhaduri", "given": "Aparna", "initials": "A"}, {"family": "Kriegstein", "given": "Arnold", "initials": "A"}, {"family": "Kvanta", "given": "Anders", "initials": "A"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2022-06-14", "journal": {"title": "Stem Cell Reports", "issn": "2213-6711", "issn-l": "2213-6711", "volume": "17", "issue": "6", "pages": "1458-1475"}, "abstract": "Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, a detailed mapping of transient cellular states during in vitro differentiation has not been performed. Here, we conduct single-cell transcriptomic profiling of an hESC-RPE differentiation protocol that has been developed for clinical use. Differentiation progressed through a culture diversification recapitulating early embryonic development, whereby cells rapidly acquired a rostral embryo patterning signature before converging toward the RPE lineage. At intermediate steps, we identified and examined the potency of an NCAM1+ retinal progenitor population and showed the ability of the protocol to suppress non-RPE fates. We demonstrated that the method produces a pure RPE pool capable of maturing further after subretinal transplantation in a large-eyed animal model. Our evaluation of hESC-RPE differentiation supports the development of safe and efficient pluripotent stem cell-based therapies for AMD.", "doi": "10.1016/j.stemcr.2022.05.005", "pmid": "35705015", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9214069"}, {"db": "pii", "key": "S2213-6711(22)00257-0"}], "notes": [], "created": "2022-08-19T08:38:01.135Z", "modified": "2023-10-12T12:29:34.915Z"}, {"entity": "publication", "iuid": "a3fdcb354f53401681344e220de54fce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3fdcb354f53401681344e220de54fce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3fdcb354f53401681344e220de54fce"}}, "title": "Long-Term Warming of Baltic Sea Coastal Waters Affects Bacterial Communities in Bottom Water and Sediments Differently.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Hendrycks", "given": "Wouter", "initials": "W"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Forsman", "given": "Anders", "initials": "A"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2022-06-10", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "issn-l": "1664-302X", "volume": "13", "issue": null, "pages": "873281"}, "abstract": "Coastal marine ecosystems are some of the most diverse natural habitats while being highly vulnerable in the face of climate change. The combination of anthropogenic influence from land and ongoing climate change will likely have severe effects on the environment, but the precise response remains uncertain. This study compared an unaffected \"control\" Baltic Sea bay to a \"heated\" bay that has undergone artificial warming from cooling water release from a nuclear power plant for ~50 years. This heated the water in a similar degree to IPCC SSP5-8.5 predictions by 2100 as natural systems to study temperature-related climate change effects. Bottom water and surface sediment bacterial communities and their biogeochemical processes were investigated to test how future coastal water warming alters microbial communities; shifts seasonal patterns, such as increased algae blooming; and influences nutrient and energy cycling, including elevated respiration rates. 16S rRNA gene amplicon sequencing and geochemical parameters demonstrated that heated bay bottom water bacterial communities were influenced by increased average temperatures across changing seasons, resulting in an overall Shannon's H diversity loss and shifts in relative abundances. In contrast, Shannon's diversity increased in the heated surface sediments. The results also suggested a trend toward smaller-sized microorganisms within the heated bay bottom waters, with a 30% increased relative abundance of small size picocyanobacteria in the summer (June). Furthermore, bacterial communities in the heated bay surface sediment displayed little seasonal variability but did show potential changes of long-term increased average temperature in the interplay with related effects on bottom waters. Finally, heated bay metabolic gene predictions from the 16S rRNA gene sequences suggested raised anaerobic processes closer to the sediment-water interface. In conclusion, climate change will likely alter microbial seasonality and diversity, leading to prolonged and increased algae blooming and elevated respiration rates within coastal waters.", "doi": "10.3389/fmicb.2022.873281", "pmid": "35755995", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9226639"}], "notes": [], "created": "2022-08-19T08:37:50.580Z", "modified": "2024-01-16T13:48:36.152Z"}, {"entity": "publication", "iuid": "fc535be61b6b43f8869dd1955c2d0546", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc535be61b6b43f8869dd1955c2d0546.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc535be61b6b43f8869dd1955c2d0546"}}, "title": "Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.", "authors": [{"family": "Suarez", "given": "Carolina", "initials": "C", "orcid": "0000-0001-5988-4048", "researcher": {"href": "https://publications.scilifelab.se/researcher/86cadb16f7cf45eca8030af1a8ae860e.json"}}, {"family": "Sedlacek", "given": "Christopher J", "initials": "CJ"}, {"family": "Gustavsson", "given": "David J I", "initials": "DJI"}, {"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Modin", "given": "Oskar", "initials": "O", "orcid": "0000-0002-9232-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cfa2dd97cc472c9307498a65b5a8c6.json"}}, {"family": "Hermansson", "given": "Malte", "initials": "M"}, {"family": "Persson", "given": "Frank", "initials": "F", "orcid": "0000-0002-0269-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/40290cae1a7e44c1939801323653b31c.json"}}], "type": "journal article", "published": "2022-06-08", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "issn-l": "2055-5008", "volume": "8", "issue": "1", "pages": "47"}, "abstract": "The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.", "doi": "10.1038/s41522-022-00308-w", "pmid": "35676296", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9178042"}, {"db": "pii", "key": "10.1038/s41522-022-00308-w"}], "notes": [], "created": "2022-08-19T08:38:09.681Z", "modified": "2024-01-16T13:48:36.210Z"}, {"entity": "publication", "iuid": "1263db35dcf5464c8840a71f59c535e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1263db35dcf5464c8840a71f59c535e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1263db35dcf5464c8840a71f59c535e6"}}, "title": "Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.", "authors": [{"family": "Srigyan", "given": "Megha", "initials": "M"}, {"family": "Bol\u00edvar", "given": "H\u00e9ctor", "initials": "H", "orcid": "0000-0001-5898-643X", "researcher": {"href": "https://publications.scilifelab.se/researcher/acff178f29e34a368b3f1c0105d473b7.json"}}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I", "orcid": "0000-0001-9724-9977", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b02b033776f4758acc477c75e4ec1ed.json"}}, {"family": "Santana", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9615-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a4f0fc23b847b98e0d57d22a8a756d.json"}}, {"family": "Petersen", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3882-0867", "researcher": {"href": "https://publications.scilifelab.se/researcher/69701b12d455487a9dd1ab55f9904327.json"}}, {"family": "Iriarte", "given": "Eneko", "initials": "E", "orcid": "0000-0001-8365-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/112f0c5761e84deea89b2b7cb68521ce.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "Mora", "given": "Alice", "initials": "A", "orcid": "0000-0002-0313-8545", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ca97200bd0442c3a9d41b84e57c448e.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Abdo", "given": "Khaled", "initials": "K"}, {"family": "Braemer", "given": "Frank", "initials": "F"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Iba\u00f1ez", "given": "Juan Jos\u00e9", "initials": "JJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}], "type": "journal article", "published": "2022-06-07", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "554"}, "abstract": "The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices).", "doi": "10.1038/s42003-022-03508-4", "pmid": "35672445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9174286"}, {"db": "pii", "key": "10.1038/s42003-022-03508-4"}], "notes": [], "created": "2022-08-19T08:37:53.525Z", "modified": "2024-01-16T13:48:36.218Z"}, {"entity": "publication", "iuid": "974ebae89bc14ac6bd30ac79677563c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/974ebae89bc14ac6bd30ac79677563c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/974ebae89bc14ac6bd30ac79677563c6"}}, "title": "Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis.", "authors": [{"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Pohl", "given": "Fabio", "initials": "F"}, {"family": "Langseth", "given": "Christoffer Mattsson", "initials": "CM"}, {"family": "Kukanja", "given": "Petra", "initials": "P"}, {"family": "Lee", "given": "Hower", "initials": "H"}, {"family": "Albiach", "given": "Alejandro Mossi", "initials": "AM"}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal article", "published": "2022-06-06", "journal": {"title": "Dev. Cell", "issn": "1878-1551", "issn-l": "1534-5807", "volume": "57", "issue": "11", "pages": "1421-1436.e5"}, "abstract": "Oligodendrogenesis in the human central nervous system has been observed mainly at the second trimester of gestation, a much later developmental stage compared to oligodendrogenesis in mice. Here, we characterize the transcriptomic neural diversity in the human forebrain at post-conception weeks (PCW) 8-10. Using single-cell RNA sequencing, we find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level through the use of single-cell ATAC-seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of 50 key genes through the use of in situ sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mice and humans and describe regulatory mechanisms involved in human OPC specification.", "doi": "10.1016/j.devcel.2022.04.016", "pmid": "35523173", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1534-5807(22)00282-9"}], "notes": [], "created": "2022-08-19T08:37:41.778Z", "modified": "2025-10-17T13:02:17.519Z"}, {"entity": "publication", "iuid": "8688bf4021944174a60cf4a78486b2ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8688bf4021944174a60cf4a78486b2ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8688bf4021944174a60cf4a78486b2ce"}}, "title": "Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.", "authors": [{"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78aae6139714fa3ae8221f3fb380b5a.json"}}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/82499805c5c24c46b8c2ec6427345c89.json"}}, {"family": "Adler", "given": "Andrew F", "initials": "AF"}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M"}, {"family": "van Lunteren", "given": "Josina Anna", "initials": "JA"}, {"family": "Nolbrant", "given": "Sara", "initials": "S", "orcid": "0000-0003-2184-1741", "researcher": {"href": "https://publications.scilifelab.se/researcher/91ab50f5e5874992a0703470230a8462.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Vasylovska", "given": "Svitlana", "initials": "S", "orcid": "0000-0003-0682-3449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e24070d9f82243b8a3159739b054aa90.json"}}, {"family": "Yoshitake", "given": "Takashi", "initials": "T"}, {"family": "Kehr", "given": "Jan", "initials": "J"}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M", "orcid": "0000-0003-1658-1631", "researcher": {"href": "https://publications.scilifelab.se/researcher/88931dd9e39c48e2820b89080c3945ad.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a093b1609b74f74a8a8546f02946782.json"}}], "type": "journal article", "published": "2022-06-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "3046"}, "abstract": "Stem cell therapies for Parkinson's disease (PD) have entered first-in-human clinical trials using a set of technically related methods to produce mesencephalic dopamine (mDA) neurons from human pluripotent stem cells (hPSCs). Here, we outline an approach for high-yield derivation of mDA neurons that principally differs from alternative technologies by utilizing retinoic acid (RA) signaling, instead of WNT and FGF8 signaling, to specify mesencephalic fate. Unlike most morphogen signals, where precise concentration determines cell fate, it is the duration of RA exposure that is the key-parameter for mesencephalic specification. This concentration-insensitive patterning approach provides robustness and reduces the need for protocol-adjustments between hPSC-lines. RA-specified progenitors promptly differentiate into functional mDA neurons in vitro, and successfully engraft and relieve motor deficits after transplantation in a rat PD model. Our study provides a potential alternative route for cell therapy and disease modelling that due to its robustness could be particularly expedient when use of autologous- or immunologically matched cells is considered.", "doi": "10.1038/s41467-022-30777-8", "pmid": "35650213", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9160024"}, {"db": "pii", "key": "10.1038/s41467-022-30777-8"}], "notes": [], "created": "2022-08-19T08:37:46.809Z", "modified": "2024-01-16T13:48:36.237Z"}, {"entity": "publication", "iuid": "c0bb50ac623641d88b32b975f7e3b455", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0bb50ac623641d88b32b975f7e3b455.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0bb50ac623641d88b32b975f7e3b455"}}, "title": "The mosaic oat genome gives insights into a uniquely healthy cereal crop.", "authors": [{"family": "Kamal", "given": "Nadia", "initials": "N"}, {"family": "Tsardakas Renhuldt", "given": "Nikos", "initials": "N", "orcid": "0000-0001-7216-5320", "researcher": {"href": "https://publications.scilifelab.se/researcher/117e1cc25e4545298e212d86b3ee8ce3.json"}}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Gundlach", "given": "Heidrun", "initials": "H", "orcid": "0000-0002-6757-0943", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e6d69126dd4a9a9a99827c672b5fa5.json"}}, {"family": "Haberer", "given": "Georg", "initials": "G", "orcid": "0000-0002-6612-6939", "researcher": {"href": "https://publications.scilifelab.se/researcher/5313eb519bd24ee3b92a090746ad93a3.json"}}, {"family": "Juh\u00e1sz", "given": "Ang\u00e9la", "initials": "A"}, {"family": "Lux", "given": "Thomas", "initials": "T", "orcid": "0000-0002-5543-1911", "researcher": {"href": "https://publications.scilifelab.se/researcher/076281817e274a45819ff2f53f9047cf.json"}}, {"family": "Bose", "given": "Utpal", "initials": "U"}, {"family": "Tye-Din", "given": "Jason A", "initials": "JA", "orcid": "0000-0001-7687-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dacb233f9d747f7802937fdbfa63d07.json"}}, {"family": "Lang", "given": "Daniel", "initials": "D", "orcid": "0000-0002-2166-0716", "researcher": {"href": "https://publications.scilifelab.se/researcher/a42c82d2c3944382811323db528b074f.json"}}, {"family": "van Gessel", "given": "Nico", "initials": "N", "orcid": "0000-0002-0606-246X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f634bf44243b4c9e8862d2fcbb637357.json"}}, {"family": "Reski", "given": "Ralf", "initials": "R", "orcid": "0000-0002-5496-6711", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f01ef88d61741e8a2fa6ad36d545f52.json"}}, {"family": "Fu", "given": "Yong-Bi", "initials": "YB"}, {"family": "Sp\u00e9gel", "given": "Peter", "initials": "P", "orcid": "0000-0002-6092-2387", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e06a5bbd6114a248eafb168782d0b27.json"}}, {"family": "Ceplitis", "given": "Alf", "initials": "A"}, {"family": "Himmelbach", "given": "Axel", "initials": "A"}, {"family": "Waters", "given": "Amanda J", "initials": "AJ"}, {"family": "Bekele", "given": "Wubishet A", "initials": "WA"}, {"family": "Colgrave", "given": "Michelle L", "initials": "ML"}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}, {"family": "Stein", "given": "Nils", "initials": "N", "orcid": "0000-0003-3011-8731", "researcher": {"href": "https://publications.scilifelab.se/researcher/11ef5173e1214a9f920bcadad30afc70.json"}}, {"family": "Mayer", "given": "Klaus F X", "initials": "KFX", "orcid": "0000-0001-6484-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd32d600030146e9891b324e80708362.json"}}, {"family": "Jellen", "given": "Eric N", "initials": "EN", "orcid": "0000-0002-7906-4845", "researcher": {"href": "https://publications.scilifelab.se/researcher/83594761835445f9a5c92cad770ca372.json"}}, {"family": "Maughan", "given": "Peter J", "initials": "PJ", "orcid": "0000-0003-3714-3411", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f53b85b82e4ccfbb9220754ae0d59a.json"}}, {"family": "Tinker", "given": "Nicholas A", "initials": "NA", "orcid": "0000-0002-2452-4779", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef54eb854d47488f88ffc97360bfef59.json"}}, {"family": "Mascher", "given": "Martin", "initials": "M", "orcid": "0000-0001-6373-6013", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad2d033b05734d53a888db3e03edee0a.json"}}, {"family": "Olsson", "given": "Olof", "initials": "O"}, {"family": "Spannagl", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0701-7035", "researcher": {"href": "https://publications.scilifelab.se/researcher/88a57f18a3794d1aaf7af7c579697860.json"}}, {"family": "Sirijovski", "given": "Nick", "initials": "N", "orcid": "0000-0002-6191-3845", "researcher": {"href": "https://publications.scilifelab.se/researcher/040fc49df77d4171bf2695ae420f2302.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "606", "issue": "7912", "pages": "113-119"}, "abstract": "Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.", "doi": "10.1038/s41586-022-04732-y", "pmid": "35585233", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9159951"}, {"db": "pii", "key": "10.1038/s41586-022-04732-y"}], "notes": [], "created": "2022-08-19T08:37:48.764Z", "modified": "2024-01-16T13:48:36.250Z"}, {"entity": "publication", "iuid": "6174ffa3b7814304b002c1cd4c00f22f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6174ffa3b7814304b002c1cd4c00f22f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6174ffa3b7814304b002c1cd4c00f22f"}}, "title": "Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.", "authors": [{"family": "Dahlin", "given": "Maria", "initials": "M"}, {"family": "Singleton", "given": "Stephanie S", "initials": "SS"}, {"family": "David", "given": "John A", "initials": "JA"}, {"family": "Basuchoudhary", "given": "Atin", "initials": "A"}, {"family": "Wickstr\u00f6m", "given": "Ronny", "initials": "R"}, {"family": "Mazumder", "given": "Raja", "initials": "R"}, {"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S"}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "EBioMedicine", "issn": "2352-3964", "issn-l": "2352-3964", "volume": "80", "issue": null, "pages": "104061"}, "abstract": "Recently, studies have suggested a role for the gut microbiota in epilepsy. Gut microbial changes during ketogenic diet (KD) treatment of drug-resistant epilepsy have been described. Inflammation is associated with certain types of epilepsy and specific inflammation markers decrease during KD. The gut microbiota plays an important role in the regulation of the immune system and inflammation.\n\n28 children with drug-resistant epilepsy treated with the ketogenic diet were followed in this observational study. Fecal and serum samples were collected at baseline and three months after dietary intervention.\n\nWe identified both gut microbial and inflammatory changes during treatment. KD had a general anti-inflammatory effect. Novel bioinformatics and machine learning approaches identified signatures of specific Bifidobacteria and TNF (tumor necrosis factor) associated with responders before starting KD. During KD, taxonomic and inflammatory profiles between responders and non-responders were more similar than at baseline.\n\nOur results suggest that children with drug-resistant epilepsy are more likely to benefit from KD treatment when specific Bifidobacteria and TNF are elevated. We here present a novel signature of interaction of the gut microbiota and the immune system associated with anti-epileptic response to KD treatment. This signature could be used as a prognostic biomarker to identify potential responders to KD before starting treatment. Our findings may also contribute to the development of new anti-seizure therapies by targeting specific components of the gut microbiota.\n\nThis study was supported by the Swedish Brain Foundation, Margarethahemmet Society, Stiftelsen Sunnerdahls Handikappfond, Linnea & Josef Carlssons Foundation, and The McCormick Genomic & Proteomic Center.", "doi": "10.1016/j.ebiom.2022.104061", "pmid": "35598439", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9126955"}, {"db": "pii", "key": "S2352-3964(22)00242-0"}], "notes": [], "created": "2022-08-19T08:38:03.769Z", "modified": "2024-01-16T13:48:36.303Z"}, {"entity": "publication", "iuid": "e5278ea801b7484c8284dbeecf36e468", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5278ea801b7484c8284dbeecf36e468.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5278ea801b7484c8284dbeecf36e468"}}, "title": "Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater.", "authors": [{"family": "Hellman", "given": "Maria", "initials": "M"}, {"family": "Valhondo", "given": "Cristina", "initials": "C"}, {"family": "Mart\u00ednez-Landa", "given": "Lurdes", "initials": "L"}, {"family": "Carrera", "given": "Jes\u00fas", "initials": "J"}, {"family": "Juhanson", "given": "Jaanis", "initials": "J"}, {"family": "Hallin", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2022-05-24", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "issn-l": "1664-302X", "volume": "13", "issue": null, "pages": "877990"}, "abstract": "Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes.", "doi": "10.3389/fmicb.2022.877990", "pmid": "35685927", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9171435"}], "notes": [], "created": "2022-08-19T08:38:05.074Z", "modified": "2024-01-16T13:48:36.460Z"}, {"entity": "publication", "iuid": "05252c2ee2e24c1caba55097e6100408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05252c2ee2e24c1caba55097e6100408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05252c2ee2e24c1caba55097e6100408"}}, "title": "Touch signaling and thigmomorphogenesis are regulated by complementary CAMTA3- and JA-dependent pathways.", "authors": [{"family": "Darwish", "given": "Essam", "initials": "E", "orcid": "0000-0002-8204-0772", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a087f251f64ef3a0e21fe0909a8841.json"}}, {"family": "Ghosh", "given": "Ritesh", "initials": "R", "orcid": "0000-0002-2528-7277", "researcher": {"href": "https://publications.scilifelab.se/researcher/73d9fdc04f7e44b697cc669014c7bbd3.json"}}, {"family": "Ontiveros-Cisneros", "given": "Abraham", "initials": "A", "orcid": "0000-0003-3983-8380", "researcher": {"href": "https://publications.scilifelab.se/researcher/f47950d286194253814b41b1899440c6.json"}}, {"family": "Tran", "given": "Huy Cuong", "initials": "HC", "orcid": "0000-0002-7670-2215", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf057352ae445079a2e9dc51b6326a7.json"}}, {"family": "Petersson", "given": "Marcus", "initials": "M", "orcid": "0000-0002-2466-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c80b9fcb01144528c230d9844da4dad.json"}}, {"family": "De Milde", "given": "Liesbeth", "initials": "L"}, {"family": "Broda", "given": "Martyna", "initials": "M", "orcid": "0000-0003-0591-7814", "researcher": {"href": "https://publications.scilifelab.se/researcher/115370b9582d4b079cda461027833ae3.json"}}, {"family": "Goossens", "given": "Alain", "initials": "A", "orcid": "0000-0002-1599-551X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe20d16e62445b9b734a7c12da3b71d.json"}}, {"family": "Van Moerkercke", "given": "Alex", "initials": "A"}, {"family": "Khan", "given": "Kasim", "initials": "K", "orcid": "0000-0001-7336-2764", "researcher": {"href": "https://publications.scilifelab.se/researcher/76561aa1400a457aa3aff29a105097f8.json"}}, {"family": "Van Aken", "given": "Olivier", "initials": "O", "orcid": "0000-0003-4024-968X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8174aa4d9e4031822ea281b6f0f9dd.json"}}], "type": "journal article", "published": "2022-05-20", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "20", "pages": "eabm2091"}, "abstract": "Plants respond to mechanical stimuli to direct their growth and counteract environmental threats. Mechanical stimulation triggers rapid gene expression changes and affects plant appearance (thigmomorphogenesis) and flowering. Previous studies reported the importance of jasmonic acid (JA) in touch signaling. Here, we used reverse genetics to further characterize the molecular mechanisms underlying touch signaling. We show that Piezo mechanosensitive ion channels have no major role in touch-induced gene expression and thigmomorphogenesis. In contrast, the receptor-like kinase Feronia acts as a strong negative regulator of the JA-dependent branch of touch signaling. Last, we show that calmodulin-binding transcriptional activators CAMTA1/2/3 are key regulators of JA-independent touch signaling. CAMTA1/2/3 cooperate to directly bind the promoters and activate gene expression of JA-independent touch marker genes like TCH2 and TCH4. In agreement, camta3 mutants show a near complete loss of thigmomorphogenesis and touch-induced delay of flowering. In conclusion, we have now identified key regulators of two independent touch-signaling pathways.", "doi": "10.1126/sciadv.abm2091", "pmid": "35594358", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9122320"}], "notes": [], "created": "2022-08-19T08:38:07.571Z", "modified": "2023-10-16T11:24:07.553Z"}, {"entity": "publication", "iuid": "96c09c8b62a449159fb912e1596c2f28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96c09c8b62a449159fb912e1596c2f28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96c09c8b62a449159fb912e1596c2f28"}}, "title": "Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.", "authors": [{"family": "Laber", "given": "Christien P", "initials": "CP"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C"}, {"family": "Di Leo", "given": "Danilo", "initials": "D"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Farnelid", "given": "Hanna", "initials": "H"}], "type": "journal article", "published": "2022-05-09", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "issn-l": "1664-302X", "volume": "13", "issue": null, "pages": "828459"}, "abstract": "The picophytoplankton Synechococcus is a globally abundant autotroph that contributes significantly to primary production in the oceans and coastal areas. These cyanobacteria constitute a diverse genus of organisms that have developed independent niche spaces throughout aquatic environments. Here, we use the 16S V3-V4 rRNA gene region and flow cytometry to explore the diversity of Synechococcus within the picophytoplankton community in the Gullmar Fjord, on the west coast of Sweden. We conducted a station-based 1-year time series and two transect studies of the fjord. Our analysis revealed that within the large number of Synechococcus amplicon sequence variants (ASVs; 239 in total), prevalent ASVs phylogenetically clustered with clade representatives in both marine subcluster 5.1 and 5.2. The near-surface composition of ASVs shifted from spring to summer, when a 5.1 subcluster dominated community developed along with elevated Synechococcus abundances up to 9.3 \u00d7 104 cells ml-1. This seasonal dominance by subcluster 5.1 was observed over the length of the fjord (25 km), where shifts in community composition were associated with increasing depth. Unexpectedly, the community shift was not associated with changes in salinity. Synechococcus abundance dynamics also differed from that of the photosynthetic picoeukaryote community. These results highlight how seasonal variations in environmental conditions influence the dynamics of Synechococcus clades in a high latitude threshold fjord.", "doi": "10.3389/fmicb.2022.828459", "pmid": "35615500", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9125215"}], "notes": [], "created": "2022-08-19T08:37:45.474Z", "modified": "2024-01-16T13:48:36.589Z"}, {"entity": "publication", "iuid": "9c25f649010d4c10b0c89f067f250b61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61"}}, "title": "Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.", "authors": [{"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "H\u00f6glund", "given": "Julia", "initials": "J", "orcid": "0000-0001-8061-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b02049b625d47a69324be23e35f5b58.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4143a879fa2043e7873be9e2aa72d051.json"}}, {"family": "Lo Faro", "given": "Valeria", "initials": "V", "orcid": "0000-0003-4931-7327", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e77657632e1469d9f0382673f54d071.json"}}, {"family": "Schmitz", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4480-891X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b1d0c4505854c7d9ab7a2ed3116b7ae.json"}}, {"family": "Ek", "given": "Weronica E", "initials": "WE", "orcid": "0000-0003-2194-496X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7398a2bfa9154e15a4295828bc0f5bb8.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}], "type": "journal article", "published": "2022-05-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "2532"}, "abstract": "Despite the success of genome-wide association studies, much of the genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, to evaluate the contribution of rare genetic variants to 414 plasma proteins. The frequency distribution of genetic variants is skewed towards the rare spectrum, and damaging variants are more often rare. We estimate that less than 4.3% of the narrow-sense heritability is expected to be explained by rare variants in our cohort. Using a gene-based approach, we identify Cis-associations for 237 of the proteins, which is slightly more compared to a GWAS (N = 213), and we identify 34 associated loci in Trans. Several associations are driven by rare variants, which have larger effects, on average. We therefore conclude that rare variants could be of importance for precision medicine applications, but have a more limited contribution to the missing heritability of complex diseases.", "doi": "10.1038/s41467-022-30208-8", "pmid": "35534486", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9085767"}, {"db": "pii", "key": "10.1038/s41467-022-30208-8"}], "notes": [], "created": "2022-06-10T08:49:57.584Z", "modified": "2024-01-16T13:48:36.679Z"}, {"entity": "publication", "iuid": "a21aae4fea454a37a843e4ee311e249f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a21aae4fea454a37a843e4ee311e249f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a21aae4fea454a37a843e4ee311e249f"}}, "title": "Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression.", "authors": [{"family": "Faucillion", "given": "Marie-Line", "initials": "ML"}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Larsson", "given": "Jan", "initials": "J", "orcid": "0000-0003-4373-6790", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6f8e41628d4534879edaf229575dec.json"}}], "type": "journal article", "published": "2022-05-06", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "50", "issue": "8", "pages": "4372-4388"}, "abstract": "The steady state levels of RNAs, often referred to as expression levels, result from a well-balanced combination of RNA transcription and decay. Alterations in RNA levels will therefore result from tight regulation of transcription rates, decay rates or both. Here, we explore the role of RNA stability in achieving balanced gene expression and present genome-wide RNA stabilities in Drosophila melanogaster male and female cells as well as male cells depleted of proteins essential for dosage compensation. We identify two distinct RNA-stability mediated responses involved in regulation of gene expression. The first of these responds to acute and global changes in transcription and thus counteracts potentially harmful gene mis-expression by shifting the RNA stability in the direction opposite to the transcriptional change. The second response enhances inter-individual differential gene expression by adjusting the RNA stability in the same direction as a transcriptional change. Both mechanisms are global, act on housekeeping as well as non-housekeeping genes and were observed in both flies and mammals. Additionally, we show that, in contrast to mammals, modulation of RNA stability does not detectably contribute to dosage compensation of the sex-chromosomes in D. melanogaster.", "doi": "10.1093/nar/gkac208", "pmid": "35390159", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9071389"}, {"db": "pii", "key": "6564801"}], "notes": [], "created": "2022-08-19T08:37:16.435Z", "modified": "2023-10-12T11:27:55.185Z"}, {"entity": "publication", "iuid": "551c288a5ec247cc99cca4008efbf761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/551c288a5ec247cc99cca4008efbf761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/551c288a5ec247cc99cca4008efbf761"}}, "title": "Evaluating metagenomic assembly approaches for biome-specific gene catalogues.", "authors": [{"family": "Delgado", "given": "Luis Fernando", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2022-05-06", "journal": {"title": "Microbiome", "issn": "2049-2618", "issn-l": "2049-2618", "volume": "10", "issue": "1", "pages": "72"}, "abstract": "For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene calling on the assembled contigs. The assembly is typically conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is preferable. Thus, both approaches have potential pros and cons, but it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: (1) assembly on individual samples followed by clustering of the resulting genes, (2) co-assembly on all samples, and (3) mix assembly, combining individual and co-assembly.\n\nThe mix-assembly approach resulted in a more extensive nonredundant gene set than the other approaches and with more genes predicted to be complete and that could be functionally annotated. The mix assembly consists of 67 million genes (Baltic Sea gene set, BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (< 95% amino acid identity) to the Tara Oceans gene dataset, and hence, BAGS represents a valuable resource for brackish water research.\n\nThe mix-assembly approach represents a feasible approach to increase the information obtained from metagenomic samples. Video abstract.", "doi": "10.1186/s40168-022-01259-2", "pmid": "35524337", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9074274"}, {"db": "pii", "key": "10.1186/s40168-022-01259-2"}], "notes": [], "created": "2022-08-19T08:37:40.525Z", "modified": "2024-01-16T13:48:36.706Z"}, {"entity": "publication", "iuid": "ecc31d5772fa4ea4babb02dab123322d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecc31d5772fa4ea4babb02dab123322d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecc31d5772fa4ea4babb02dab123322d"}}, "title": "FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.", "authors": [{"family": "Pe\u00f1a-P\u00e9rez", "given": "Luc\u00eda", "initials": "L"}, {"family": "Kharazi", "given": "Shabnam", "initials": "S"}, {"family": "Frengen", "given": "Nicolai", "initials": "N"}, {"family": "Krstic", "given": "Aleksandra", "initials": "A"}, {"family": "Bouderlique", "given": "Thibault", "initials": "T"}, {"family": "Hauenstein", "given": "Julia", "initials": "J"}, {"family": "He", "given": "Minghui", "initials": "M"}, {"family": "Somuncular", "given": "Ece", "initials": "E"}, {"family": "Li Wang", "given": "Xiaoze", "initials": "X"}, {"family": "Dahlberg", "given": "Carin", "initials": "C"}, {"family": "Gustafsson", "given": "Charlotte", "initials": "C"}, {"family": "Johansson", "given": "Ann-Sofie", "initials": "AS"}, {"family": "Walfridsson", "given": "Julian", "initials": "J"}, {"family": "Kadri", "given": "Nadir", "initials": "N"}, {"family": "Woll", "given": "Petter", "initials": "P"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Westerberg", "given": "Lisa", "initials": "L"}, {"family": "Luc", "given": "Sidinh", "initials": "S"}, {"family": "M\u00e5nsson", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2022-05-04", "journal": {"title": "Front Immunol", "issn": "1664-3224", "issn-l": "1664-3224", "volume": "13", "issue": null, "pages": "880668"}, "abstract": "The development of B cells relies on an intricate network of transcription factors critical for developmental progression and lineage commitment. In the B cell developmental trajectory, a temporal switch from predominant Foxo3 to Foxo1 expression occurs at the CLP stage. Utilizing VAV-iCre mediated conditional deletion, we found that the loss of FOXO3 impaired B cell development from LMPP down to B cell precursors, while the loss of FOXO1 impaired B cell commitment and resulted in a complete developmental block at the CD25 negative proB cell stage. Strikingly, the combined loss of FOXO1 and FOXO3 resulted in the failure to restrict the myeloid potential of CLPs and the complete loss of the B cell lineage. This is underpinned by the failure to enforce the early B-lineage gene regulatory circuitry upon a predominantly pre-established open chromatin landscape. Altogether, this demonstrates that FOXO3 and FOXO1 cooperatively govern early lineage restriction and initiation of B-lineage commitment in CLPs.", "doi": "10.3389/fimmu.2022.880668", "pmid": "35603175", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9116193"}], "notes": [], "created": "2022-08-19T08:38:02.479Z", "modified": "2024-01-16T13:48:36.743Z"}, {"entity": "publication", "iuid": "658d38b5c3c841b1b3fd8242018b4b4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/658d38b5c3c841b1b3fd8242018b4b4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/658d38b5c3c841b1b3fd8242018b4b4e"}}, "title": "Genomic Impact of Whaling in North Atlantic Fin Whales.", "authors": [{"family": "Wolf", "given": "Magnus", "initials": "M", "orcid": "0000-0001-9212-9861", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d66a031b0e64d8a882d0c9cb19d1960.json"}}, {"family": "de Jong", "given": "Menno", "initials": "M", "orcid": "0000-0003-2131-9048", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a695ce1588409c8a22db7feeeac66b.json"}}, {"family": "Halld\u00f3rsson", "given": "Sverrir Dan\u00edel", "initials": "SD", "orcid": "0000-0002-0037-8543", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b5254497c7e433c8d61e35b5f504fa8.json"}}, {"family": "\u00c1rnason", "given": "\u00dalfur", "initials": "\u00da", "orcid": "0000-0002-4285-9492", "researcher": {"href": "https://publications.scilifelab.se/researcher/e13ddfbab43341de828601ee9715a0c6.json"}}, {"family": "Janke", "given": "Axel", "initials": "A", "orcid": "0000-0002-9394-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d649283c9584ff3b6d6415462026721.json"}}], "type": "journal article", "published": "2022-05-03", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "5", "pages": null}, "abstract": "It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained largely unaddressed because of the paucity of adequate samples and the limitation of applicable techniques. Here, we have examined the effect of whaling on the North Atlantic fin whale based on genomes of 51 individuals from Icelandic waters, representing three temporally separated intervals, 1989, 2009 and 2018 and provide a reference genome for the species. Demographic models suggest a noticeable drop of the effective population size of the North Atlantic fin whale around a century ago. The present results suggest that the genome-wide heterozygosity is not markedly reduced and has remained comparable with other baleen whale species. Similarly, there are no signs of apparent inbreeding, as measured by the proportion of long runs of homozygosity, or of a distinctively increased mutational load, as measured by the amount of putative deleterious mutations. Compared with other baleen whales, the North Atlantic fin whale appears to be less affected by anthropogenic influences than other whales such as the North Atlantic right whale, consistent with the presence of long runs of homozygosity and higher levels of mutational load in an otherwise more heterozygous genome. Thus, genome-wide assessments of other species and populations are essential for future, more specific, conservation efforts.", "doi": "10.1093/molbev/msac094", "pmid": "35512360", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9113106"}, {"db": "pii", "key": "6580755"}], "notes": [], "created": "2022-08-19T08:37:42.957Z", "modified": "2023-10-12T11:40:08.615Z"}, {"entity": "publication", "iuid": "9769ee1e0cc34f988fe4ea50b0f9f3c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9769ee1e0cc34f988fe4ea50b0f9f3c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9769ee1e0cc34f988fe4ea50b0f9f3c5"}}, "title": "The outcome of targeted NGS screening in patients with syndromic forms of sagittal and pansynostosis - IL11RA is an emerging core-gene for pansynostosis.", "authors": [{"family": "Topa", "given": "Alexandra", "initials": "A"}, {"family": "Rohlin", "given": "Anna", "initials": "A"}, {"family": "Andersson", "given": "Mattias K", "initials": "MK"}, {"family": "Fehr", "given": "Andr\u00e9", "initials": "A"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Stenman", "given": "G\u00f6ran", "initials": "G"}, {"family": "K\u00f6lby", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Eur J Med Genet", "issn": "1878-0849", "issn-l": "1769-7212", "volume": "65", "issue": "5", "pages": "104476"}, "abstract": "Here, we have studied the prevalence and spectrum of genetic alterations in syndromic forms of sagittal and pansynostosis. Eighteen patients with sagittal synostosis (isolated or combined with other synostoses, except coronal) or pansynostosis were phenotypically assessed by retrospective analysis of medical records, three-dimensional computed tomography skull reconstructions, and registered photos. Patient DNAs were analyzed using a targeted next-generation sequencing (NGS) panel including 63 craniosynostosis (CS) related genes. Pathogenic and likely pathogenic variants were found in 72% of the cases, mainly affecting FGFR2, TWIST1, IL11RA, and SKI. Two patients that were negative at NGS screening - one with a supernumerary marker chromosome with duplication of 15q25.2q26.3 and one with a pathogenic PHEX variant - were identified using microarray and single gene analysis, respectively. The overall diagnostic rate in the cohort was thus 83%. We identified two novel likely pathogenic variants in FGFR2 (NM_022970.3: c.811_812delGGinsCC, p.Gly271Pro) and TWIST1 (NM_000474.3: c.476T > A, p.Leu159His), and a novel variant of unclear phenotypic significance in RUNX2 (NM_001024630.3: c.340G > A, p.Val114Ile) which could suggest a modulatory effect. Notably, we also identified three new patients with pansynostosis and a Crouzon-like phenotype with IL11RA mutation. Targeted NGS using a broad panel of CS-related genes is a simple and powerful tool for detecting pathogenic mutations in patients with syndromic forms of CS and multiple suture involvement, in particular pansynostosis. Our results provide additional evidence of an association between pansynostosis and IL11RA, an emerging core gene for autosomal recessive CS.", "doi": "10.1016/j.ejmg.2022.104476", "pmid": "35331937", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1769-7212(22)00057-X"}], "notes": [], "created": "2022-08-19T08:37:20.168Z", "modified": "2024-01-16T13:48:36.775Z"}, {"entity": "publication", "iuid": "3d2c0be8738f4321b47129d5ca7625b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d2c0be8738f4321b47129d5ca7625b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d2c0be8738f4321b47129d5ca7625b1"}}, "title": "Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.", "authors": [{"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Li", "given": "Ke", "initials": "K"}, {"family": "Hoetzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-1932-6479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6324668ed1db48a787d75bd996d5358c.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "issn-l": "1462-2912", "volume": "24", "issue": "5", "pages": "2270-2281"}, "abstract": "Phages modulate bacterial metabolism during infection by regulating gene expression, which influences aquatic nutrient cycling. However, the effects of shifting nutrient regimes are less understood. Here, we analyzed transcriptomes of an ecologically relevant Gammaproteobacterium and its lytic phage in high (HNM) and low (LNM) nutrient medium. Despite different infection characteristics, including reduced burst size and longer latent period in LNM, the phage had a fixed expression profile. Bacterial transcription was instead different depending on nutrient regime, with HNM bacteria focusing on growth while LNM bacteria focused on motility and membrane transport. Additionally, phage infection had a larger effect on bacterial gene expression in LNM compared to HNM, e.g. suppressing increased iron uptake and altering expression of phosphorus uptake genes. Overall, phage infection influenced host metabolism more in LNM, which was more similar to natural conditions, emphasizing the importance of considering natural conditions to understand phage and host ecology.", "doi": "10.1111/1462-2920.15904", "pmid": "35049095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9305737"}], "notes": [], "created": "2022-03-29T13:48:07.622Z", "modified": "2024-01-16T13:48:36.787Z"}, {"entity": "publication", "iuid": "a956d64b6ab24e9d965b0f87d4ee55f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a956d64b6ab24e9d965b0f87d4ee55f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a956d64b6ab24e9d965b0f87d4ee55f3"}}, "title": "Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.", "authors": [{"family": "Eroglu", "given": "Elif", "initials": "E", "orcid": "0000-0003-3952-3178", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f528128b8d46d4b6773c78f74d2f27.json"}}, {"family": "Yen", "given": "Christopher Y T", "initials": "CYT", "orcid": "0000-0001-5999-6306", "researcher": {"href": "https://publications.scilifelab.se/researcher/16c21e09bed648d09277181129eac844.json"}}, {"family": "Tsoi", "given": "Yat-Long", "initials": "YL", "orcid": "0000-0002-8890-3989", "researcher": {"href": "https://publications.scilifelab.se/researcher/c58e997420f2443dab668d9aad863006.json"}}, {"family": "Witman", "given": "Nevin", "initials": "N", "orcid": "0000-0002-1109-778X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b19cd00ecdc47838411d6ab8fe58498.json"}}, {"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Joven Araus", "given": "Alberto", "initials": "A", "orcid": "0000-0002-0926-4665", "researcher": {"href": "https://publications.scilifelab.se/researcher/11c7df4727464e1c95bdaa9372ce7409.json"}}, {"family": "Wang", "given": "Heng", "initials": "H", "orcid": "0000-0002-1727-9226", "researcher": {"href": "https://publications.scilifelab.se/researcher/1861054d4a744bc885fa876e97591208.json"}}, {"family": "Szattler", "given": "Tamara", "initials": "T", "orcid": "0000-0002-1562-1278", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa689c60e4dc4a79b082369bbf25b46b.json"}}, {"family": "Umeano", "given": "Chimezie H", "initials": "CH"}, {"family": "Sohlm\u00e9r", "given": "Jesper", "initials": "J", "orcid": "0000-0003-2607-7500", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e770e2f774bb68ed8059bc6aa2aef.json"}}, {"family": "Goedel", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5980-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/866e8580c3d8462da0f3ee3b8909ea6f.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A", "orcid": "0000-0002-1018-1891", "researcher": {"href": "https://publications.scilifelab.se/researcher/96bdae99574843959cede3393f727ee0.json"}}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "issn-l": null, "volume": "24", "issue": "5", "pages": "645-658"}, "abstract": "The contribution of the epicardium, the outermost layer of the heart, to cardiac regeneration has remained controversial due to a lack of suitable analytical tools. By combining genetic marker-independent lineage-tracing strategies with transcriptional profiling and loss-of-function methods, we report here that the epicardium of the highly regenerative salamander species Pleurodeles waltl has an intrinsic capacity to differentiate into cardiomyocytes. Following cryoinjury, CLDN6+ epicardium-derived cells appear at the lesion site, organize into honeycomb-like structures connected via focal tight junctions and undergo transcriptional reprogramming that results in concomitant differentiation into de novo cardiomyocytes. Ablation of CLDN6+ differentiation intermediates as well as disruption of their tight junctions impairs cardiac regeneration. Salamanders constitute the evolutionarily closest species to mammals with an extensive ability to regenerate heart muscle and our results highlight the epicardium and tight junctions as key targets in efforts to promote cardiac regeneration.", "doi": "10.1038/s41556-022-00902-2", "pmid": "35550612", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9106584"}, {"db": "pii", "key": "10.1038/s41556-022-00902-2"}], "notes": [], "created": "2022-08-19T08:37:51.908Z", "modified": "2024-01-16T13:48:36.843Z"}, {"entity": "publication", "iuid": "99397d7788074cf99808f5c18d8ef9ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99397d7788074cf99808f5c18d8ef9ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99397d7788074cf99808f5c18d8ef9ea"}}, "title": "Multi-omics protein-coding units as massively parallel Bayesian networks: Empirical validation of causality structure.", "authors": [{"family": "Zenere", "given": "Alberto", "initials": "A"}, {"family": "Rundquist", "given": "Olof", "initials": "O"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}, {"family": "Altafini", "given": "Claudio", "initials": "C"}], "type": "journal article", "published": "2022-04-15", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "4", "pages": "104048"}, "abstract": "In this article we use high-throughput epigenomics, transcriptomics, and proteomics data to construct fine-graded models of the \"protein-coding units\" gathering all transcript isoforms and chromatin accessibility peaks associated with more than 4000 genes in humans. Each protein-coding unit has the structure of a directed acyclic graph (DAG) and can be represented as a Bayesian network. The factorization of the joint probability distribution induced by the DAGs imposes a number of conditional independence relationships among the variables forming a protein-coding unit, corresponding to the missing edges in the DAGs. We show that a large fraction of these conditional independencies are indeed verified by the data. Factors driving this verification appear to be the structural and functional annotation of the transcript isoforms, as well as a notion of structural balance (or frustration-free) of the corresponding sample correlation graph, which naturally leads to reduction of correlation (and hence to independence) upon conditioning.", "doi": "10.1016/j.isci.2022.104048", "pmid": "35355520", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8958332"}, {"db": "pii", "key": "S2589-0042(22)00318-2"}], "notes": [], "created": "2022-08-19T08:37:22.690Z", "modified": "2023-10-12T11:35:33.813Z"}, {"entity": "publication", "iuid": "b8fea114a14342328b67a204d5da01a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8fea114a14342328b67a204d5da01a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8fea114a14342328b67a204d5da01a1"}}, "title": "Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.", "authors": [{"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Kempe Lagerholm", "given": "Vendela", "initials": "V"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Danilov", "given": "Gleb K", "initials": "GK"}, {"family": "Mortensen", "given": "Peter", "initials": "P"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2022-04-13", "journal": {"title": "Genes", "issn": "2073-4425", "issn-l": "2073-4425", "volume": "13", "issue": "4", "pages": null}, "abstract": "Rapid and cost-effective retrieval of endogenous DNA from ancient specimens remains a limiting factor in palaeogenomic research. Many methods have been developed to increase ancient DNA yield, but modifications to existing protocols are often based on personal experience rather than systematic testing. Here, we present a new silica column-based extraction protocol, where optimizations were tested in controlled experiments. Using relatively well-preserved permafrost samples, we tested the efficiency of pretreatment of bone and tooth powder with a bleach wash and a predigestion step. We also tested the recovery efficiency of MinElute and QIAquick columns, as well as Vivaspin columns with two molecular weight cut-off values. Finally, we tested the effect of uracil-treatment with two different USER enzyme concentrations. We find that neither bleach wash combined with a predigestion step, nor predigestion by itself, significantly increased sequencing efficiency. Initial results, however, suggest that MinElute columns are more efficient for ancient DNA extractions than QIAquick columns, whereas different molecular weight cut-off values in centrifugal concentrator columns did not have an effect. Uracil treatments are effective at removing DNA damage even at concentrations of 0.15 U/\u00b5L (as compared to 0.3 U/\u00b5L) of ancient DNA extracts.", "doi": "10.3390/genes13040687", "pmid": "35456493", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9032354"}, {"db": "pii", "key": "genes13040687"}], "notes": [], "created": "2022-08-19T08:37:18.957Z", "modified": "2024-01-16T13:48:37.051Z"}, {"entity": "publication", "iuid": "64118dce7d1343469bcff7d1753b674f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64118dce7d1343469bcff7d1753b674f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64118dce7d1343469bcff7d1753b674f"}}, "title": "Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.", "authors": [{"family": "Lewerentz", "given": "Jacob", "initials": "J", "orcid": "0000-0001-5013-9498", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb6f36f637804d6e9a9d58d28ce5bd92.json"}}, {"family": "Johansson", "given": "Anna-Mia", "initials": "A"}, {"family": "Larsson", "given": "Jan", "initials": "J"}, {"family": "Stenberg", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2022-04-07", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "276"}, "abstract": "Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure.\r\n\r\nUsing a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (> 80% of SVs), with Gypsy retrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in other D. melanogaster cell lines.\r\n\r\nThe S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.", "doi": "10.1186/s12864-022-08472-1", "pmid": "35392795", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8991648"}, {"db": "pii", "key": "10.1186/s12864-022-08472-1"}], "notes": [], "created": "2022-08-19T08:37:15.097Z", "modified": "2024-01-16T13:48:37.069Z"}, {"entity": "publication", "iuid": "f2b8e797bc1f449fa623e9ccef692699", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2b8e797bc1f449fa623e9ccef692699.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2b8e797bc1f449fa623e9ccef692699"}}, "title": "Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.", "authors": [{"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "van Tuijn", "given": "Cassandra A", "initials": "CA"}, {"family": "Heskol", "given": "Abeer", "initials": "A"}, {"family": "Zheng", "given": "Chao", "initials": "C"}, {"family": "Mendanha Falc\u00e3o", "given": "Ana", "initials": "A"}, {"family": "Bartosovic", "given": "Marek", "initials": "M"}, {"family": "Kirby", "given": "Leslie", "initials": "L"}, {"family": "Calini", "given": "Daniela", "initials": "D"}, {"family": "Johnson", "given": "Michael R", "initials": "MR"}, {"family": "Corces", "given": "M Ryan", "initials": "MR"}, {"family": "Montine", "given": "Thomas J", "initials": "TJ"}, {"family": "Chen", "given": "Xingqi", "initials": "X"}, {"family": "Chang", "given": "Howard Y", "initials": "HY"}, {"family": "Malhotra", "given": "Dheeraj", "initials": "D"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal article", "published": "2022-04-06", "journal": {"title": "Neuron", "issn": "1097-4199", "issn-l": "0896-6273", "volume": "110", "issue": "7", "pages": "1193-1210.e13"}, "abstract": "Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and myelin by immune cells, which are thought to be the main drivers of MS susceptibility. We found that immune genes exhibit a primed chromatin state in single mouse and human OLG in a non-disease context, compatible with transitions to immune-competent states in MS. We identified BACH1 and STAT1 as transcription factors involved in immune gene regulation in oligodendrocyte precursor cells (OPCs). A subset of immune genes presents bivalency of H3K4me3/H3K27me3 in OPCs, with Polycomb inhibition leading to their increased activation upon interferon gamma (IFN-\u03b3) treatment. Some MS susceptibility single-nucleotide polymorphisms (SNPs) overlap with these regulatory regions in mouse and human OLG. Treatment of mouse OPCs with IFN-\u03b3 leads to chromatin architecture remodeling at these loci and altered expression of interacting genes. Thus, the susceptibility for MS may involve OLG, which therefore constitutes novel targets for immunological-based therapies for MS.", "doi": "10.1016/j.neuron.2021.12.034", "pmid": "35093191", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Single cell": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-6273(21)01089-8"}], "notes": [], "created": "2022-03-29T13:48:05.164Z", "modified": "2024-02-12T08:46:45.499Z"}, {"entity": "publication", "iuid": "6e36dcb6fc944e67ba802034b10f625c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e36dcb6fc944e67ba802034b10f625c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e36dcb6fc944e67ba802034b10f625c"}}, "title": "Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.", "authors": [{"family": "von Grothusen", "given": "Carolina", "initials": "C", "orcid": "0000-0002-1508-8952", "researcher": {"href": "https://publications.scilifelab.se/researcher/d114195666f34b3ab78b054a13ceede1.json"}}, {"family": "Frisendahl", "given": "Caroline", "initials": "C", "orcid": "0000-0001-5283-6692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc410e454e8d4eec949737d3f29d945a.json"}}, {"family": "Modhukur", "given": "Vijayachitra", "initials": "V"}, {"family": "Lalitkumar", "given": "Parameswaran Grace", "initials": "PG", "orcid": "0000-0001-6733-533X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce39a89ff7c2470f9333cc5bcf9ad412.json"}}, {"family": "Peters", "given": "Maire", "initials": "M"}, {"family": "Faridani", "given": "Omid R", "initials": "OR"}, {"family": "Salumets", "given": "Andres", "initials": "A", "orcid": "0000-0002-1251-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dcf4bacf5c4792bbfd111495d43595.json"}}, {"family": "Boggavarapu", "given": "Nageswara Rao", "initials": "NR"}, {"family": "Gemzell-Danielsson", "given": "Kristina", "initials": "K", "orcid": "0000-0001-6516-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/44544a9f401c4db8a5cbdeca3d31e4b2.json"}}], "type": "journal article", "published": "2022-04-01", "journal": {"title": "Hum. Reprod.", "issn": "1460-2350", "issn-l": "0268-1161", "volume": "37", "issue": "4", "pages": "734-746"}, "abstract": "Is the composition of microRNAs (miRNAs) in uterine fluid (UF) of women with recurrent implantation failure (RIF) different from that of healthy fertile women?\r\n\r\nThe composition of miRNAs in UF of women with RIF is different from that of healthy fertile women and the dysregulated miRNAs are associated with impaired endometrial receptivity and embryo implantation.\r\n\r\nIt has previously been demonstrated that the miRNAs secreted from endometrial cells into the UF contribute to the achievement of endometrial receptivity. Endometrial miRNAs are dysregulated in women with RIF.\r\n\r\nIn this descriptive laboratory case-control study, miRNA abundancy was compared between UF collected during implantation phase from healthy fertile women (n = 17) and women with RIF (n = 34), which was defined as three failed IVF cycles with high-quality embryos.\r\n\r\nRecruitment of study subjects and sampling of UF were performed at two university clinics in Stockholm, Sweden and Tartu, Estonia. The study participants monitored their menstrual cycles using an LH test kit. The UF samples were collected on Day LH + 7-9 by flushing with saline. Samples were processed for small RNA sequencing and mapped for miRNAs. The differential abundance of miRNAs in UF was compared between the two groups using differential expression analysis (DESeq2). Further downstream analyses, including miRNA target gene prediction (miRTarBase), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (g:Profiler) and external validation using relevant published data, were performed on the dysregulated miRNAs. Two miRNAs were technically validated with quantitative real-time PCR (RT-PCR).\r\n\r\nAfter processing of the sequencing data, there were 15 samples in the healthy fertile group and 33 samples in the RIF group. We found 61 differentially abundant UF miRNAs (34 upregulated and 27 downregulated) in RIF compared to healthy women with a false discovery rate of <0.05 and a fold change (FC) of \u2264-2 or \u22652. When analyzed with published literature, we found that several of the differentially abundant miRNAs are expressed in endometrial epithelial cells and have been reported in endometrial extracellular vesicles and in association with endometrial receptivity and RIF. Their predicted target genes were further expressed both in the trophectodermal cells of blastocyst-stage embryos and endometrial mid-secretory epithelial cells, as assessed by publicly available single-cell transcriptome-sequencing studies. Pathway analysis further revealed that 25 pathways, having key roles in endometrial receptivity and implantation, were significantly enriched. Hsa-miR-486-5p (FC -20.32; P-value = 0.004) and hsa-miR-92b-3p (FC -9.72; P-value = 0.004) were successfully technically validated with RT-PCR.\r\n\r\nThe data are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/ with GEO accession number: GSE173289.\r\n\r\nThis is a descriptive study with a limited number of study participants. Moreover, the identified differentially abundant miRNAs should be validated in a larger study cohort, and the predicted miRNA target genes and enriched pathways in RIF need to be confirmed and further explored in vitro.\r\n\r\nRIF is a major challenge in the current IVF setting with no diagnostic markers nor effective treatment options at hand. For the first time, total miRNAs have been extensively mapped in receptive phase UF of both healthy women with proven fertility and women diagnosed with RIF. Our observations shed further light on the molecular mechanisms behind RIF, with possible implications in future biomarker and clinical treatment studies.\r\n\r\nThis work was financially supported by the Swedish Research Council (2017-00932), a joint grant from Region Stockholm and Karolinska Institutet (ALF Medicine 2020, FoUI-954072), Estonian Research Council (PRG1076), Horizon 2020 innovation (ERIN, EU952516) and European Commission and Enterprise Estonia (EU48695). The authors have no competing interests to declare for the current study.", "doi": "10.1093/humrep/deac019", "pmid": "35147192", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8971651"}, {"db": "pii", "key": "6526798"}], "notes": [], "created": "2022-12-01T13:48:42.298Z", "modified": "2024-01-16T13:48:37.141Z"}, {"entity": "publication", "iuid": "a5940ec7da224843a42c98a9c7baa6ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5940ec7da224843a42c98a9c7baa6ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5940ec7da224843a42c98a9c7baa6ba"}}, "title": "Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.", "authors": [{"family": "Ferreira", "given": "Paola de Lima", "initials": "PdL"}, {"family": "Batista", "given": "Romina", "initials": "R"}, {"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Groppo", "given": "Milton", "initials": "M"}, {"family": "Bacon", "given": "Christine D", "initials": "CD"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2022-04-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "issn-l": "1055-7903", "volume": "169", "issue": null, "pages": "107432"}, "abstract": "Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samples are commonly excluded from downstream analyses, even though they may still contain valuable information. On the other hand, including data-poor loci may bias phylogenetic analyses. Here we use a target sequence capture dataset of an ecologically and taxonomically diverse group of spiny sunflowers (Asteraceae, or Compositae: Barnadesioideae) to test how the inclusion or exclusion of such data-poor loci affects phylogenetic inference. We investigate the sensitivity of concatenation and coalescent approaches to missing data with matrices of varying taxonomic completeness by filtering loci with different proportions of missing samples prior to data analysis. We find that missing data affect both the topology and branch support of the resulting phylogenies. The matrix containing all loci yielded the overall highest node support values, independently of the amount of missing nucleotides. These results provide empirical support to earlier suggestions based on single genes and data simulations that taxa with high amounts of missing data should not be readily dismissed as they can provide essential information for phylogenomic reconstruction.", "doi": "10.1016/j.ympev.2022.107432", "pmid": "35131421", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(22)00045-8"}], "notes": [], "created": "2022-03-29T13:47:57.279Z", "modified": "2022-08-18T14:56:55.394Z"}, {"entity": "publication", "iuid": "9ebcad7df6fc4b52a1198f4a36faeb0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ebcad7df6fc4b52a1198f4a36faeb0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ebcad7df6fc4b52a1198f4a36faeb0e"}}, "title": "Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines.", "authors": [{"family": "Leo", "given": "Isabelle Rose", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/21185d9c6a2343f189397cbbb95c6e71.json"}}, {"family": "Aswad", "given": "Luay", "initials": "L", "orcid": "0000-0002-8730-9208", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01cefe048a541c7bdab2727d9cfc79d.json"}}, {"family": "Stahl", "given": "Matthias", "initials": "M", "orcid": "0000-0002-0176-9386", "researcher": {"href": "https://publications.scilifelab.se/researcher/f113f8aa6e77444d9492b5fed0067b25.json"}}, {"family": "Kunold", "given": "Elena", "initials": "E"}, {"family": "Post", "given": "Frederik", "initials": "F", "orcid": "0000-0003-0376-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/439eb72d3314446da93915e854774caf.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Struyf", "given": "Nona", "initials": "N", "orcid": "0000-0002-6975-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/1295c3be31024c4fa2da10cffe42c406.json"}}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Joshi", "given": "Rubin Narayan", "initials": "RN"}, {"family": "Gracia-Villacampa", "given": "Eva", "initials": "E", "orcid": "0000-0003-0353-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf72d81feea4b7899197c67131a85ba.json"}}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Kallioniemi", "given": "Olli P", "initials": "OP"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/481b2a2329634f9086cf52fb808edea5.json"}}], "type": "journal article", "published": "2022-03-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "1691"}, "abstract": "Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Although standard-of-care chemotherapeutics are sufficient for most ALL cases, there are subsets of patients with poor response who relapse in disease. The biology underlying differences between subtypes and their response to therapy has only partially been explained by genetic and transcriptomic profiling. Here, we perform comprehensive multi-omic analyses of 49 readily available childhood ALL cell lines, using proteomics, transcriptomics, and pharmacoproteomic characterization. We connect the molecular phenotypes with drug responses to 528 oncology drugs, identifying drug correlations as well as lineage-dependent correlations. We also identify the diacylglycerol-analog bryostatin-1 as a therapeutic candidate in the MEF2D-HNRNPUL1 fusion high-risk subtype, for which this drug activates pro-apoptotic ERK signaling associated with molecular mediators of pre-B cell negative selection. Our data is the foundation for the interactive online Functional Omics Resource of ALL (FORALL) with navigable proteomics, transcriptomics, and drug sensitivity profiles at https://proteomics.se/forall .", "doi": "10.1038/s41467-022-29224-5", "pmid": "35354797", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8967900"}, {"db": "pii", "key": "10.1038/s41467-022-29224-5"}], "notes": [], "created": "2022-08-19T08:37:13.488Z", "modified": "2024-01-16T13:48:37.216Z"}, {"entity": "publication", "iuid": "1b65a28d95bf4b53a0ae5ad7f46da0ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b65a28d95bf4b53a0ae5ad7f46da0ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b65a28d95bf4b53a0ae5ad7f46da0ae"}}, "title": "GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.", "authors": [{"family": "Rezaei", "given": "Shiva", "initials": "S"}, {"family": "Uffenorde", "given": "Julia", "initials": "J"}, {"family": "Gimm", "given": "Oliver", "initials": "O"}, {"family": "Hosseinpour Feizi", "given": "Mohammad Ali", "initials": "MA"}, {"family": "Miemczyk", "given": "Stefan", "initials": "S"}, {"family": "Coutinho", "given": "Luiz Lehmann", "initials": "LL"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}], "type": "journal article", "published": "2022-03-18", "journal": {"title": "STAR Protoc", "issn": "2666-1667", "issn-l": null, "volume": "3", "issue": "1", "pages": "101202"}, "abstract": "The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.", "doi": "10.1016/j.xpro.2022.101202", "pmid": "35257114", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S2666-1667(22)00082-X"}, {"db": "pmc", "key": "PMC8897576"}], "notes": [], "created": "2022-03-29T13:48:48.683Z", "modified": "2022-08-18T14:57:15.276Z"}, {"entity": "publication", "iuid": "09ec8012bd3846dd8c8f324e636f0700", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09ec8012bd3846dd8c8f324e636f0700.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09ec8012bd3846dd8c8f324e636f0700"}}, "title": "Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis.", "authors": [{"family": "Eriksson", "given": "Kaja", "initials": "K"}, {"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Delgado", "given": "Luis F", "initials": "LF"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Fei", "given": "Guozhong", "initials": "G"}, {"family": "Lee", "given": "Linkiat", "initials": "L"}, {"family": "Fei", "given": "Carina", "initials": "C"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Jansson", "given": "Leif", "initials": "L"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2022-03-14", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "issn-l": "2235-2988", "volume": "12", "issue": null, "pages": "841139"}, "abstract": "Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study was to compare the oral microbial composition and host\u00b4s inflammatory mediator profile of saliva samples obtained from subjects with periodontitis, with and without RA, as well as to predict biomarkers, of bacterial pathogens and/or inflammatory mediators, for classification of samples associated with periodontitis and RA.\n\nSalivary samples were obtained from 53 patients with periodontitis and RA and 48 non-RA with chronic periodontitis. The microbial composition was identified using 16S rRNA gene sequencing and compared across periodontitis patients with and without RA. Levels of inflammatory mediators were determined using a multiplex bead assay, compared between the groups and correlated to the microbial profile. The achieved data was analysed using PCoA, DESeq2 and two machine learning algorithms, OPLS-DA and sPLS-DA.\n\nDifferential abundance DESeq2 analyses showed that the four most highly enriched (log2 FC >20) amplicon sequence variants (ASVs) in the non-RA periodontitis group included Alloprevotella sp., Prevotella sp., Haemophilus sp., and Actinomyces sp. whereas Granulicatella sp., Veillonella sp., Megasphaera sp., and Fusobacterium nucleatum were the most highly enriched ASVs (log2 FC >20) in the RA group. OPLS-DA with log2 FC analyses demonstrated that the top ASVs with the highest importance included Vampirovibrio sp. having a positive correlation with non-RA group, and seven ASVs belonging to Sphingomonas insulae, Sphingobium sp., Novosphingobium aromaticivorans, Delftia acidovorans, Aquabacterium spp. and Sphingomonas echinoides with a positive correlation with RA group. Among the detected inflammatory mediators in saliva samples, TWEAK/TNFSF12, IL-35, IFN-\u03b12, pentraxin-3, gp130/sIL6Rb, sIL-6Ra, IL-19 and sTNF-R1 were found to be significantly increased in patients with periodontitis and RA compared to non-RA group with periodontitis. Moreover, correlations between ASVs and inflammatory mediators using sPLS-DA analysis revealed that TWEAK/TNFSF12, pentraxin-3 and IL-19 were positively correlated with the ASVs Sphingobium sp., Acidovorax delafieldii, Novosphingobium sp., and Aquabacterium sp.\n\nOur results suggest that the combination of microbes and host inflammatory mediators could be more efficient to be used as a predictable biomarker associated with periodontitis and RA, as compared to microbes and inflammatory mediators alone.", "doi": "10.3389/fcimb.2022.841139", "pmid": "35360114", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8964114"}], "notes": [], "created": "2022-08-19T08:37:11.943Z", "modified": "2024-01-16T13:48:37.246Z"}, {"entity": "publication", "iuid": "01b396ca14784d979d8f1a5282eb9c7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01b396ca14784d979d8f1a5282eb9c7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01b396ca14784d979d8f1a5282eb9c7c"}}, "title": "Downregulation and Hypermethylation of GABPB1 Is Associated with Aggressive Thyroid Cancer Features.", "authors": [{"family": "Xing", "given": "Xiangling", "initials": "X"}, {"family": "Mu", "given": "Ninni", "initials": "N", "orcid": "0000-0002-3887-880X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b478578ad34b40ecb865f915e86e59b6.json"}}, {"family": "Yuan", "given": "Xiaotian", "initials": "X", "orcid": "0000-0002-1501-518X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b10c4020514185be7da4077f78e4f2.json"}}, {"family": "Wang", "given": "Na", "initials": "N"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}, {"family": "Str\u00e5\u00e5t", "given": "Klas", "initials": "K"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}, {"family": "Neo", "given": "Shi Yong", "initials": "SY"}, {"family": "Xu", "given": "Dawei", "initials": "D", "orcid": "0000-0003-3141-4524", "researcher": {"href": "https://publications.scilifelab.se/researcher/a90bfbbe83364a1087de699dc3b4b80c.json"}}], "type": "journal article", "published": "2022-03-08", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "issn-l": "2072-6694", "volume": "14", "issue": "6", "pages": null}, "abstract": "Promoter mutations of the telomerase reverse transcriptase (TERT) gene occur frequently in thyroid carcinoma (TC), including papillary (PTC) and anaplastic subtypes (ATC). Given that the ETS family transcription factors GABPA and GABPB1 activate the mutant TERT promoter and induce TERT expression for telomerase activation, GABPB1 has been proposed as a cancer therapeutic target to inhibit telomerase. Here, we sought to determine the role of GABPB1 in TC pathogenesis. In TC-derived cells carrying the mutated TERT promoter, GABPB1 knockdown led to diminished TERT expression but significantly increased invasive potentials in vitro and metastatic potential in a xenograft zebrafish model and altered expression of markers for epithelial-to-mesenchymal transition. GABPB1 expression was downregulated in aggressive TCs. Low GABPB1 expression correlated with its promoter hypermethylation, which in turn was also associated with shorter disease-free survival. Consistently, DNA methylation inhibitors enhanced GABPB1 expression, as observed upon reduced promoter methylation. Our results suggest that GABPB1 is required for TERT expression and telomerase activation, but itself serves as a tumor suppressor to inhibit TC progression. Furthermore, aberrant DNA methylation leads to GABPB1 silencing, thereby promoting TC aggressiveness. Thus, caution is needed if targeting GABPB1 for cancer therapy is considered.", "doi": "10.3390/cancers14061385", "pmid": "35326537", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8946831"}, {"db": "pii", "key": "cancers14061385"}], "notes": [], "created": "2023-01-13T12:59:08.053Z", "modified": "2024-01-02T13:08:48.641Z"}, {"entity": "publication", "iuid": "aad25a1a0abd468badc8972835965e79", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aad25a1a0abd468badc8972835965e79.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aad25a1a0abd468badc8972835965e79"}}, "title": "Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.", "authors": [{"family": "Stenudd", "given": "Moa", "initials": "M"}, {"family": "Sabelstr\u00f6m", "given": "Hanna", "initials": "H"}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E"}, {"family": "Zamboni", "given": "Margherita", "initials": "M"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H"}, {"family": "Zhang", "given": "Shupei", "initials": "S"}, {"family": "Basak", "given": "Onur", "initials": "O"}, {"family": "Clevers", "given": "Hans", "initials": "H"}, {"family": "G\u00f6ritz", "given": "Christian", "initials": "C"}, {"family": "Barnab\u00e9-Heider", "given": "Fanie", "initials": "F"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2022-03-01", "journal": {"title": "Cell Rep", "issn": "2211-1247", "issn-l": null, "volume": "38", "issue": "9", "pages": "110440"}, "abstract": "Spinal cord ependymal cells display neural stem cell properties in vitro and generate scar-forming astrocytes and remyelinating oligodendrocytes after injury. We report that ependymal cells are functionally heterogeneous and identify a small subpopulation (8% of ependymal cells and 0.1% of all cells in a spinal cord segment), which we denote ependymal A (EpA) cells, that accounts for the in vitro stem cell potential in the adult spinal cord. After spinal cord injury, EpA cells undergo self-renewing cell division as they give rise to differentiated progeny. Single-cell transcriptome analysis revealed a loss of ependymal cell gene expression programs as EpA cells gained signaling entropy and dedifferentiated to a stem-cell-like transcriptional state after an injury. We conclude that EpA cells are highly differentiated cells that can revert to a stem cell state and constitute a therapeutic target for spinal cord repair.", "doi": "10.1016/j.celrep.2022.110440", "pmid": "35235796", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Single cell": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(22)00167-X"}], "notes": [], "created": "2022-03-07T18:13:15.523Z", "modified": "2024-01-16T13:48:37.311Z"}, {"entity": "publication", "iuid": "204bd002be2540c08b0fe0a4629bb135", "links": {"self": {"href": "https://publications.scilifelab.se/publication/204bd002be2540c08b0fe0a4629bb135.json"}, "display": {"href": "https://publications.scilifelab.se/publication/204bd002be2540c08b0fe0a4629bb135"}}, "title": "Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern.", "authors": [{"family": "Ernst", "given": "Mario", "initials": "M", "orcid": "0000-0002-4155-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/b739558f798a4b1d85e252bc2eb7d013.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X", "volume": "128", "issue": "3", "pages": "159-168"}, "abstract": "A taxonomic classification that accurately captures evolutionary history is essential for conservation. Genomics provides powerful tools for delimiting species and understanding their evolutionary relationships. This allows for a more accurate and detailed view on conservation status compared with other, traditionally used, methods. However, from a practical and ethical perspective, gathering sufficient samples for endangered taxa may be difficult. Here, we use museum specimens to trace the evolutionary history and species boundaries in an Asian oriole clade. The endangered silver oriole has long been recognized as a distinct species based on its unique coloration, but a recent study suggested that it might be nested within the maroon oriole-species complex. To evaluate species designation, population connectivity, and the corresponding conservation implications, we assembled a de novo genome and used whole-genome resequencing of historical specimens. Our results show that the silver orioles form a monophyletic lineage within the maroon oriole complex and that maroon and silver forms continued to interbreed after initial divergence, but do not show signs of recent gene flow. Using a genome scan, we identified genes that may form the basis for color divergence and act as reproductive barriers. Taken together, our results confirm the species status of the silver oriole and highlight that taxonomic revision of the maroon forms is urgently needed. Our study demonstrates how genomics and Natural History Collections (NHC) can be utilized to shed light on the taxonomy and evolutionary history of natural populations and how such insights can directly benefit conservation practitioners when assessing wild populations.", "doi": "10.1038/s41437-022-00499-0", "pmid": "35082388", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-022-00499-0"}, {"db": "pmc", "key": "PMC8897408"}], "notes": [], "created": "2022-03-29T13:47:58.452Z", "modified": "2024-01-16T13:48:37.328Z"}, {"entity": "publication", "iuid": "7bae925b3e40438c820b6ac9f99547d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7bae925b3e40438c820b6ac9f99547d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7bae925b3e40438c820b6ac9f99547d9"}}, "title": "Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.", "authors": [{"family": "Mueller", "given": "Jakob C", "initials": "JC", "orcid": "0000-0001-6676-7595", "researcher": {"href": "https://publications.scilifelab.se/researcher/5236c473e0434e97b48f4259fc28149b.json"}}, {"family": "Botero-Delgadillo", "given": "Esteban", "initials": "E", "orcid": "0000-0003-4653-7551", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9cd6146d3304ca98e1ec2648068b6ff.json"}}, {"family": "Esp\u00edndola-Hern\u00e1ndez", "given": "Pamela", "initials": "P"}, {"family": "Gilsenan", "given": "Carol", "initials": "C"}, {"family": "Ewels", "given": "Phil", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Kempenaers", "given": "Bart", "initials": "B", "orcid": "0000-0002-7505-5458", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b734c25f792436ba8d004ab4018dad2.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "31", "issue": "5", "pages": "1504-1514"}, "abstract": "Understanding the genomic landscape of adaptation is central to understanding microevolution in wild populations. Genomic targets of selection and the underlying genomic mechanisms of adaptation can be elucidated by genome-wide scans for past selective sweeps or by scans for direct fitness associations. We sequenced and assembled 150 haplotypes of 75 blue tits (Cyanistes caeruleus) of a single Central European population by a linked-read technology. We used these genome data in combination with coalescent simulations (i) to estimate an historical effective population size of ~250,000, which recently declined to ~10,000, and (ii) to identify genome-wide distributed selective sweeps of beneficial variants probably originating from standing genetic variation (soft sweeps). The genes linked to these soft sweeps, but also those linked to hard sweeps based on new beneficial mutants, showed a significant enrichment for functions associated with gene expression and transcription regulation. This emphasizes the importance of regulatory evolution in the population's adaptive history. Soft sweeps were further enriched for genes related to axon and synapse development, indicating the significance of neuronal connectivity changes in the brain potentially linked to behavioural adaptations. A previous scan of heterozygosity-fitness correlations revealed a consistent negative effect on arrival date at the breeding site for a single microsatellite in the MDGA2 gene. Here, we used the haplotype structure around this microsatellite to explain the effect as a local and direct outbreeding effect of a gene involved in synapse development.", "doi": "10.1111/mec.16345", "pmid": "34995389", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-03-29T13:48:45.916Z", "modified": "2022-08-18T14:59:56.937Z"}, {"entity": "publication", "iuid": "12756343a43441109cb2cec8e32aeb4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12756343a43441109cb2cec8e32aeb4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12756343a43441109cb2cec8e32aeb4c"}}, "title": "Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris).", "authors": [{"family": "Kardum Hjort", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-9901-9478", "researcher": {"href": "https://publications.scilifelab.se/researcher/eca2d55964664a0e8959f7f0fef324fa.json"}}, {"family": "Paris", "given": "Josephine R", "initials": "JR"}, {"family": "Olsson", "given": "Peter", "initials": "P"}, {"family": "Herbertsson", "given": "Lina", "initials": "L"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR"}, {"family": "Dudaniec", "given": "Rachael Y", "initials": "RY"}, {"family": "Smith", "given": "Henrik G", "initials": "HG"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "issn-l": "1752-4571", "volume": "15", "issue": "3", "pages": "365-382"}, "abstract": "The global movement of bees for agricultural pollination services can affect local pollinator populations via hybridization. When commercial bumblebees are of the same species but of different geographic origin, intraspecific hybridization may result in beneficial integration of new genetic variation, or alternatively may disrupt locally adapted gene complexes. However, neither the existence nor the extent of genomic introgression and evolutionary divergence between wild and commercial bumblebees is fully understood. We obtained whole-genome sequencing data from wild and commercial Bombus terrestris collected from sites in Southern Sweden with and without long-term use of commercially imported B. terrestris. We search for evidence of introgression, dispersal and genome-wide differentiation in a comparative genomic analysis of wild and commercial bumblebees. Commercial B. terrestris were found in natural environments near sites where commercial bumblebees were used, as well as drifting wild B. terrestris in commercial bumblebee colonies. However, we found no evidence for widespread, recent genomic introgression of commercial B. terrestris into local wild conspecific populations. We found that wild B. terrestris had significantly higher nucleotide diversity (Nei's pi, \u03c0), while the number of segregating sites (Watterson's theta, \u03b8w) was higher in commercial B. terrestris. A highly divergent region on chromosome 11 was identified in commercial B. terrestris and found to be enriched with structural variants. The genes present in this region are involved in flight muscle contraction and structure and pathogen immune response, providing evidence for differing evolutionary processes operating in wild and commercial B. terrestris. We did not find evidence for recent introgression, suggesting that co-occurring commercial B. terrestris have not disrupted evolutionary processes in wild B. terrestris populations.", "doi": "10.1111/eva.13346", "pmid": "35386397", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8965379"}, {"db": "pii", "key": "EVA13346"}], "notes": [], "created": "2022-08-19T08:37:21.470Z", "modified": "2025-11-27T14:14:31.904Z"}, {"entity": "publication", "iuid": "a9377e38c4fb4ae1920a4247903d1f42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9377e38c4fb4ae1920a4247903d1f42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9377e38c4fb4ae1920a4247903d1f42"}}, "title": "Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.", "authors": [{"family": "Ratz", "given": "Michael", "initials": "M", "orcid": "0000-0002-9795-8033", "researcher": {"href": "https://publications.scilifelab.se/researcher/a481899ca58a467499f56af4feb5457c.json"}}, {"family": "von Berlin", "given": "Leonie", "initials": "L", "orcid": "0000-0002-7790-0395", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c69f77dcc374d63b6717bef930206f9.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "25", "issue": "3", "pages": "285-294"}, "abstract": "The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the nervous system, but the lineage relationships between mature cell types and progenitor cells are not well understood. Here we show in vivo barcoding of early progenitors to simultaneously profile cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. By reconstructing thousands of clones, we discovered fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. We combined spatial transcriptomics with clonal barcoding and disentangled migration patterns of clonally related cells in densely labeled tissue sections. Our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture.", "doi": "10.1038/s41593-022-01011-x", "pmid": "35210624", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Single cell": "Service", "NGI Spatial omics": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8904259"}, {"db": "pii", "key": "10.1038/s41593-022-01011-x"}], "notes": [], "created": "2022-02-25T08:59:35.886Z", "modified": "2024-01-16T13:48:37.372Z"}, {"entity": "publication", "iuid": "b919fcbcfc42445690be42dfbb7fdfba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b919fcbcfc42445690be42dfbb7fdfba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b919fcbcfc42445690be42dfbb7fdfba"}}, "title": "ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.", "authors": [{"family": "Widmark", "given": "Albin", "initials": "A"}, {"family": "Sagredo", "given": "Eduardo A", "initials": "EA"}, {"family": "Karlstr\u00f6m", "given": "Victor", "initials": "V"}, {"family": "Behm", "given": "Mikaela", "initials": "M"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Daniel", "given": "Chammiran", "initials": "C"}, {"family": "\u00d6hman", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "J. Biol. Chem.", "issn": "1083-351X", "issn-l": "0021-9258", "volume": "298", "issue": "3", "pages": "101682"}, "abstract": "miRNAs are short noncoding RNA molecules that regulate gene expression by inhibiting translation or inducing degradation of target mRNAs. miRNAs are often expressed as polycistronic transcripts, so-called miRNA clusters, containing several miRNA precursors. The largest mammalian miRNA cluster, the miR-379-410 cluster, is expressed primarily during embryonic development and in the adult brain; however, downstream regulation of this cluster is not well understood. Here, we investigated adenosine deamination to inosine (RNA editing) in the miR-379-410 cluster by adenosine deaminase acting on RNA (ADAR) enzymes as a possible mechanism modulating the expression and activity of these miRNAs in a brain-specific manner. We show that the levels of editing in the majority of mature miRNAs are lower than the editing levels of the corresponding site in primary miRNA precursors. However, for one miRNA, miR-376b-3p, editing was significantly higher in the mature form than in the primary precursor. We found miR-376b-3p maturation is negatively regulated by ADAR2 in an editing activity-independent manner, whereas ADAR1-mediated and ADAR2-mediated editing were observed to be competitive. In addition, the edited miR-376b-3p targets a different set of mRNAs than unedited miR-376b-3p, including 4-aminobutyrate aminotransferase, encoding the enzyme responsible for the catabolism of the neurotransmitter gamma aminobutyric acid (GABA). Expression of edited miR-376b-3p led to increased intracellular GABA levels as well as increased cell surface presentation of GABA type A receptors. Our results indicate that both editing and editing-independent effects modulate the expression of miR-376b-3p, with the potential to regulate GABAergic signaling in the brain.", "doi": "10.1016/j.jbc.2022.101682", "pmid": "35124003", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8892144"}, {"db": "pii", "key": "S0021-9258(22)00122-3"}], "notes": [], "created": "2022-03-29T13:47:29.079Z", "modified": "2024-01-16T13:48:37.394Z"}, {"entity": "publication", "iuid": "08f15b6b8d674af294f91bd5ad4005d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08f15b6b8d674af294f91bd5ad4005d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08f15b6b8d674af294f91bd5ad4005d3"}}, "title": "The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.", "authors": [{"family": "Sturk-Andreaggi", "given": "Kimberly", "initials": "K", "orcid": "0000-0001-6857-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1cbf7b4fd94b17b1c37712634b7638.json"}}, {"family": "Ring", "given": "Joseph D", "initials": "JD"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Bodner", "given": "Martin", "initials": "M", "orcid": "0000-0002-3870-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/455fefcf430d4b7e8433b3c7b3856b4b.json"}}, {"family": "Parson", "given": "Walther", "initials": "W", "orcid": "0000-0002-5692-2392", "researcher": {"href": "https://publications.scilifelab.se/researcher/84574a9a6f03419ea3a37a6dd0470082.json"}}, {"family": "Marshall", "given": "Charla", "initials": "C", "orcid": "0000-0002-8495-1748", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b9e14fcfae4eeea425cf685cf6d6ba.json"}}, {"family": "Allen", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "23", "issue": "4", "pages": null}, "abstract": "Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612-13,105 and 16,390-16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.", "doi": "10.3390/ijms23042244", "pmid": "35216360", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8876724"}, {"db": "pii", "key": "ijms23042244"}], "notes": [], "created": "2022-03-29T04:39:22.438Z", "modified": "2024-01-16T13:48:37.438Z"}, {"entity": "publication", "iuid": "2488c6cb0e74465fb22eafbfe10e83fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2488c6cb0e74465fb22eafbfe10e83fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2488c6cb0e74465fb22eafbfe10e83fc"}}, "title": "Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.", "authors": [{"family": "Andr\u00e9", "given": "Domenique", "initials": "D"}, {"family": "Zambrano", "given": "Jos\u00e9 Alfredo", "initials": "JA"}, {"family": "Zhang", "given": "Bo", "initials": "B"}, {"family": "Lee", "given": "Keh Chien", "initials": "KC"}, {"family": "R\u00fchl", "given": "Mark", "initials": "M"}, {"family": "Marcon", "given": "Alice", "initials": "A"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}], "type": "journal article", "published": "2022-02-17", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "13", "issue": null, "pages": "823019"}, "abstract": "SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.", "doi": "10.3389/fpls.2022.823019", "pmid": "35251092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8891642"}], "notes": [], "created": "2022-03-29T13:48:44.625Z", "modified": "2024-01-16T13:48:37.467Z"}, {"entity": "publication", "iuid": "b1a6f3fb64d34dc5b599349bc378a722", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1a6f3fb64d34dc5b599349bc378a722.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1a6f3fb64d34dc5b599349bc378a722"}}, "title": "Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D", "orcid": "0000-0002-9391-5722", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebb422a68344362a76e1bd23bfb5b49.json"}}, {"family": "Carlberg", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-1774-6058", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e018cce30794ae08a4d7b5096914169.json"}}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Hildebrandt", "given": "Franziska", "initials": "F"}, {"family": "Korotkova", "given": "Marina", "initials": "M"}, {"family": "Hensvold", "given": "Aase H", "initials": "AH"}, {"family": "Catrina", "given": "Anca I", "initials": "AI"}, {"family": "Sorger", "given": "Peter K", "initials": "PK", "orcid": "0000-0002-3364-1838", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c63ad2d92e943b89ea7590c8a928ad9.json"}}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "129"}, "abstract": "The inflamed rheumatic joint is a highly heterogeneous and complex tissue with dynamic recruitment and expansion of multiple cell types that interact in multifaceted ways within a localized area. Rheumatoid arthritis synovium has primarily been studied either by immunostaining or by molecular profiling after tissue homogenization. Here, we use Spatial Transcriptomics, where tissue-resident RNA is spatially labeled in situ with barcodes in a transcriptome-wide fashion, to study local tissue interactions at the site of chronic synovial inflammation. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Combining morphological features and high-throughput spatially resolved transcriptomics may be able to provide higher statistical power and more insights into monitoring disease severity and treatment-specific responses in seropositive and seronegative rheumatoid arthritis.", "doi": "10.1038/s42003-022-03050-3", "pmid": "35149753", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-022-03050-3"}, {"db": "pmc", "key": "PMC8837632"}], "notes": [], "created": "2022-03-29T13:47:26.413Z", "modified": "2022-08-19T09:06:49.671Z"}, {"entity": "publication", "iuid": "ec581b66240c426ca45bd1ab1951a61a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec581b66240c426ca45bd1ab1951a61a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec581b66240c426ca45bd1ab1951a61a"}}, "title": "The spatial transcriptomic landscape of the healing mouse intestine following damage.", "authors": [{"family": "Parigi", "given": "Sara M", "initials": "SM"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Das", "given": "Srustidhar", "initials": "S"}, {"family": "Ramirez Flores", "given": "Ricardo O", "initials": "RO", "orcid": "0000-0003-0087-371X", "researcher": {"href": "https://publications.scilifelab.se/researcher/51f01d7b57044e628850bb9705e03ed0.json"}}, {"family": "Frede", "given": "Annika", "initials": "A"}, {"family": "Tripathi", "given": "Kumar P", "initials": "KP"}, {"family": "Diaz", "given": "Oscar E", "initials": "OE", "orcid": "0000-0001-7622-7832", "researcher": {"href": "https://publications.scilifelab.se/researcher/9aae40d7294841989eee4629596395d3.json"}}, {"family": "Selin", "given": "Katja", "initials": "K", "orcid": "0000-0002-8888-0529", "researcher": {"href": "https://publications.scilifelab.se/researcher/64550a7d2143443dbf3f1575ab3f870d.json"}}, {"family": "Morales", "given": "Rodrigo A", "initials": "RA", "orcid": "0000-0003-4382-5777", "researcher": {"href": "https://publications.scilifelab.se/researcher/61802da2579446d5b2a73c4f06b9969e.json"}}, {"family": "Luo", "given": "Xinxin", "initials": "X"}, {"family": "Monasterio", "given": "Gustavo", "initials": "G"}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Gagliani", "given": "Nicola", "initials": "N", "orcid": "0000-0001-8514-1395", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cc11473c8944eebc0974780d1c6919.json"}}, {"family": "Saez-Rodriguez", "given": "Julio", "initials": "J", "orcid": "0000-0002-8552-8976", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0043f77cad4f6e8ab9641d7f42c420.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Villablanca", "given": "Eduardo J", "initials": "EJ", "orcid": "0000-0001-9522-9729", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c6a2dde2d8f40ef82dfba0cf1b52c0d.json"}}], "type": "journal article", "published": "2022-02-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "828"}, "abstract": "The intestinal barrier is composed of a complex cell network defining highly compartmentalized and specialized structures. Here, we use spatial transcriptomics to define how the transcriptomic landscape is spatially organized in the steady state and healing murine colon. At steady state conditions, we demonstrate a previously unappreciated molecular regionalization of the colon, which dramatically changes during mucosal healing. Here, we identified spatially-organized transcriptional programs defining compartmentalized mucosal healing, and regions with dominant wired pathways. Furthermore, we showed that decreased p53 activation defined areas with increased presence of proliferating epithelial stem cells. Finally, we mapped transcriptomics modules associated with human diseases demonstrating the translational potential of our dataset. Overall, we provide a publicly available resource defining principles of transcriptomic regionalization of the colon during mucosal healing and a framework to develop and progress further hypotheses.", "doi": "10.1038/s41467-022-28497-0", "pmid": "35149721", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Spatial omics": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-28497-0"}, {"db": "pmc", "key": "PMC8837647"}], "notes": [], "created": "2022-03-29T13:47:22.254Z", "modified": "2022-08-19T09:06:40.669Z"}, {"entity": "publication", "iuid": "227835dd47d040b1b51f9f718b8e46e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/227835dd47d040b1b51f9f718b8e46e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/227835dd47d040b1b51f9f718b8e46e2"}}, "title": "Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids.", "authors": [{"family": "Hou", "given": "Xiao-Qing", "initials": "XQ"}, {"family": "Zhang", "given": "Dan-Dan", "initials": "DD"}, {"family": "Powell", "given": "Daniel", "initials": "D"}, {"family": "Wang", "given": "Hong-Lei", "initials": "HL"}, {"family": "Andersson", "given": "Martin N", "initials": "MN"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C", "orcid": "0000-0002-3116-6922", "researcher": {"href": "https://publications.scilifelab.se/researcher/68150ac5a3d44f26af3fa81a5209c535.json"}}], "type": "journal article", "published": "2022-02-07", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "issn-l": "1741-7007", "volume": "20", "issue": "1", "pages": "34"}, "abstract": "In insects, airborne chemical signals are mainly detected by two receptor families, odorant receptors (ORs) and ionotropic receptors (IRs). Functions of ORs have been intensively investigated in Diptera and Lepidoptera, while the functions and evolution of the more ancient IR family remain largely unexplored beyond Diptera.\n\nHere, we identified a repertoire of 26 IRs from transcriptomes of female and male antennae, and ovipositors in the moth Agrotis segetum. We observed that a large clade formed by IR75p and IR75q expansions is closely related to the acid-sensing IRs identified in Diptera. We functionally assayed each of the five AsegIRs from this clade using Xenopus oocytes and found that two receptors responded to the tested ligands. AsegIR75p.1 responded to several compounds but hexanoic acid was revealed to be the primary ligand, and AsegIR75q.1 responded primarily to octanoic acid, and less so to nonanoic acid. It has been reported that the C6-C10 medium-chain fatty acids repel various insects including many drosophilids and mosquitos. We show that the C6-C10 medium-chain fatty acids elicited antennal responses of both sexes of A. segetum, while only octanoic acid had repellent effect to the moths in a behavioral assay. In addition, using fluorescence in situ hybridization, we demonstrated that the five IRs and their co-receptor AsegIR8a are not located in coeloconic sensilla as found in Drosophila, but in basiconic or trichoid sensilla.\n\nOur results significantly expand the current knowledge of the insect IR family. Based on the functional data in combination with phylogenetic analysis, we propose that subfunctionalization after gene duplication plays an important role in the evolution of ligand specificities of the acid-sensing IRs in Lepidoptera.", "doi": "10.1186/s12915-022-01235-0", "pmid": "35130883", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-022-01235-0"}, {"db": "pmc", "key": "PMC8822749"}], "notes": [], "created": "2022-03-29T13:48:29.753Z", "modified": "2024-01-16T13:48:37.525Z"}, {"entity": "publication", "iuid": "a55225efd1884cc69dcd9e06cf662675", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a55225efd1884cc69dcd9e06cf662675.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a55225efd1884cc69dcd9e06cf662675"}}, "title": "Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.", "authors": [{"family": "Schuy", "given": "Jakob", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Shahrokhshahi", "given": "Niloofar", "initials": "N"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Shahsavani", "given": "Mansoureh", "initials": "M"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2022-02-04", "journal": {"title": "Front Genet", "issn": "1664-8021", "issn-l": "1664-8021", "volume": "12", "issue": null, "pages": "803683"}, "abstract": "Induced pluripotent stem cells (iPSCs) from patients are an attractive disease model to study tissues with poor accessibility such as the brain. Using this approach, we and others have shown that trisomy 21 results in genome-wide transcriptional dysregulations. The effects of loss of genes on chromosome 21 is much less characterized. Here, we use patient-derived neural cells from an individual with neurodevelopmental delay and a ring chromosome 21 with two deletions spanning 3.8 Mb at the terminal end of 21q22.3, containing 60 protein-coding genes. To investigate the molecular perturbations of the partial monosomy on neural cells, we established patient-derived iPSCs from fibroblasts retaining the ring chromosome 21, and we then induced iPSCs into neuroepithelial stem cells. RNA-Seq analysis of NESCs with the ring chromosome revealed downregulation of 18 genes within the deleted region together with global transcriptomic dysregulations when compared to euploid NESCs. Since the deletions on chromosome 21 represent a genetic \"contrary\" to trisomy of the corresponding region, we further compared the dysregulated transcriptomic profile in with that of two NESC lines with trisomy 21. The analysis revealed opposed expression changes for 23 genes on chromosome 21 as well as 149 non-chromosome 21 genes. Taken together, our results bring insights into the effects on the global and chromosome 21 specific gene expression from a partial monosomy of chromosome 21qter during early neuronal differentiation.", "doi": "10.3389/fgene.2021.803683", "pmid": "35186010", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8854775"}, {"db": "pii", "key": "803683"}], "notes": [], "created": "2022-03-29T13:48:02.703Z", "modified": "2024-01-16T13:48:37.541Z"}, {"entity": "publication", "iuid": "e015c071dbe0428fb3ca40635d198713", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e015c071dbe0428fb3ca40635d198713.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e015c071dbe0428fb3ca40635d198713"}}, "title": "Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.", "authors": [{"family": "Le Duc", "given": "Diana", "initials": "D", "orcid": "0000-0001-7289-2552", "researcher": {"href": "https://publications.scilifelab.se/researcher/43cb1e364fc8408296ed8020b7196f53.json"}}, {"family": "Velluva", "given": "Akhil", "initials": "A", "orcid": "0000-0003-0859-3624", "researcher": {"href": "https://publications.scilifelab.se/researcher/22bf0c696d2e40a38ddcf60b09165339.json"}}, {"family": "Cassatt-Johnstone", "given": "Molly", "initials": "M", "orcid": "0000-0001-7278-8333", "researcher": {"href": "https://publications.scilifelab.se/researcher/a008c2a3fd42458f93fb3c6256aeba9b.json"}}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Baleka", "given": "Sina", "initials": "S", "orcid": "0000-0002-8850-9420", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8c3c655ce8649608799b0d7aa9fa705.json"}}, {"family": "Lin", "given": "Chen-Ching", "initials": "C"}, {"family": "Lemke", "given": "Johannes R", "initials": "JR", "orcid": "0000-0002-4435-6610", "researcher": {"href": "https://publications.scilifelab.se/researcher/352294fdf9cd493da90292c31a9c6a7e.json"}}, {"family": "Southon", "given": "John R", "initials": "JR"}, {"family": "Burdin", "given": "Alexander", "initials": "A", "orcid": "0000-0001-5701-1008", "researcher": {"href": "https://publications.scilifelab.se/researcher/acd72ad931e1472bbb9c6caefc9d2b44.json"}}, {"family": "Wang", "given": "Ming-Shan", "initials": "M"}, {"family": "Grunewald", "given": "Sonja", "initials": "S", "orcid": "0000-0002-2165-6274", "researcher": {"href": "https://publications.scilifelab.se/researcher/a409fad52d1647e0b4f55bb290f6c56f.json"}}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Joger", "given": "Ulrich", "initials": "U"}, {"family": "Rutschmann", "given": "Sereina", "initials": "S"}, {"family": "Hildebrandt", "given": "Thomas B", "initials": "TB", "orcid": "0000-0001-8685-4733", "researcher": {"href": "https://publications.scilifelab.se/researcher/466fd7cfdc934d328cea5823f5728c98.json"}}, {"family": "Fritsch", "given": "Guido", "initials": "G", "orcid": "0000-0002-1296-9586", "researcher": {"href": "https://publications.scilifelab.se/researcher/38901590e3c448e2b2bad86b6cf588a3.json"}}, {"family": "Estes", "given": "James A", "initials": "JA", "orcid": "0000-0002-3632-4555", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8c15b28e41944238e6871fb21116f1a.json"}}, {"family": "Kelso", "given": "Janet", "initials": "J", "orcid": "0000-0002-3618-322X", "researcher": {"href": "https://publications.scilifelab.se/researcher/57db79fef05b4743bff8345f8c3dfc04.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M", "orcid": "0000-0003-0441-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/f18713dbd0044cb2bd6dfc3bad1cf349.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Sch\u00f6neberg", "given": "Torsten", "initials": "T", "orcid": "0000-0001-5313-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/27274c04fd23401f8da747f5cc7f70b0.json"}}], "type": "journal article", "published": "2022-02-04", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "5", "pages": "eabl6496"}, "abstract": "Steller's sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller's descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller's sea cow and cetaceans but not extant sirenians, suggesting a role of several genes in adaptation to cold aquatic (or marine) environments. Among these are inactivations of lipoxygenase genes, which in humans and mouse models cause ichthyosis, a skin disease characterized by a thick, hyperkeratotic epidermis that recapitulates Steller's sea cows' reportedly bark-like skin. We also found that Steller's sea cows' abundance was continuously declining for tens of thousands of years before their description, implying that environmental changes also contributed to their extinction.", "doi": "10.1126/sciadv.abl6496", "pmid": "35119923", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8816345"}], "notes": [], "created": "2022-03-29T13:47:31.563Z", "modified": "2024-01-16T13:48:37.573Z"}, {"entity": "publication", "iuid": "95fc46bcb7654466ac708cc088b05da0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95fc46bcb7654466ac708cc088b05da0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95fc46bcb7654466ac708cc088b05da0"}}, "title": "Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.", "authors": [{"family": "Hernandez-Castro", "given": "Luis E", "initials": "LE", "orcid": "0000-0002-2342-1655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a3d9ad2f09c48088c1e4534f174abea.json"}}, {"family": "Villac\u00eds", "given": "Anita G", "initials": "AG"}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Cheaib", "given": "Bachar", "initials": "B", "orcid": "0000-0002-0325-823X", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b88320f2a54e299d7465e63ad65d9f.json"}}, {"family": "Day", "given": "Casey C", "initials": "CC", "orcid": "0000-0001-6096-3448", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9bbc7fd2e524a149935d04e43d14d93.json"}}, {"family": "Oca\u00f1a-Mayorga", "given": "Sof\u00eda", "initials": "S", "orcid": "0000-0003-3861-9784", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0019340458d49089833e986a1d780fc.json"}}, {"family": "Yumiseva", "given": "Cesar A", "initials": "CA"}, {"family": "Bacigalupo", "given": "Antonella", "initials": "A", "orcid": "0000-0003-1661-8916", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf83a4fc78244f93981bac5e050afdf1.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-4624-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85416dce306436ab0c4cdeea22a1f59.json"}}, {"family": "Matthews", "given": "Louise", "initials": "L", "orcid": "0000-0003-4420-8367", "researcher": {"href": "https://publications.scilifelab.se/researcher/00c9c18fa9ac4a769dc607c9ec348e77.json"}}, {"family": "Landguth", "given": "Erin L", "initials": "EL", "orcid": "0000-0002-7044-346X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d218881fdff49339ac0d9f3cdbbbe54.json"}}, {"family": "Costales", "given": "Jaime A", "initials": "JA", "orcid": "0000-0001-9418-6640", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c4d4a83625f4e0ab3b82cbec4b1d996.json"}}, {"family": "Llewellyn", "given": "Martin S", "initials": "MS", "orcid": "0000-0001-9856-1591", "researcher": {"href": "https://publications.scilifelab.se/researcher/89a41a3c068943b9ac42025d7d4b6136.json"}}, {"family": "Grijalva", "given": "Mario J", "initials": "MJ", "orcid": "0000-0003-1964-1425", "researcher": {"href": "https://publications.scilifelab.se/researcher/de30f95bb60248639fd5995abee30c17.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "18", "issue": "2", "pages": "e1010019"}, "abstract": "Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches.", "doi": "10.1371/journal.pgen.1010019", "pmid": "35120121", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-21-00937"}, {"db": "pmc", "key": "PMC8849464"}], "notes": [], "created": "2022-03-29T13:48:50.208Z", "modified": "2022-08-19T08:58:50.879Z"}, {"entity": "publication", "iuid": "bac07fae3c0e4214bca1d4ff1a326f39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39"}}, "title": "A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Whitley", "given": "Kaitlyn M", "initials": "KM"}, {"family": "Sullivan", "given": "Isabel", "initials": "I"}, {"family": "Geib", "given": "Jennifer C", "initials": "JC"}, {"family": "Miller-Struttmann", "given": "Nicole E", "initials": "NE"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "31", "issue": "4", "pages": "1111-1127"}, "abstract": "Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species (\"incognitus\"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.", "doi": "10.1111/mec.16291", "pmid": "34837435", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Long read": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-11-30T12:41:55.744Z", "modified": "2024-01-16T13:48:37.663Z"}, {"entity": "publication", "iuid": "069fec14ac8c4841a7bc3127fa86355d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/069fec14ac8c4841a7bc3127fa86355d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/069fec14ac8c4841a7bc3127fa86355d"}}, "title": "Occasional paternal inheritance of the germline-restricted chromosome in songbirds.", "authors": [{"family": "Pei", "given": "Yifan", "initials": "Y", "orcid": "0000-0002-2411-4454", "researcher": {"href": "https://publications.scilifelab.se/researcher/af91cebf5fa04abb9656aaf9123ad53b.json"}}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-5984-8925", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a07a11116004a05adea2ee593ba7cc9.json"}}, {"family": "Ruiz-Ruano", "given": "Francisco J", "initials": "FJ", "orcid": "0000-0002-5391-301X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37ccedb49884e27aeffed3b49085ddf.json"}}, {"family": "Mueller", "given": "Jakob C", "initials": "JC", "orcid": "0000-0001-6676-7595", "researcher": {"href": "https://publications.scilifelab.se/researcher/5236c473e0434e97b48f4259fc28149b.json"}}, {"family": "Cabrero", "given": "Josefa", "initials": "J", "orcid": "0000-0002-5848-6985", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c5b1ae3e51f47d4989a39089796dd38.json"}}, {"family": "Camacho", "given": "Juan Pedro M", "initials": "JPM", "orcid": "0000-0002-2507-9814", "researcher": {"href": "https://publications.scilifelab.se/researcher/f41fae6a46f84c21a907ded6544574cf.json"}}, {"family": "Alch\u00e9", "given": "Juan D", "initials": "JD", "orcid": "0000-0002-7547-6025", "researcher": {"href": "https://publications.scilifelab.se/researcher/df53deb79fd14668b7ecfd5fc14959e9.json"}}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Hoeppner", "given": "Marc", "initials": "M"}, {"family": "B\u00f6rno", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7990-9625", "researcher": {"href": "https://publications.scilifelab.se/researcher/a75924a21f5c4db59b4d449acfc4ae5a.json"}}, {"family": "Gessara", "given": "Ivana", "initials": "I", "orcid": "0000-0001-9834-9013", "researcher": {"href": "https://publications.scilifelab.se/researcher/c32eab7ad57044df9f693f283736fb4c.json"}}, {"family": "Hertel", "given": "Moritz", "initials": "M"}, {"family": "Teltscher", "given": "Kim", "initials": "K", "orcid": "0000-0003-3997-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/7653b22be14c499b854f3c9d0d9563af.json"}}, {"family": "Knief", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-6959-3033", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8858c7c7b44a008a172bc637957ce1.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Kempenaers", "given": "Bart", "initials": "B", "orcid": "0000-0002-7505-5458", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b734c25f792436ba8d004ab4018dad2.json"}}], "type": "journal article", "published": "2022-01-25", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "119", "issue": "4", "pages": null}, "abstract": "Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.", "doi": "10.1073/pnas.2103960119", "pmid": "35058355", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8794876"}, {"db": "pii", "key": "2103960119"}], "notes": [], "created": "2022-03-29T13:48:24.377Z", "modified": "2024-01-16T13:48:37.688Z"}, {"entity": "publication", "iuid": "00097c342d474f85a1fe229a74798c7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00097c342d474f85a1fe229a74798c7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00097c342d474f85a1fe229a74798c7b"}}, "title": "Massive genome inversion drives coexistence of divergent morphs in common quails.", "authors": [{"family": "Sanchez-Donoso", "given": "Ines", "initials": "I", "orcid": "0000-0003-2773-9844", "researcher": {"href": "https://publications.scilifelab.se/researcher/917f54b110bd4aca8efbcf3cd9aef4e7.json"}}, {"family": "Ravagni", "given": "Sara", "initials": "S", "orcid": "0000-0003-0320-3447", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cb16a7faa1a4952b3247d440d2cdf5f.json"}}, {"family": "Rodr\u00edguez-Teijeiro", "given": "J Domingo", "initials": "JD"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Huang", "given": "Yan", "initials": "Y"}, {"family": "Maldonado-Linares", "given": "Andros", "initials": "A"}, {"family": "Puigcerver", "given": "Manel", "initials": "M"}, {"family": "Jim\u00e9nez-Blasco", "given": "Irene", "initials": "I"}, {"family": "Andrade", "given": "Pedro", "initials": "P"}, {"family": "Gon\u00e7alves", "given": "David", "initials": "D"}, {"family": "Friis", "given": "Guillermo", "initials": "G", "orcid": "0000-0002-0731-6468", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa844934c3544b37ba2c9874ed8f9b8d.json"}}, {"family": "Roig", "given": "Ignasi", "initials": "I", "orcid": "0000-0003-0313-3581", "researcher": {"href": "https://publications.scilifelab.se/researcher/138805893cb940d39e98c8347f909260.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}, {"family": "Leonard", "given": "Jennifer A", "initials": "JA"}, {"family": "Vil\u00e0", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2022-01-24", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "2", "pages": "462-469.e6"}, "abstract": "The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats,1,2 and whose females may lay successive clutches at different locations while migrating.3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jim\u00e9nez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.", "doi": "10.1016/j.cub.2021.11.019", "pmid": "34847353", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)01543-8"}], "notes": [], "created": "2021-11-30T12:50:56.211Z", "modified": "2022-08-19T08:57:48.552Z"}, {"entity": "publication", "iuid": "c185eca3b3494dcdabeca9eb7b35ee47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c185eca3b3494dcdabeca9eb7b35ee47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c185eca3b3494dcdabeca9eb7b35ee47"}}, "title": "Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.", "authors": [{"family": "Berggren", "given": "Hanna", "initials": "H"}, {"family": "Tibblin", "given": "Petter", "initials": "P"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Ye\u015ferin", "initials": "Y"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Larsson", "given": "Per", "initials": "P"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Forsman", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2022-01-21", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "issn-l": "1664-302X", "volume": "12", "issue": null, "pages": "767770"}, "abstract": "Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.", "doi": "10.3389/fmicb.2021.767770", "pmid": "35126324", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8813977"}], "notes": [], "created": "2022-03-29T13:48:25.889Z", "modified": "2024-01-16T13:48:37.705Z"}, {"entity": "publication", "iuid": "45d2428a38a64c9c9e56907065a2e49a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45d2428a38a64c9c9e56907065a2e49a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45d2428a38a64c9c9e56907065a2e49a"}}, "title": "Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.", "authors": [{"family": "\u00d6hlund", "given": "Pontus", "initials": "P"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Hayer", "given": "Juliette", "initials": "J", "orcid": "0000-0003-4899-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9535fdd81a2347528a48540c78decf1e.json"}}, {"family": "Hesson", "given": "Jenny C", "initials": "JC", "orcid": "0000-0003-2489-4400", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc38909bfe20449f9de91560a1aee6ce.json"}}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}], "type": "journal article", "published": "2022-01-14", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "23", "issue": "2", "pages": null}, "abstract": "Understanding the flavivirus infection process in mosquito hosts is important and fundamental in the search for novel control strategies that target the mosquitoes' ability to carry and transmit pathogenic arboviruses. A group of viruses known as insect-specific viruses (ISVs) has been shown to interfere with the infection and replication of a secondary arbovirus infection in mosquitoes and mosquito-derived cell lines. However, the molecular mechanisms behind this interference are unknown. Therefore, in the present study, we infected the Aedes albopictus cell line U4.4 with either the West Nile virus (WNV), the insect-specific Lammi virus (LamV) or an infection scheme whereby cells were pre-infected with LamV 24 h prior to WNV challenge. The qPCR analysis showed that the dual-infected U4.4 cells had a reduced number of WNV RNA copies compared to WNV-only infected cells. The transcriptome profiles of the different infection groups showed a variety of genes with altered expression. WNV-infected cells had an up-regulation of a broad range of immune-related genes, while in LamV-infected cells, many genes related to stress, such as different heat-shock proteins, were up-regulated. The transcriptome profile of the dual-infected cells was a mix of up- and down-regulated genes triggered by both viruses. Furthermore, we observed an up-regulation of signal peptidase complex (SPC) proteins in all infection groups. These SPC proteins have shown importance for flavivirus assembly and secretion and could be potential targets for gene modification in strategies for the interruption of flavivirus transmission by mosquitoes.", "doi": "10.3390/ijms23020875", "pmid": "35055061", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8777793"}, {"db": "pii", "key": "ijms23020875"}], "notes": [], "created": "2022-03-29T13:48:43.380Z", "modified": "2024-01-16T13:48:37.721Z"}, {"entity": "publication", "iuid": "f19a9fcf2233411d89334859fc9ac0d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f19a9fcf2233411d89334859fc9ac0d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f19a9fcf2233411d89334859fc9ac0d6"}}, "title": "Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.", "authors": [{"family": "Ghadamgahi", "given": "Farideh", "initials": "F", "orcid": "0000-0001-6614-0944", "researcher": {"href": "https://publications.scilifelab.se/researcher/721f37e18c6b438e9f292da5a360f8ab.json"}}, {"family": "Tarighi", "given": "Saeed", "initials": "S", "orcid": "0000-0003-1021-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d34fda31b0654a0d9a743ee040c48be2.json"}}, {"family": "Taheri", "given": "Parissa", "initials": "P", "orcid": "0000-0002-2848-337X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d1403da909541aeb07e37e94600ad42.json"}}, {"family": "Saripella", "given": "Ganapathi Varma", "initials": "GV", "orcid": "0000-0003-3504-9333", "researcher": {"href": "https://publications.scilifelab.se/researcher/494b3df440974bb7a42af6843c9ad415.json"}}, {"family": "Anzalone", "given": "Alice", "initials": "A"}, {"family": "Kalyandurg", "given": "Pruthvi Balachandra", "initials": "PB", "orcid": "0000-0003-2091-2739", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cad320bef7747728d926284f00ce25e.json"}}, {"family": "Catara", "given": "Vittoria", "initials": "V", "orcid": "0000-0001-8076-258X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae7b3ef0d25245918786cbe672960b3a.json"}}, {"family": "Ortiz", "given": "Rodomiro", "initials": "R", "orcid": "0000-0002-1739-7206", "researcher": {"href": "https://publications.scilifelab.se/researcher/63be215302d140b58050b7f04060d1ca.json"}}, {"family": "Vetukuri", "given": "Ramesh Raju", "initials": "RR", "orcid": "0000-0001-7129-5326", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbb5fb93506a4b3a8faacc38397a741c.json"}}], "type": "journal article", "published": "2022-01-14", "journal": {"title": "Biology (Basel)", "issn": "2079-7737", "issn-l": null, "volume": "11", "issue": "1", "pages": null}, "abstract": "P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent.", "doi": "10.3390/biology11010140", "pmid": "35053136", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "biology11010140"}, {"db": "pmc", "key": "PMC8773043"}], "notes": [], "created": "2022-03-29T13:48:28.310Z", "modified": "2022-08-19T08:55:20.686Z"}, {"entity": "publication", "iuid": "92f07130682a4fa283e3b89d3d9a1249", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f07130682a4fa283e3b89d3d9a1249.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f07130682a4fa283e3b89d3d9a1249"}}, "title": "The formation of avian montane diversity across barriers and along elevational gradients.", "authors": [{"family": "Pujolar", "given": "Jos\u00e9 Mart\u00edn", "initials": "JM"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH"}, {"family": "Kennedy", "given": "Jonathan D", "initials": "JD", "orcid": "0000-0002-2843-122X", "researcher": {"href": "https://publications.scilifelab.se/researcher/efdccdbf3f5a44b39a66d7ece5f174f7.json"}}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ"}, {"family": "Korneliussen", "given": "Thorfinn S", "initials": "TS"}, {"family": "Freeman", "given": "Benjamin G", "initials": "BG", "orcid": "0000-0001-6131-6832", "researcher": {"href": "https://publications.scilifelab.se/researcher/e05aaf37772b4f50a12b20db5d2db3c8.json"}}, {"family": "Sam", "given": "Katerina", "initials": "K"}, {"family": "Linck", "given": "Ethan", "initials": "E"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "Iova", "given": "Bulisa", "initials": "B"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Maiah", "given": "Gibson", "initials": "G"}, {"family": "Paul", "given": "Luda", "initials": "L"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}], "type": "journal article", "published": "2022-01-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "268"}, "abstract": "Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.", "doi": "10.1038/s41467-021-27858-5", "pmid": "35022441", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27858-5"}, {"db": "pmc", "key": "PMC8755808"}], "notes": [], "created": "2022-03-29T13:48:03.888Z", "modified": "2024-01-16T13:48:37.739Z"}, {"entity": "publication", "iuid": "d1c02b37ff1e42cf98540d9d4d2e9035", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1c02b37ff1e42cf98540d9d4d2e9035.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1c02b37ff1e42cf98540d9d4d2e9035"}}, "title": "Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.", "authors": [{"family": "Westmeijer", "given": "George", "initials": "G", "orcid": "0000-0002-5529-2237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2146c3e286d4f858efb5787cb3c74a2.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Alakangas", "given": "Linda", "initials": "L"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "37"}, "abstract": "The deep biosphere is an energy constrained ecosystem yet fosters diverse microbial communities that are key in biogeochemical cycling. Whether microbial communities in deep biosphere groundwaters are shaped by infiltration of allochthonous surface microorganisms or the evolution of autochthonous species remains unresolved. In this study, 16S rRNA gene amplicon analyses showed that few groups of surface microbes infiltrated deep biosphere groundwaters at the \u00c4sp\u00f6 Hard Rock Laboratory, Sweden, but that such populations constituted up to 49% of the microbial abundance. The dominant persisting phyla included Patescibacteria, Proteobacteria, and Epsilonbacteraeota. Despite the hydrological connection of the Baltic Sea with the studied groundwaters, infiltrating microbes predominantly originated from deep soil groundwater. Most deep biosphere groundwater populations lacked surface representatives, suggesting that they have evolved from ancient autochthonous populations. We propose that deep biosphere groundwater communities in the Fennoscandian Shield consist of selected infiltrated and indigenous populations adapted to the prevailing conditions.", "doi": "10.1038/s42003-021-02980-8", "pmid": "35017653", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8752596"}, {"db": "pii", "key": "10.1038/s42003-021-02980-8"}], "notes": [], "created": "2022-03-29T13:47:23.684Z", "modified": "2024-01-16T13:48:37.771Z"}, {"entity": "publication", "iuid": "818045cf427e448a88ca0016ae161e99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/818045cf427e448a88ca0016ae161e99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/818045cf427e448a88ca0016ae161e99"}}, "title": "Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.", "authors": [{"family": "Chachoua", "given": "Ilyas", "initials": "I"}, {"family": "Tzelepis", "given": "Ilias", "initials": "I", "orcid": "0000-0001-5777-6334", "researcher": {"href": "https://publications.scilifelab.se/researcher/18d93209d4bd4173bebec63d50462fe5.json"}}, {"family": "Dai", "given": "Hao", "initials": "H"}, {"family": "Lim", "given": "Jia Pei", "initials": "JP"}, {"family": "Lewandowska-Ronnegren", "given": "Anna", "initials": "A"}, {"family": "Casagrande", "given": "Felipe Beccaria", "initials": "FB", "orcid": "0000-0003-1117-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec52e8f2c91840858ed9c496481bc97b.json"}}, {"family": "Wu", "given": "Shuangyang", "initials": "S"}, {"family": "Vestlund", "given": "Johanna", "initials": "J", "orcid": "0000-0001-7158-905X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1589ce6268784aa6b599b3fd07caeb9d.json"}}, {"family": "Mallet de Lima", "given": "Carolina Diettrich", "initials": "CD"}, {"family": "Bhartiya", "given": "Deeksha", "initials": "D"}, {"family": "Scholz", "given": "Barbara A", "initials": "BA"}, {"family": "Martino", "given": "Mirco", "initials": "M", "orcid": "0000-0002-0954-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d73809cbf204985a5d90befd9f65766.json"}}, {"family": "Mehmood", "given": "Rashid", "initials": "R", "orcid": "0000-0002-3488-9413", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e41df49c1e8470a9851829de9cf6a08.json"}}, {"family": "G\u00f6nd\u00f6r", "given": "Anita", "initials": "A", "orcid": "0000-0002-1523-4411", "researcher": {"href": "https://publications.scilifelab.se/researcher/611abc86936c400e91670eaee7a91fec.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "204"}, "abstract": "Abnormal WNT signaling increases MYC expression in colon cancer cells in part via oncogenic super-enhancer-(OSE)-mediated gating of the active MYC to the nuclear pore in a poorly understood process. We show here that the principal tenet of the WNT-regulated MYC gating, facilitating nuclear export of the MYC mRNA, is regulated by a CTCF binding site (CTCFBS) within the OSE to confer growth advantage in HCT-116 cells. To achieve this, the CTCFBS directs the WNT-dependent trafficking of the OSE to the nuclear pore from intra-nucleoplasmic positions in a stepwise manner. Once the OSE reaches a peripheral position, which is triggered by a CTCFBS-mediated CCAT1 eRNA activation, its final stretch (\u22640.7 \u03bcm) to the nuclear pore requires the recruitment of AHCTF1, a key nucleoporin, to the CTCFBS. Thus, a WNT/\u00df-catenin-AHCTF1-CTCF-eRNA circuit enables the OSE to promote pathological cell growth by coordinating the trafficking of the active MYC gene within the 3D nuclear architecture.", "doi": "10.1038/s41467-021-27868-3", "pmid": "35017527", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-27868-3"}, {"db": "pmc", "key": "PMC8752836"}], "notes": [], "created": "2022-03-29T13:48:00.967Z", "modified": "2024-01-16T13:48:37.783Z"}, {"entity": "publication", "iuid": "23d7ef3496e949c7b6f354ee8b433bbc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23d7ef3496e949c7b6f354ee8b433bbc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23d7ef3496e949c7b6f354ee8b433bbc"}}, "title": "Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.", "authors": [{"family": "Romdhane", "given": "Sana", "initials": "S"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A"}, {"family": "Banerjee", "given": "Samiran", "initials": "S"}, {"family": "Breuil", "given": "Marie-Christine", "initials": "M"}, {"family": "Bru", "given": "David", "initials": "D"}, {"family": "Chabbi", "given": "Abad", "initials": "A"}, {"family": "Hallin", "given": "Sara", "initials": "S"}, {"family": "van der Heijden", "given": "Marcel G A", "initials": "MGA"}, {"family": "Saghai", "given": "Aur\u00e9lien", "initials": "A"}, {"family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}}], "type": "journal article", "published": "2022-01-06", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "issn-l": null, "volume": "17", "issue": "1", "pages": "1"}, "abstract": "Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks.\r\n\r\nWe showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses.\r\n\r\nOur findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.", "doi": "10.1186/s40793-021-00396-9", "pmid": "34991714", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40793-021-00396-9"}, {"db": "pmc", "key": "PMC8740439"}], "notes": [], "created": "2022-03-29T13:48:27.073Z", "modified": "2022-08-19T08:54:32.507Z"}, {"entity": "publication", "iuid": "9acb1bb14347433d9f52a2ccf0633011", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9acb1bb14347433d9f52a2ccf0633011.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9acb1bb14347433d9f52a2ccf0633011"}}, "title": "Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.", "authors": [{"family": "Saha", "given": "Atal", "initials": "A", "orcid": "0000-0003-1334-928X", "researcher": {"href": "https://publications.scilifelab.se/researcher/db74704a8f08424cbe68784b8b72e529.json"}}, {"family": "Andersson", "given": "Anastasia", "initials": "A", "orcid": "0000-0002-5698-4948", "researcher": {"href": "https://publications.scilifelab.se/researcher/53b4f2c97b3d4261874f12f7142e3630.json"}}, {"family": "Kurland", "given": "Sara", "initials": "S", "orcid": "0000-0002-5370-1236", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdfc16fe9c7c4065b3e3d3f6877424f7.json"}}, {"family": "Keehnen", "given": "Naomi L P", "initials": "NLP", "orcid": "0000-0002-8782-3477", "researcher": {"href": "https://publications.scilifelab.se/researcher/524a74275ed848a8a6ccbdf5509e90e0.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "H\u00f6ssjer", "given": "Ola", "initials": "O", "orcid": "0000-0003-2767-8818", "researcher": {"href": "https://publications.scilifelab.se/researcher/09226c21334345f086f157d9e7f3136a.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Karlsson", "given": "Sten", "initials": "S"}, {"family": "Kardos", "given": "Marty", "initials": "M"}, {"family": "St\u00e5hl", "given": "Gunnar", "initials": "G"}, {"family": "Allendorf", "given": "Fred W", "initials": "FW", "orcid": "0000-0003-3663-6425", "researcher": {"href": "https://publications.scilifelab.se/researcher/a877524fe9d343f0a7b92711dbf8f608.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "31", "issue": "2", "pages": "498-511", "issn-l": "0962-1083"}, "abstract": "The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersj\u00f6arna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST \u2248 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.", "doi": "10.1111/mec.16252", "pmid": "34699656", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "RefSeq", "key": "GCA_901001165.1"}], "notes": [], "created": "2021-11-10T08:24:51.845Z", "modified": "2024-01-16T13:48:37.867Z"}, {"entity": "publication", "iuid": "ecc57c7fbab145cba4fe6464713c2501", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecc57c7fbab145cba4fe6464713c2501.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecc57c7fbab145cba4fe6464713c2501"}}, "title": "Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.", "authors": [{"family": "Benz", "given": "Caroline", "initials": "C", "orcid": "0000-0002-5166-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/86628e15252f4dd98f08759d59fad848.json"}}, {"family": "Ali", "given": "Muhammad", "initials": "M", "orcid": "0000-0002-8858-6776", "researcher": {"href": "https://publications.scilifelab.se/researcher/3056d2aefea64cfb99be29c977fa81c7.json"}}, {"family": "Krystkowiak", "given": "Izabella", "initials": "I", "orcid": "0000-0002-8863-7086", "researcher": {"href": "https://publications.scilifelab.se/researcher/f37aace7a7944e02a23ac1ccb2a95fba.json"}}, {"family": "Simonetti", "given": "Leandro", "initials": "L", "orcid": "0000-0003-1283-9770", "researcher": {"href": "https://publications.scilifelab.se/researcher/23530c1a3cef4f499a460ac59c674261.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Kliche", "given": "Johanna", "initials": "J", "orcid": "0000-0003-3179-4635", "researcher": {"href": "https://publications.scilifelab.se/researcher/fae2a374b1664635a7ab0eabd28cc999.json"}}, {"family": "Andersson", "given": "Eva", "initials": "E"}, {"family": "Jemth", "given": "Per", "initials": "P", "orcid": "0000-0003-1516-7228", "researcher": {"href": "https://publications.scilifelab.se/researcher/91bb46ceba74462498354a328886b982.json"}}, {"family": "Davey", "given": "Norman E", "initials": "NE", "orcid": "0000-0001-6988-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/c239a7f1b8a344948d80b9104a5fcc96.json"}}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-7081-3846", "researcher": {"href": "https://publications.scilifelab.se/researcher/f51534acce8c4214a55a3e7387850d53.json"}}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "issn-l": "1744-4292", "volume": "18", "issue": "1", "pages": "e10584"}, "abstract": "Specific protein-protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein-protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type-specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide-phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)-binding domains and confirmed the quality of the produced data by complementary biophysical or cell-based assays. Finally, we show how the amino acid resolution-binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome-wide discovery of SLiM-based interactions.", "doi": "10.15252/msb.202110584", "pmid": "35044719", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8769072"}], "notes": [], "created": "2022-03-29T13:48:47.202Z", "modified": "2022-08-19T08:54:16.880Z"}, {"entity": "publication", "iuid": "651f205cc503452bad97d24143804bae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/651f205cc503452bad97d24143804bae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/651f205cc503452bad97d24143804bae"}}, "title": "Biased TCR gene usage in citrullinated Tenascin C specific T-cells in rheumatoid arthritis.", "authors": [{"family": "Sharma", "given": "Ravi K", "initials": "RK"}, {"family": "Boddul", "given": "Sanjay V", "initials": "SV"}, {"family": "Yoosuf", "given": "Niyaz", "initials": "N"}, {"family": "Turcinov", "given": "Sara", "initials": "S"}, {"family": "Dubnovitsky", "given": "Anatoly", "initials": "A"}, {"family": "Kozhukh", "given": "Genadiy", "initials": "G"}, {"family": "Wermeling", "given": "Fredrik", "initials": "F"}, {"family": "Kwok", "given": "William W", "initials": "WW"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V", "orcid": "0000-0001-9251-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/34027fbf97444632a470b33e446d4d67.json"}}], "type": "journal article", "published": "2021-12-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24512", "issn-l": "2045-2322"}, "abstract": "We aimed to search for common features in the autoreactive T cell receptor (TCR) repertoire in patients with rheumatoid arthritis (RA), focusing on the newly identified candidate antigen citrullinated Tenascin C (cit-TNC). Mononuclear cells from peripheral blood or synovial fluid of eight RA-patients positive for the RA-associated HLA-DRB1*04:01 allele were in-vitro cultured with recently identified citrullinated peptides from Tenascin C. Antigen-specific T cells were isolated using peptide-HLA tetramer staining and subsequently single-cell sequenced for paired alpha/beta TCR analyses by bioinformatic tools. TCRs were re-expressed for further studies of antigen-specificity and T cell responses. Autoreactive T cell lines could be grown out from both peripheral blood and synovial fluid. We demonstrate the feasibility of retrieving true autoreactive TCR sequences by validating antigen-specificity in T cell lines with re-expressed TCRs. One of the Tenascin C peptides, cit-TNC22, gave the most robust T cell responses including biased TCR gene usage patterns. The shared TCR-beta chain signature among the cit-TNC22-specific TCRs was evident in blood and synovial fluid of different patients. The identification of common elements in the autoreactive TCR repertoire gives promise to the possibility of both immune monitoring of the autoimmune components in RA and of future antigen- or TCR-targeted specific intervention in subsets of patients.", "doi": "10.1038/s41598-021-04291-8", "pmid": "34972837", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-04291-8"}, {"db": "pmc", "key": "PMC8720095"}], "notes": [], "created": "2022-03-29T13:47:59.715Z", "modified": "2022-03-29T13:47:59.743Z"}, {"entity": "publication", "iuid": "9b5f41c85c154d97a689abf4c3ad468b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b5f41c85c154d97a689abf4c3ad468b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b5f41c85c154d97a689abf4c3ad468b"}}, "title": "Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice.", "authors": [{"family": "L\u00f3pez-P\u00e9rez", "given": "Ana", "initials": "A"}, {"family": "Norlin", "given": "Stefan", "initials": "S"}, {"family": "Steneberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Remeseiro", "given": "Silvia", "initials": "S"}, {"family": "Edlund", "given": "Helena", "initials": "H"}, {"family": "H\u00f6rnblad", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2021-12-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24410", "issn-l": "2045-2322"}, "abstract": "AMP-activated protein kinase (AMPK) has an important role in cellular energy homeostasis and has emerged as a promising target for treatment of Type 2 Diabetes (T2D) due to its beneficial effects on insulin sensitivity and glucose homeostasis. O304 is a pan-AMPK activator that has been shown to improve glucose homeostasis in both mouse models of diabetes and in human T2D subjects. Here, we describe the genome-wide transcriptional profile and chromatin landscape of pancreatic islets following O304 treatment of mice fed high-fat diet (HFD). O304 largely prevented genome-wide gene expression changes associated with HFD feeding in CBA mice and these changes were associated with remodelling of active and repressive chromatin marks. In particular, the increased expression of the \u03b2-cell stress marker Aldh1a3 in islets from HFD-mice is completely abrogated following O304 treatment, which is accompanied by loss of active chromatin marks in the promoter as well as distant non-coding regions upstream of the Aldh1a3 gene. Moreover, O304 treatment restored dysfunctional glucose homeostasis as well as expression of key markers associated with \u03b2-cell function in mice with already established obesity. Our findings provide preclinical evidence that O304 is a promising therapeutic compound not only for T2D remission but also for restoration of \u03b2-cell function following remission of T2D diabetes.", "doi": "10.1038/s41598-021-03567-3", "pmid": "34949756", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-03567-3"}, {"db": "pmc", "key": "PMC8702551"}], "notes": [], "created": "2022-03-29T13:48:23.081Z", "modified": "2022-03-29T13:48:23.093Z"}, {"entity": "publication", "iuid": "fc66b426f2b0449c89a990b030c97298", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc66b426f2b0449c89a990b030c97298.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc66b426f2b0449c89a990b030c97298"}}, "title": "Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord.", "authors": [{"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "Gonz\u00e1lez", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-9926-3323", "researcher": {"href": "https://publications.scilifelab.se/researcher/985211e3b6354b6e9fe4be56a9c2b5b2.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2021-12-21", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "6", "issue": "6", "pages": "e0057521", "issn-l": "2379-5077"}, "abstract": "A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean's interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.", "doi": "10.1128/mSystems.00575-21", "pmid": "34904860", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8670421"}], "notes": [], "created": "2022-03-29T13:47:25.000Z", "modified": "2022-03-29T13:47:25.112Z"}, {"entity": "publication", "iuid": "2580178a81f6434f9c0146ac18759ecc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2580178a81f6434f9c0146ac18759ecc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2580178a81f6434f9c0146ac18759ecc"}}, "title": "Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities.", "authors": [{"family": "Albert", "given": "S\u00e9r\u00e9na", "initials": "S"}, {"family": "Hedberg", "given": "Per", "initials": "P"}, {"family": "Motwani", "given": "Nisha H", "initials": "NH"}, {"family": "Sj\u00f6ling", "given": "Sara", "initials": "S"}, {"family": "Winder", "given": "Monika", "initials": "M"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2021-12-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "24033", "issn-l": "2045-2322"}, "abstract": "In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.", "doi": "10.1038/s41598-021-03303-x", "pmid": "34911983", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-03303-x"}, {"db": "pmc", "key": "PMC8674317"}], "notes": [], "created": "2022-03-29T13:48:06.335Z", "modified": "2024-01-16T13:48:37.970Z"}, {"entity": "publication", "iuid": "c9474748c2934ce1a9ff72a666d0ce39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9474748c2934ce1a9ff72a666d0ce39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9474748c2934ce1a9ff72a666d0ce39"}}, "title": "Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history.", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2021-12-03", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "23384", "issn-l": "2045-2322"}, "abstract": "Coastal aquatic systems suffer from nutrient enrichment, which results in accelerated eutrophication effects due to increased microbial metabolic rates. Climate change related prolonged warming will likely accelerate existing eutrophication effects, including low oxygen concentrations. However, how the interplay between these environmental changes will alter coastal ecosystems is poorly understood. In this study, we compared 16S rRNA gene amplicon based bacterial communities in coastal sediments of a Baltic Sea basin in November 2013 and 2017 at three sites along a water depth gradient with varying bottom water oxygen histories. The shallow site showed changes of only 1.1% in relative abundance of bacterial populations in 2017 compared to 2013, while the deep oxygen-deficient site showed up to 11% changes in relative abundance including an increase of sulfate-reducing bacteria along with a 36% increase in organic matter content. The data suggested that bacterial communities in shallow sediments were more resilient to seasonal oxygen decline, while bacterial communities in sediments subjected to long-term hypoxia seemed to be sensitive to oxygen changes and were likely to be under hypoxic/anoxic conditions in the future. Our data demonstrate that future climate changes will likely fuel eutrophication related spread of low oxygen zones.", "doi": "10.1038/s41598-021-02725-x", "pmid": "34862412", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-02725-x"}, {"db": "pmc", "key": "PMC8642432"}], "notes": [], "created": "2022-03-29T13:47:33.570Z", "modified": "2024-01-16T13:48:37.994Z"}, {"entity": "publication", "iuid": "740eecf090cc480691eaa88069c34fed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/740eecf090cc480691eaa88069c34fed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/740eecf090cc480691eaa88069c34fed"}}, "title": "Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).", "authors": [{"family": "S\u00e1nchez-Barreiro", "given": "F\u00e1tima", "initials": "F", "orcid": "0000-0002-5902-0052", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c84c6755fbf476bba3d19b2782dadea.json"}}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S", "orcid": "0000-0002-2004-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/637bc46cf8094999aad02a3d646e82fd.json"}}, {"family": "Ramos-Madrigal", "given": "Jazm\u00edn", "initials": "J"}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "de Manuel", "given": "Marc", "initials": "M"}, {"family": "Margaryan", "given": "Ashot", "initials": "A"}, {"family": "Ciucani", "given": "Marta M", "initials": "MM"}, {"family": "Vieira", "given": "Filipe G", "initials": "FG"}, {"family": "Patramanis", "given": "Yannis", "initials": "Y"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC"}, {"family": "Timmons", "given": "Zena", "initials": "Z"}, {"family": "Sicheritz-Pont\u00e9n", "given": "Thomas", "initials": "T"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Marqu\u00e8s-Bonet", "given": "Tom\u00e1s", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Moodley", "given": "Yoshan", "initials": "Y"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "23", "pages": "6355-6369", "issn-l": "0962-1083"}, "abstract": "Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.", "doi": "10.1111/mec.16043", "pmid": "34176179", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:01:14.124Z", "modified": "2021-12-06T13:46:52.505Z"}, {"entity": "publication", "iuid": "7013590bb16742499cb4ab2faf44231d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7013590bb16742499cb4ab2faf44231d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7013590bb16742499cb4ab2faf44231d"}}, "title": "Evolutionary history of the extinct Sardinian dhole", "authors": [{"family": "Ciucani", "given": "Marta Maria", "initials": "MM"}, {"family": "Jensen", "given": "Julie Kragmose", "initials": "JK", "orcid": "0000-0002-7882-0450", "researcher": {"href": "https://publications.scilifelab.se/researcher/aefb3d21ea1f433284b5cac0ce2deca0.json"}}, {"family": "Sinding", "given": "Mikkel Holger S", "initials": "MHS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Smith", "given": "Oliver", "initials": "O", "orcid": "0000-0002-0146-9244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebee38f7617407897c80da437018a2f.json"}}, {"family": "Lucenti", "given": "Saverio Bartolini", "initials": "SB", "orcid": "0000-0003-1280-5378", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f6d5f7a65184e2d97c6e0ebf571c02d.json"}}, {"family": "Rosengren", "given": "Erika", "initials": "E", "orcid": "0000-0002-9658-2134", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bea6444beec43f4a24bf1b8d04202aa.json"}}, {"family": "Rook", "given": "Lorenzo", "initials": "L"}, {"family": "Tuveri", "given": "Caterinella", "initials": "C"}, {"family": "Arca", "given": "Marisa", "initials": "M"}, {"family": "Cappellini", "given": "Enrico", "initials": "E"}, {"family": "Galaverni", "given": "Marco", "initials": "M"}, {"family": "Randi", "given": "Ettore", "initials": "E"}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Sicheritz-Pont\u00e9n", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S", "orcid": "0000-0002-2004-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/637bc46cf8094999aad02a3d646e82fd.json"}}], "type": "journal-article", "published": "2021-12-00", "journal": {"title": "Current Biology", "issn": "0960-9822", "volume": "31", "issue": "24", "pages": "5571-5579.e6", "issn-l": "0960-9822"}, "abstract": "The Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene.2-5 Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor.3,6-9 Morphometric analyses3,6,8-12 have failed to clarify the evolutionary relationship with other canids.We sequenced the genome of a ca-21,100-year-old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found that it represents a separate taxon from all other living canids from Eurasia, Africa, and North America, and that the Sardinian dhole lineage diverged from the Asian dhole ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, which ended approximately 500-300 ka, when the land bridge between Sardinia and mainland Italy was already broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids-probably a result of the long-term isolation-that could have contributed to the subsequent extinction of the Sardinian dhole.", "doi": "10.1016/j.cub.2021.09.059", "pmid": "34655517", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)01315-4"}], "notes": [], "created": "2021-12-06T13:49:17.223Z", "modified": "2023-06-19T11:38:27.891Z"}, {"entity": "publication", "iuid": "dceec3c36085466ba0fa701b15600f65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dceec3c36085466ba0fa701b15600f65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dceec3c36085466ba0fa701b15600f65"}}, "title": "An atlas of the Norway spruce needle seasonal transcriptome.", "authors": [{"family": "Bag", "given": "Pushan", "initials": "P", "orcid": "0000-0003-3858-4606", "researcher": {"href": "https://publications.scilifelab.se/researcher/033b97dc712047a294d3e801ba750787.json"}}, {"family": "Lihavainen", "given": "Jenna", "initials": "J"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Riquelme", "given": "Thomas", "initials": "T"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Plant J.", "issn": "1365-313X", "volume": "108", "issue": "6", "pages": "1815-1829", "issn-l": "0960-7412"}, "abstract": "Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February), and spring (March-April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.", "doi": "10.1111/tpj.15530", "pmid": "34624161", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T13:49:14.846Z", "modified": "2024-01-16T13:48:38.046Z"}, {"entity": "publication", "iuid": "2f408cf8bc92436dbd6808898c4a9da4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f408cf8bc92436dbd6808898c4a9da4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f408cf8bc92436dbd6808898c4a9da4"}}, "title": "Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials.", "authors": [{"family": "Johnson", "given": "Anders", "initials": "A"}, {"family": "H\u00f6gfors-R\u00f6nnholm", "given": "Eva", "initials": "E"}, {"family": "Engblom", "given": "Sten", "initials": "S"}, {"family": "\u00d6sterholm", "given": "Peter", "initials": "P"}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2021-11-23", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "pages": "151864", "issn-l": "0048-9697"}, "abstract": "Sediments along the Baltic Sea coast can contain considerable amounts of metal sulfides that if dredged and the spoils deposited such that they are exposed to air, can release high concentrations of acid and toxic metals into recipient water bodies. Two river estuaries in western Finland were dredged from 2013 to 2018 and the dredge spoils were deposited on land previously covered with agricultural limestone to buffer the pH and mitigate acid and metal release. In this study, the geochemistry and 16S rRNA gene amplicon based bacterial communities were investigated over time to explore whether the application of lime prevented a conversion of the dredge spoils into acid producing and metal releasing soil. The pH of the dredge spoils decreased with time indicating metal sulfide oxidation and resulted in elevated sulfate concentrations along with a concomitant release of metals. However, calculations indicated only approximately 5% of the added lime had been dissolved. The bacterial communities decreased in diversity with the lowering of the pH as taxa most similar to extremely acidophilic sulfur, and in some cases iron, oxidizing Acidithiobacillus species became the dominant characterized genus in the deposited dredge spoils as the oxidation front moved deeper. In addition, other taxa characterized as involved in oxidation of iron or sulfur were identified including Gallionella, Sulfuricurvum, and Sulfurimonas. These data suggest there was a rapid conversion of the dredge spoils to severely acidic soil similar to actual acid sulfate soil and that the lime placed on the land prior to deposition of the spoils, and later ploughed into the dry dredge spoils, was insufficient to halt this process. Hence, future dredging and deposition of dredge spoils containing metal sulfides should not only take into account the amount of lime used for buffering but also its grain size and mixing into the soil.", "doi": "10.1016/j.scitotenv.2021.151864", "pmid": "34822903", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(21)06940-0"}], "notes": [], "created": "2021-12-06T13:49:34.815Z", "modified": "2024-01-16T13:48:38.054Z"}, {"entity": "publication", "iuid": "f9f4da192abc41a59c7dbafd427b7cd0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9f4da192abc41a59c7dbafd427b7cd0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9f4da192abc41a59c7dbafd427b7cd0"}}, "title": "Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.", "authors": [{"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Boyaci", "given": "Ceren", "initials": "C", "orcid": "0000-0001-5598-0243", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1a803107a224c578bf01ef65aba69ff.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/826836fefcf5440ebef1c404e046a0ca.json"}}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Moreno-Ruiz", "given": "Pablo", "initials": "P"}, {"family": "Bai", "given": "Yalai", "initials": "Y"}, {"family": "Rimm", "given": "David L", "initials": "DL", "orcid": "0000-0001-5820-4397", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bb1180d52564c48876ecc4b7e635d52.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd907ed1df0441b99789d3e045c4d890.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.json"}}], "type": "journal article", "published": "2021-11-19", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "7", "issue": "1", "pages": "144", "issn-l": null}, "abstract": "Emerging data indicate that genomic alterations can shape immune cell composition in early breast cancer. However, there is a need for complementary imaging and sequencing methods for the quantitative assessment of combined somatic copy number alteration (SCNA) and immune profiling in pathological samples. Here, we tested the feasibility of three approaches-CUTseq, for high-throughput low-input SCNA profiling, multiplexed fluorescent immunohistochemistry (mfIHC) and digital-image analysis (DIA) for quantitative immuno-profiling- in archival formalin-fixed paraffin-embedded (FFPE) tissue samples from patients enrolled in the randomized SBG-2004-1 phase II trial. CUTseq was able to reproducibly identify amplification and deletion events with a resolution of 100 kb using only 6 ng of DNA extracted from FFPE tissue and pooling together 77 samples into the same sequencing library. In the same samples, mfIHC revealed that CD4 + T-cells and CD68 + macrophages were the most abundant immune cells and they mostly expressed PD-L1 and PD-1. Combined analysis showed that the SCNA burden was inversely associated with lymphocytic infiltration. Our results set the basis for further applications of CUTseq, mfIHC and DIA to larger cohorts of early breast cancer patients.", "doi": "10.1038/s41523-021-00352-3", "pmid": "34799582", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41523-021-00352-3"}, {"db": "pmc", "key": "PMC8604966"}], "notes": [], "created": "2021-12-01T19:52:21.708Z", "modified": "2024-01-16T13:48:38.062Z"}, {"entity": "publication", "iuid": "0474c782601a4552921a9242325c6fb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0474c782601a4552921a9242325c6fb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0474c782601a4552921a9242325c6fb5"}}, "title": "MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.", "authors": [{"family": "Kang", "given": "Wenjing", "initials": "W"}, {"family": "Fromm", "given": "Bastian", "initials": "B"}, {"family": "Houben", "given": "Anna J", "initials": "AJ"}, {"family": "H\u00f8ye", "given": "Eirik", "initials": "E"}, {"family": "Bezdan", "given": "Daniela", "initials": "D"}, {"family": "Arnan", "given": "Carme", "initials": "C"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Asp", "given": "Michaela", "initials": "M"}, {"family": "Johnson", "given": "Rory", "initials": "R"}, {"family": "Biryukova", "given": "Inna", "initials": "I"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}], "type": "journal article", "published": "2021-11-16", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "37", "issue": "7", "pages": "110015", "issn-l": null}, "abstract": "Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they have been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors with a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from 20 animal species. We systematically compare the importance of known and novel sequence and structural features and test biogenesis of miRNA precursors from 10 animal and plant species in human cells. Lastly, we provide evidence that the GHG motif better predicts processing when defined as a structure rather than sequence motif, consistent with recent cryogenic electron microscopy (cryo-EM) studies. In summary, we apply a screening assay in living cells to reveal the importance of lower basal stem stability for miRNA processing and in vivo expression.", "doi": "10.1016/j.celrep.2021.110015", "pmid": "34788611", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(21)01497-2"}], "notes": [], "created": "2021-12-06T13:49:38.493Z", "modified": "2024-01-16T13:48:38.077Z"}, {"entity": "publication", "iuid": "5a0fd3eeab8e4303ade4bc3356923079", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a0fd3eeab8e4303ade4bc3356923079.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a0fd3eeab8e4303ade4bc3356923079"}}, "title": "Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.", "authors": [{"family": "Chattopadhyay", "given": "Subhayan", "initials": "S", "orcid": "0000-0002-8599-2971", "researcher": {"href": "https://publications.scilifelab.se/researcher/78358668578b4661bed1f6a37365fae4.json"}}, {"family": "Karlsson", "given": "Jenny", "initials": "J"}, {"family": "Valind", "given": "Anders", "initials": "A"}, {"family": "Andersson", "given": "Natalie", "initials": "N"}, {"family": "Gisselsson", "given": "David", "initials": "D"}], "type": "journal article", "published": "2021-11-05", "journal": {"title": "Brief. Bioinformatics", "issn": "1477-4054", "volume": "22", "issue": "6", "issn-l": "1467-5463"}, "abstract": "Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer. Two limiting factors for clonal deconvolution that have remained unresolved are variation in purity and chromosomal copy number across different samples of the same tumor. We developed a semi-supervised algorithm that tracks variant calls through multi-sample spatiotemporal tumor data. While normalizing allele frequencies based on purity, it also adjusts for copy number changes at clonal deconvolution. Absent \u00e0 priori copy number data, it renders in silico copy number estimations from bulk sequences. Using published and simulated tumor sequences, we reliably segregated clonal/subclonal variants even at a low sequencing depth (~50\u00d7). Given at least one pure tumor sample (>70% purity), we could normalize and deconvolve paired samples down to a purity of 40%. This renders a reliable clonal reconstruction well adapted to multi-regionally sampled solid tumors, which are often aneuploid and contaminated by non-cancer cells.", "doi": "10.1093/bib/bbab292", "pmid": "34343239", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "6337895"}], "notes": [], "created": "2021-10-01T09:03:47.437Z", "modified": "2021-12-06T13:48:08.580Z"}, {"entity": "publication", "iuid": "56272ae880c14e5b9c0ff4ac36a0eb98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56272ae880c14e5b9c0ff4ac36a0eb98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56272ae880c14e5b9c0ff4ac36a0eb98"}}, "title": "Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line.", "authors": [{"family": "\u00d6hlund", "given": "Pontus", "initials": "P"}, {"family": "Hayer", "given": "Juliette", "initials": "J", "orcid": "0000-0003-4899-9637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9535fdd81a2347528a48540c78decf1e.json"}}, {"family": "Hesson", "given": "Jenny C", "initials": "JC", "orcid": "0000-0003-2489-4400", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc38909bfe20449f9de91560a1aee6ce.json"}}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}], "type": "journal article", "published": "2021-10-29", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "13", "issue": "11", "issn-l": "1999-4915"}, "abstract": "RNA interference (RNAi)-mediated antiviral immunity is believed to be the primary defense against viral infection in mosquitoes. The production of virus-specific small RNA has been demonstrated in mosquitoes and mosquito-derived cell lines for viruses in all of the major arbovirus families. However, many if not all mosquitoes are infected with a group of viruses known as insect-specific viruses (ISVs), and little is known about the mosquito immune response to this group of viruses. Therefore, in this study, we sequenced small RNA from an Aedes albopictus-derived cell line infected with either Lammi virus (LamV) or Hanko virus (HakV). These viruses belong to two distinct phylogenetic groups of insect-specific flaviviruses (ISFVs). The results revealed that both viruses elicited a strong virus-derived small interfering RNA (vsiRNA) response that increased over time and that targeted the whole viral genome, with a few predominant hotspots observed. Furthermore, only the LamV-infected cells produced virus-derived Piwi-like RNAs (vpiRNAs); however, they were mainly derived from the antisense genome and did not show the typical ping-pong signatures. HakV, which is more distantly related to the dual-host flaviviruses than LamV, may lack certain unknown sequence elements or structures required for vpiRNA production. Our findings increase the understanding of mosquito innate immunity and ISFVs' effects on their host.", "doi": "10.3390/v13112181", "pmid": "34834988", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "v13112181"}, {"db": "pmc", "key": "PMC8620693"}], "notes": [], "created": "2021-12-06T13:49:46.492Z", "modified": "2024-01-16T13:48:38.155Z"}, {"entity": "publication", "iuid": "e8a3f3d6dec948ea97e5ff3b991742d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8a3f3d6dec948ea97e5ff3b991742d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8a3f3d6dec948ea97e5ff3b991742d6"}}, "title": "Microbial Plankton Community Structure and Function Responses to Vitamin B12 and B1 Amendments in an Upwelling System.", "authors": [{"family": "Joglar", "given": "Vanessa", "initials": "V", "orcid": "0000-0001-9798-7443", "researcher": {"href": "https://publications.scilifelab.se/researcher/501df1e0ac584b71a6f09cf2801d2bab.json"}}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S"}, {"family": "Fuentes-Lema", "given": "Antonio", "initials": "A"}, {"family": "P\u00e9rez-Lorenzo", "given": "Mar\u00eda", "initials": "M"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Fern\u00e1ndez", "given": "Emilio", "initials": "E"}, {"family": "Teira", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2021-10-28", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "pages": "e0152521", "volume": "87", "issue": "22", "issn-l": "0099-2240"}, "abstract": "B vitamins are essential cofactors for practically all living organisms on Earth and are produced by a selection of microorganisms. An imbalance between high demand and limited production, in concert with abiotic processes, may explain the low availability of these vitamins in marine systems. Natural microbial communities from surface shelf water in the productive area off northwestern Spain were enclosed in mesocosms in winter, spring, and summer 2016. In order to explore the impact of B-vitamin availability on microbial community composition (16S and 18S rRNA gene sequence analysis) and bacterial function (metatranscriptomics analysis) in different seasons, enrichment experiments were conducted with seawater from the mesocosms. Our findings revealed that significant increases in phytoplankton or prokaryote biomass associated with vitamin B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most of the microbial taxa benefited from the external B-vitamin supply. Metatranscriptome analysis suggested that many bacteria were potential consumers of vitamins B12 and B1, although the relative abundance of reads related to synthesis was ca. 3.6-fold higher than that related to uptake. Alteromonadales and Oceanospirillales accounted for important portions of vitamin B1 and B12 synthesis gene transcription, despite accounting for only minor portions of the bacterial community. Flavobacteriales appeared to be involved mostly in vitamin B12 and B1 uptake, and Pelagibacterales expressed genes involved in vitamin B1 uptake. Interestingly, the relative expression of vitamin B12 and B1 synthesis genes among bacteria strongly increased upon inorganic nutrient amendment. Collectively, these findings suggest that upwelling events intermittently occurring during spring and summer in productive ecosystems may ensure an adequate production of these cofactors to sustain high levels of phytoplankton growth and biomass. IMPORTANCE B vitamins are essential growth factors for practically all living organisms on Earth that are produced by a selection of microorganisms. An imbalance between high demand and limited production may explain the low concentration of these compounds in marine systems. In order to explore the impact of B-vitamin availability on bacteria and algae in the coastal waters off northwestern Spain, six experiments were conducted with natural surface water enclosed in winter, spring, and summer. Our findings revealed that increases in phytoplankton or bacterial growth associated with B12 and/or B1 amendments were not accompanied by significant changes in community composition, suggesting that most microorganisms benefited from the B-vitamin supply. Our analyses confirmed the role of many bacteria as consumers of vitamins B12 and B1, although the relative abundance of genes related to synthesis was ca. 3.6-fold higher than that related to uptake. Interestingly, prokaryote expression of B12 and B1 synthesis genes strongly increased when inorganic nutrients were added. Collectively, these findings suggest that upwelling of cold and nutrient-rich waters occurring during spring and summer in this coastal area may ensure an adequate production of B vitamins to sustain high levels of algae growth and biomass.", "doi": "10.1128/AEM.01525-21", "pmid": "34495690", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8552899"}], "notes": [], "created": "2021-10-01T09:09:01.533Z", "modified": "2024-01-16T13:48:38.162Z"}, {"entity": "publication", "iuid": "87bf78d535ce41dbbf344f9db435066f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87bf78d535ce41dbbf344f9db435066f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87bf78d535ce41dbbf344f9db435066f"}}, "title": "Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.", "authors": [{"family": "Wallander", "given": "Karin", "initials": "K"}, {"family": "Thonberg", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0003-4503-4717", "researcher": {"href": "https://publications.scilifelab.se/researcher/481958db26a2433ea8d5cc786c3b2bca.json"}}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal article", "published": "2021-10-28", "journal": {"title": "Hered Cancer Clin Pract", "issn": "1731-2302", "volume": "19", "issue": "1", "pages": "46", "issn-l": null}, "abstract": "Multiple primary cancers, defined as three or more primary tumours, are rare, and there are few genetic studies concerning them. There is a need for increased knowledge on the heritability of multiple primary cancers and genotype-phenotype correlations. We have performed whole-genome/exome sequencing (WGS/WES) in ten individuals with three or more primary tumours, with no previous findings on standard clinical genetic investigations. In one individual with a clinical diagnosis of MEN1, a likely pathogenic cryptic splice site variant was detected in the MEN1 gene. The variant (c.654C > A) is synonymous but we showed in a cDNA analysis that it affects splicing and leads to a frameshift, with the theoretical new amino acid sequence p.(Gly219Glufs*13). In one individual with metachronous colorectal cancers, ovarian cancer, endometrial cancer and chronic lymphocytic leukaemia, we found a likely pathogenic variant in the MLH1 gene (c.27G > A), and two risk factor variants in the genes CHEK2 and HOXB13. The MLH1 variant is synonymous but has previously been shown to be associated to constitutional low-grade hypermethylation of the MLH1 promoter, and segregates with disease in families with colorectal and endometrial cancer. No pathogenic single nucleotide or structural variants were detected in the remaining eight individuals in the study. The pathogenic variants found by WGS/WES were in genes already sequenced by Sanger sequencing and WES in the clinic, without any findings. We conclude that, in individuals with an unequivocal clinical diagnosis of a specific hereditary cancer syndrome, where standard clinical testing failed to detect a causative variant, re-analysis may lead to a diagnosis.", "doi": "10.1186/s13053-021-00203-z", "pmid": "34711244", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13053-021-00203-z"}, {"db": "pmc", "key": "PMC8555269"}], "notes": [], "created": "2021-11-20T12:31:14.384Z", "modified": "2024-01-16T13:48:38.170Z"}, {"entity": "publication", "iuid": "2e2f52aecc4a4656a0714ceb413d1ac4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e2f52aecc4a4656a0714ceb413d1ac4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e2f52aecc4a4656a0714ceb413d1ac4"}}, "title": "Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).", "authors": [{"family": "Rend\u00f3n-Anaya", "given": "Martha", "initials": "M"}, {"family": "Wilson", "given": "Jonathan", "initials": "J"}, {"family": "Sveinsson", "given": "S\u00e6mundur", "initials": "S"}, {"family": "Fedorkov", "given": "Aleksey", "initials": "A"}, {"family": "Cottrell", "given": "Joan", "initials": "J"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES", "orcid": "0000-0002-9788-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/3919edd84f254870a5644770152360b6.json"}}, {"family": "Ru\u0146is", "given": "Dainis", "initials": "D"}, {"family": "Lexer", "given": "Christian", "initials": "C"}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}], "type": "journal article", "published": "2021-10-27", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "38", "issue": "11", "pages": "5034-5050", "issn-l": "0737-4038"}, "abstract": "Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems, and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole-genome resequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum, we detected an adaptive introgression event in a genome region of \u223c500 kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of Northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin-probably Russian-of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results, therefore, emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.", "doi": "10.1093/molbev/msab229", "pmid": "34329481", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6332012"}, {"db": "pmc", "key": "PMC8557470"}], "notes": [], "created": "2021-10-01T09:02:36.794Z", "modified": "2024-01-16T13:48:38.184Z"}, {"entity": "publication", "iuid": "74edcc5b9fba41868b68c733c017e739", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74edcc5b9fba41868b68c733c017e739.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74edcc5b9fba41868b68c733c017e739"}}, "title": "Seasonal migration patterns and the maintenance of evolutionary diversity in a cryptic bird radiation.", "authors": [{"family": "Tang", "given": "Qindong", "initials": "Q"}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Sundev", "given": "Gombobaatar", "initials": "G"}, {"family": "Heckel", "given": "Gerald", "initials": "G", "orcid": "0000-0002-0162-323X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7865cb9352f5436da669b49f251a0430.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}], "type": "journal article", "published": "2021-10-21", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083"}, "abstract": "Morphological differentiation associated with evolutionary diversification is often explained with adaptive benefits but the processes and mechanisms maintaining cryptic diversity are still poorly understood. Using genome-wide data, we show here that the pale sand martin Riparia diluta in Central and East Asia consists of three genetically deeply differentiated lineages which vary only gradually in morphology but broadly reflect traditional taxonomy. We detected no signs of gene flow along the eastern edge of the Qinghai-Tibetan plateau between lowland south-eastern Chinese R. d. fohkienensis and high-altitude R. d. tibetana. Largely different breeding and migration timing between these low and high altitude populations as indicated by phenology data suggests that allochrony might act as prezygotic isolation mechanism in the area where their ranges abut. Mongolian populations of R. d. tibetana, however, displayed signs of limited mixed ancestries with Central Asian R. d. diluta. Their ranges meet in the area of a well-known avian migratory divide, where western lineages take a western migration route around the Qinghai-Tibetan plateau to winter quarters in South Asia, and eastern lineages take an eastern route to Southeast Asia. This might also be the case between western R. d. diluta and eastern R. d. tibetana as indicated by differing wintering grounds. We hypothesize that hybrids might have nonoptimal intermediate migration routes and selection against them might restrict gene flow. Although further potential isolation mechanisms might exist in the pale sand martin, our study points towards contrasting migration behaviour as an important factor in maintaining evolutionary diversity under morphological stasis.", "doi": "10.1111/mec.16241", "pmid": "34674334", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T13:49:42.335Z", "modified": "2024-01-16T13:48:38.214Z"}, {"entity": "publication", "iuid": "606fa1bda28743e09f8e233cf543c29d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/606fa1bda28743e09f8e233cf543c29d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/606fa1bda28743e09f8e233cf543c29d"}}, "title": "Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani.", "authors": [{"family": "Brouwer", "given": "Sophie M", "initials": "SM"}, {"family": "Brus-Szkalej", "given": "Maja", "initials": "M", "orcid": "0000-0002-9086-208X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8e5284f881040bba29ca64b38a96322.json"}}, {"family": "Saripella", "given": "Ganapathi V", "initials": "GV", "orcid": "0000-0003-3504-9333", "researcher": {"href": "https://publications.scilifelab.se/researcher/494b3df440974bb7a42af6843c9ad415.json"}}, {"family": "Liang", "given": "Dong", "initials": "D"}, {"family": "Liljeroth", "given": "Erland", "initials": "E", "orcid": "0000-0002-6950-2434", "researcher": {"href": "https://publications.scilifelab.se/researcher/2443cbfdd86d415baee28853462b1078.json"}}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2021-10-18", "journal": {"title": "Plants (Basel)", "issn": "2223-7747", "volume": "10", "issue": "10", "issn-l": null}, "abstract": "Potato early blight is caused by the necrotrophic fungus Alternaria solani and can result in yield losses of up to 50% if left uncontrolled. At present, the disease is controlled by chemical fungicides, yet rapid development of fungicide resistance renders current control strategies unsustainable. On top of that, a lack of understanding of potato defences and the quantitative nature of resistance mechanisms against early blight hinders the development of more sustainable control methods. Necrotrophic pathogens, compared to biotrophs, pose an extra challenge to the plant, since common defence strategies to biotic stresses such as the hypersensitive response and programmed cell death are often beneficial for necrotrophs. With the aim of unravelling plant responses to both the early infection stages (i.e., before necrosis), such as appressorium formation and penetration, as well as to later responses to the onset of necrosis, we present here a transcriptome analysis of potato interactions with A. solani from 1 h after inoculation when the conidia have just commenced germination, to 48 h post inoculation when multiple cell necrosis has begun. Potato transcripts with putative functions related to biotic stress tolerance and defence against pathogens were upregulated, including a putative Nudix hydrolase that may play a role in defence against oxidative stress. A. solani transcripts encoding putative pathogenicity factors, such as cell wall degrading enzymes and metabolic processes that may be important for infection. We therefore identified the differential expression of several potato and A. solani transcripts that present a group of valuable candidates for further studies into their roles in immunity or disease development.", "doi": "10.3390/plants10102212", "pmid": "34686023", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "plants10102212"}, {"db": "pmc", "key": "PMC8539873"}], "notes": [], "created": "2021-12-06T13:49:39.694Z", "modified": "2024-01-16T13:48:38.222Z"}, {"entity": "publication", "iuid": "06cb8c44cb724e169b03c31f68350a39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06cb8c44cb724e169b03c31f68350a39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06cb8c44cb724e169b03c31f68350a39"}}, "title": "Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions.", "authors": [{"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9ffc7de05a040c48011a6ba639d5851.json"}}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4393e30947441519e7ab28fccb9bc3a.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Ehinger", "given": "Anna", "initials": "A", "orcid": "0000-0001-9225-7396", "researcher": {"href": "https://publications.scilifelab.se/researcher/f500d5e3ba094e208ea53b4c42e44ce8.json"}}, {"family": "Wu", "given": "Sunny Z", "initials": "SZ", "orcid": "0000-0002-6153-0449", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b354bd9c024e0d9fae3b77b5f7ca3a.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G", "orcid": "0000-0002-1137-1726", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d06a9f413f04f7490b1724c375537c0.json"}}, {"family": "Roden", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2393-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ee5b95b08b243e49af7a837ab9f9d39.json"}}, {"family": "Swarbrick", "given": "Alex", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications.scilifelab.se/researcher/25d712c54077427abf4a5ac7cbe2b5a6.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5819-458X", "researcher": {"href": "https://publications.scilifelab.se/researcher/23064ee2ac9b4c2fb1eb94e61f92148e.json"}}, {"family": "Engblom", "given": "Camilla", "initials": "C", "orcid": "0000-0001-5090-4161", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ae4350efff0421393356f3ff1f2a971.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2021-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "6012", "issn-l": "2041-1723"}, "abstract": "In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.", "doi": "10.1038/s41467-021-26271-2", "pmid": "34650042", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8516894"}, {"db": "pii", "key": "10.1038/s41467-021-26271-2"}], "notes": [], "created": "2021-12-06T13:49:12.030Z", "modified": "2024-01-16T13:48:38.238Z"}, {"entity": "publication", "iuid": "238d3aa204584626b4262aea39c30cc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/238d3aa204584626b4262aea39c30cc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/238d3aa204584626b4262aea39c30cc5"}}, "title": "Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound.", "authors": [{"family": "Giovannucci", "given": "Tatiana A", "initials": "TA", "orcid": "0000-0001-8978-6318", "researcher": {"href": "https://publications.scilifelab.se/researcher/56b2f3f196874ef8b62a8768286c136a.json"}}, {"family": "Salomons", "given": "Florian A", "initials": "FA"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Elfman", "given": "Lotta H M", "initials": "LHM"}, {"family": "Wickstr\u00f6m", "given": "Malin", "initials": "M", "orcid": "0000-0001-5214-9956", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd8b895bc0a4dca89c4170f85d3ebb4.json"}}, {"family": "Young", "given": "Patrick", "initials": "P"}, {"family": "Lundb\u00e4ck", "given": "Thomas", "initials": "T", "orcid": "0000-0002-8145-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/e13df787cb884549bcf333aba4e6f010.json"}}, {"family": "Eirich", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0003-0963-1872", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec48b74a3727482d944088601c310a38.json"}}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/481b2a2329634f9086cf52fb808edea5.json"}}, {"family": "Gustavsson", "given": "Anna-Lena", "initials": "AL"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI", "orcid": "0000-0003-1277-812X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5b7b4c780349afacf3063e311c334e.json"}}, {"family": "Dantuma", "given": "Nico P", "initials": "NP", "orcid": "0000-0002-6090-4170", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ccdd02c787d4a699efd24d297040aa0.json"}}], "type": "journal article", "published": "2021-10-06", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "issn-l": "2041-4889", "volume": "12", "issue": "10", "pages": "914"}, "abstract": "Malignant cells display an increased sensitivity towards drugs that reduce the function of the ubiquitin-proteasome system (UPS), which is the primary proteolytic system for destruction of aberrant proteins. Here, we report on the discovery of the bioactivatable compound CBK77, which causes an irreversible collapse of the UPS, accompanied by a general accumulation of ubiquitylated proteins and caspase-dependent cell death. CBK77 caused accumulation of ubiquitin-dependent, but not ubiquitin-independent, reporter substrates of the UPS, suggesting a selective effect on ubiquitin-dependent proteolysis. In a genome-wide CRISPR interference screen, we identified the redox enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1) as a critical mediator of CBK77 activity, and further demonstrated its role as the compound bioactivator. Through affinity-based proteomics, we found that CBK77 covalently interacts with ubiquitin. In vitro experiments showed that CBK77-treated ubiquitin conjugates were less susceptible to disassembly by deubiquitylating enzymes. In vivo efficacy of CBK77 was validated by reduced growth of NQO1-proficient human adenocarcinoma cells in nude mice treated with CBK77. This first-in-class NQO1-activatable UPS inhibitor suggests that it may be possible to exploit the intracellular environment in malignant cells for leveraging the impact of compounds that impair the UPS.", "doi": "10.1038/s41419-021-04191-9", "pmid": "34615851", "labels": {"CRISPR Functional Genomics": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Global Proteomics and Proteogenomics": "Service", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41419-021-04191-9"}, {"db": "pmc", "key": "PMC8494907"}], "notes": [], "created": "2021-10-16T09:54:38.919Z", "modified": "2025-10-17T13:04:28.026Z"}, {"entity": "publication", "iuid": "8d8a7c48cf414bbd9c480513a1994913", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d8a7c48cf414bbd9c480513a1994913.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d8a7c48cf414bbd9c480513a1994913"}}, "title": "The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation.", "authors": [{"family": "Lindehell", "given": "Henrik", "initials": "H", "orcid": "0000-0003-1195-2341", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffc62dbca3145d8849c0dbbb16d44b3.json"}}, {"family": "Glotov", "given": "Alexander", "initials": "A"}, {"family": "Dorafshan", "given": "Eshagh", "initials": "E"}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB", "orcid": "0000-0003-4790-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2751a236629d4b8bb9fff42cad6ff614.json"}}, {"family": "Larsson", "given": "Jan", "initials": "J", "orcid": "0000-0003-4373-6790", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6f8e41628d4534879edaf229575dec.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "40", "pages": "eabh4390", "issn-l": "2375-2548"}, "abstract": "[Figure: see text].", "doi": "10.1126/sciadv.abh4390", "pmid": "34597135", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T13:49:37.169Z", "modified": "2024-01-16T13:48:38.326Z"}, {"entity": "publication", "iuid": "f6799d3e01e6445788993dca4c841552", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6799d3e01e6445788993dca4c841552.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6799d3e01e6445788993dca4c841552"}}, "title": "Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Spinek", "given": "Anna El\u017cbieta", "initials": "AE", "orcid": "0000-0003-0304-081X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb733a1bd8454c729d03ebd221cdf9ef.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Pasterkiewicz", "given": "Wojciech", "initials": "W"}, {"family": "Florek", "given": "Marek", "initials": "M"}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Mnich", "given": "Barbara", "initials": "B"}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Kozie\u0142", "given": "S\u0142awomir", "initials": "S"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "historical article", "published": "2021-10-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "issn-l": "0002-9483", "volume": "176", "issue": "2", "pages": "223-236"}, "abstract": "We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe.\n\nWe conducted ancient DNA studies from populations associated with Z\u0142ota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture.\n\nThe maternal genetic composition found in Z\u0142ota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Z\u0142ota group, Globular Amphora, and Funnel Beaker cultures.\n\nThe prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Z\u0142ota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Z\u0142ota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.", "doi": "10.1002/ajpa.24372", "pmid": "34308549", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:03:18.631Z", "modified": "2024-01-16T13:48:38.387Z"}, {"entity": "publication", "iuid": "cf455f938530449ea97efa2baec43961", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf455f938530449ea97efa2baec43961.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf455f938530449ea97efa2baec43961"}}, "title": "High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.", "authors": [{"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A", "orcid": "0000-0001-6585-0944", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b111d2b20a447a88a3a95af425cf14.json"}}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Chitayat", "given": "David", "initials": "D"}, {"family": "Handa", "given": "Atsuhiko", "initials": "A", "orcid": "0000-0001-6401-4629", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b3be1c4b2174983a06b8e69e339bca9.json"}}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Bartocci", "given": "Marco", "initials": "M"}, {"family": "Basel", "given": "Donald", "initials": "D"}, {"family": "Batkovskyte", "given": "Dominyka", "initials": "D"}, {"family": "Beleza-Meireles", "given": "Ana", "initials": "A"}, {"family": "Conner", "given": "Peter", "initials": "P"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Girisha", "given": "Katta M", "initials": "KM"}, {"family": "Chung", "given": "Brian Hon-Yin", "initials": "BH", "orcid": "0000-0002-7044-5916", "researcher": {"href": "https://publications.scilifelab.se/researcher/73f2da34809a40ffbbc77e47e786baa2.json"}}, {"family": "Horemuzova", "given": "Eva", "initials": "E"}, {"family": "Hyodo", "given": "Hironobu", "initials": "H", "orcid": "0000-0002-1859-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4cacab0283346f083200ac21d749de6.json"}}, {"family": "Kor\u0146ejeva", "given": "Liene", "initials": "L"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K", "orcid": "0000-0001-9848-0468", "researcher": {"href": "https://publications.scilifelab.se/researcher/63d275105d9b4253944abaa311c986ee.json"}}, {"family": "Lin", "given": "Angela E", "initials": "AE"}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M"}, {"family": "Moosa", "given": "Shahida", "initials": "S"}, {"family": "Nayak", "given": "Shalini S", "initials": "SS"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Ohashi", "given": "Hirofumi", "initials": "H"}, {"family": "Ohashi-Fukuda", "given": "Naoko", "initials": "N"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Traberg", "given": "Rasa", "initials": "R"}, {"family": "Voss", "given": "Ulrika", "initials": "U"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Nishimura", "given": "Gen", "initials": "G"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G", "orcid": "0000-0001-9601-3137", "researcher": {"href": "https://publications.scilifelab.se/researcher/684864357acd490cb627f38fed3b82a4.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "J. Hum. Genet.", "issn": "1435-232X", "volume": "66", "issue": "10", "pages": "995-1008", "issn-l": "1434-5161"}, "abstract": "Skeletal ciliopathies are a heterogenous group of disorders with overlapping clinical and radiographic features including bone dysplasia and internal abnormalities. To date, pathogenic variants in at least 30 genes, coding for different structural cilia proteins, are reported to cause skeletal ciliopathies. Here, we summarize genetic and phenotypic features of 34 affected individuals from 29 families with skeletal ciliopathies. Molecular diagnostic testing was performed using massively parallel sequencing (MPS) in combination with copy number variant (CNV) analyses and in silico filtering for variants in known skeletal ciliopathy genes. We identified biallelic disease-causing variants in seven genes: DYNC2H1, KIAA0753, WDR19, C2CD3, TTC21B, EVC, and EVC2. Four variants located in non-canonical splice sites of DYNC2H1, EVC, and KIAA0753 led to aberrant splicing that was shown by sequencing of cDNA. Furthermore, CNV analyses showed an intragenic deletion of DYNC2H1 in one individual and a 6.7 Mb de novo deletion on chromosome 1q24q25 in another. In five unsolved cases, MPS was performed in family setting. In one proband we identified a de novo variant in PRKACA and in another we found a homozygous intragenic deletion of IFT74, removing the first coding exon and leading to expression of a shorter message predicted to result in loss of 40 amino acids at the N-terminus. These findings establish IFT74 as a new skeletal ciliopathy gene. In conclusion, combined single nucleotide variant, CNV and cDNA analyses lead to a high yield of genetic diagnoses (90%) in a cohort of patients with skeletal ciliopathies.", "doi": "10.1038/s10038-021-00925-x", "pmid": "33875766", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s10038-021-00925-x"}, {"db": "pmc", "key": "PMC8472897"}], "notes": [], "created": "2021-04-26T21:54:07.828Z", "modified": "2024-01-16T13:48:38.399Z"}, {"entity": "publication", "iuid": "a01c0f9e1e8e43ee84cc57054dbeba25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a01c0f9e1e8e43ee84cc57054dbeba25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a01c0f9e1e8e43ee84cc57054dbeba25"}}, "title": "Ecologically coherent population structure of uncultivated bacterioplankton.", "authors": [{"family": "Sj\u00f6qvist", "given": "Conny", "initials": "C"}, {"family": "Delgado", "given": "Luis Fernando", "initials": "LF"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "15", "issue": "10", "pages": "3034-3049"}, "abstract": "Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities are structured in time and space, relatively little is known about intraspecies diversity patterns and their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic diversity and differentiation in metagenome-assembled genomes from the Baltic Sea, and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. The majority of the investigated species, representing several major bacterioplankton clades, displayed population structures correlating significantly with environmental factors such as salinity and temperature. Population differentiation was more pronounced over spatial than temporal scales. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along with the salinity range. This in turn implies the broad existence of ecotypes that may remain undetected by rRNA gene sequencing. Our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species.", "doi": "10.1038/s41396-021-00985-z", "pmid": "33953362", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-021-00985-z"}, {"db": "pmc", "key": "PMC8443644"}], "notes": [], "created": "2021-10-01T09:00:18.178Z", "modified": "2024-01-16T13:48:38.415Z"}, {"entity": "publication", "iuid": "905b33ff17fa45b69f16c281ae963e70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/905b33ff17fa45b69f16c281ae963e70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/905b33ff17fa45b69f16c281ae963e70"}}, "title": "Composition and Seasonality of Membrane Transporters in Marine Picoplankton.", "authors": [{"family": "Hagstr\u00f6m", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Zweifel", "given": "Ulla Li", "initials": "UL"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "M\u00fcller-Karulis", "given": "B\u00e4rbel", "initials": "B"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2021-09-28", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "714732", "issn-l": "1664-302X"}, "abstract": "In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3\u03bcm-0.2\u03bcm size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models.", "doi": "10.3389/fmicb.2021.714732", "pmid": "34650527", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8507841"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4508144.v2"}], "notes": [], "created": "2021-12-06T13:49:16.062Z", "modified": "2024-01-16T13:48:38.439Z"}, {"entity": "publication", "iuid": "474380e733ea4bffaeeccbb1bfa94ade", "links": {"self": {"href": "https://publications.scilifelab.se/publication/474380e733ea4bffaeeccbb1bfa94ade.json"}, "display": {"href": "https://publications.scilifelab.se/publication/474380e733ea4bffaeeccbb1bfa94ade"}}, "title": "Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.", "authors": [{"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}, {"family": "Ure", "given": "Agustin Enrique", "initials": "AE"}, {"family": "Sundstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Hultin", "given": "Emilie", "initials": "E"}], "type": "journal article", "published": "2021-09-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "18852", "issn-l": "2045-2322"}, "abstract": "Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.", "doi": "10.1038/s41598-021-98452-4", "pmid": "34552145", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-98452-4"}, {"db": "pmc", "key": "PMC8458301"}], "notes": [], "created": "2021-10-01T09:09:05.660Z", "modified": "2021-12-06T13:48:44.578Z"}, {"entity": "publication", "iuid": "d909e7138f8d4a4bbf569e34763080a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d909e7138f8d4a4bbf569e34763080a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d909e7138f8d4a4bbf569e34763080a0"}}, "title": "Single-Cell Analysis Reveals Major Histocompatibility Complex II\u2012Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.", "authors": [{"family": "Li", "given": "Dongqing", "initials": "D", "orcid": "0000-0003-0588-9390", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d51ff81e8ec4cc5a429dd095a0c315f.json"}}, {"family": "Cheng", "given": "Shangli", "initials": "S", "orcid": "0000-0002-8501-086X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bf07f88c8ac4612afe3375e1401e253.json"}}, {"family": "Pei", "given": "Yu", "initials": "Y", "orcid": "0000-0002-6219-3587", "researcher": {"href": "https://publications.scilifelab.se/researcher/894972d5fc5b410fae8b1b2352ff2f30.json"}}, {"family": "Sommar", "given": "Pehr", "initials": "P", "orcid": "0000-0002-9789-9221", "researcher": {"href": "https://publications.scilifelab.se/researcher/a79e955554a84d189f83f289c46b011b.json"}}, {"family": "K\u00e4rner", "given": "Jaanika", "initials": "J", "orcid": "0000-0002-3548-5023", "researcher": {"href": "https://publications.scilifelab.se/researcher/20de765c88db4d40bc67a75253c38eb9.json"}}, {"family": "Herter", "given": "Eva K", "initials": "EK", "orcid": "0000-0001-5525-4663", "researcher": {"href": "https://publications.scilifelab.se/researcher/73cd22c3a7a34fe6903c6599b20089e8.json"}}, {"family": "Toma", "given": "Maria A", "initials": "MA", "orcid": "0000-0002-4766-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/80f80639a3774c5bb5007d1f9af63a0e.json"}}, {"family": "Zhang", "given": "Letian", "initials": "L", "orcid": "0000-0002-0987-0905", "researcher": {"href": "https://publications.scilifelab.se/researcher/7285787b20e54bb5bdc3fce0eab58939.json"}}, {"family": "Pham", "given": "Kim", "initials": "K", "orcid": "0000-0002-6628-1146", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd9d80797f8c4923a837632347876e7c.json"}}, {"family": "Cheung", "given": "Yuen Ting", "initials": "YT", "orcid": "0000-0002-1140-3222", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c34b39bca1247869376613ca9529711.json"}}, {"family": "Liu", "given": "Zhuang", "initials": "Z", "orcid": "0000-0001-8938-0086", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6a97736a68f4bc2bb059487e75b85c9.json"}}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Eidsmo", "given": "Liv", "initials": "L", "orcid": "0000-0001-9237-8374", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e083936a8144a19f0b2eb14dab6898.json"}}, {"family": "Deng", "given": "Qiaolin", "initials": "Q", "orcid": "0000-0001-5934-7816", "researcher": {"href": "https://publications.scilifelab.se/researcher/b74efaba0fab49acb7164a45beca5cd9.json"}}, {"family": "Xu Land\u00e9n", "given": "Ning", "initials": "N", "orcid": "0000-0003-4868-3798", "researcher": {"href": "https://publications.scilifelab.se/researcher/c55a2caeb6cd4858aa3326b6e92d09c6.json"}}], "type": "journal article", "published": "2021-09-16", "journal": {"title": "J. Invest. Dermatol.", "issn": "1523-1747", "issn-l": "0022-202X"}, "abstract": "Pressure ulcer (PU) is a chronic wound often seen in patients with spinal cord injury and other bed-bound individuals, particularly in the elderly population. Despite its association with high mortality, the pathophysiology of PU remains poorly understood. In this study, we compared single-cell transcriptomic profiles of human epidermal cells from PU wound edges with those from uninjured skin and acute wounds in healthy donors. We identified significant shifts in the cell composition and gene expression patterns in PU. In particular, we found that major histocompatibility complex class II\u2012expressing keratinocytes were enriched in patients with worse healing outcomes. Furthermore, we showed that the IFN-\u03b3 in PU-derived wound fluid could induce major histocompatibility complex II expression in keratinocytes and that these wound fluid\u2012treated keratinocytes inhibited autologous T-cell activation. In line with this observation, we found that T cells from PUs enriched with major histocompatibility complex II+ keratinocytes produced fewer inflammatory cytokines. Overall, our study provides a high-resolution molecular map of human PU compared with that of acute wounds and intact skin, providing insights into PU pathology and the future development of tailored wound therapy.", "doi": "10.1016/j.jid.2021.07.176", "pmid": "34536485", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-202X(21)02167-9"}], "notes": [], "created": "2021-10-01T09:09:09.479Z", "modified": "2024-01-16T13:48:38.471Z"}, {"entity": "publication", "iuid": "4e382676e4e14ad396c85b058fdd2640", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e382676e4e14ad396c85b058fdd2640.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e382676e4e14ad396c85b058fdd2640"}}, "title": "Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.", "authors": [{"family": "Liu", "given": "Shanlin", "initials": "S", "orcid": "0000-0001-8118-8313", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8eebb29461c4496a1b4e1b033f1afec.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Mitchell", "given": "Kieren J", "initials": "KJ", "orcid": "0000-0002-3921-0262", "researcher": {"href": "https://publications.scilifelab.se/researcher/10db4b20d5a7487899186d6c65fa5f0c.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Duch\u00eane", "given": "David A", "initials": "DA"}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Heiniger", "given": "Holly", "initials": "H"}, {"family": "S\u00e1nchez-Barreiro", "given": "F\u00e1tima", "initials": "F"}, {"family": "Margaryan", "given": "Ashot", "initials": "A"}, {"family": "Andr\u00e9-Olsen", "given": "Remi", "initials": "R"}, {"family": "De Cahsan", "given": "Binia", "initials": "B", "orcid": "0000-0002-6978-6633", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a80844d21584199ab3acdd49cef8b37.json"}}, {"family": "Meng", "given": "Guanliang", "initials": "G", "orcid": "0000-0002-6488-1527", "researcher": {"href": "https://publications.scilifelab.se/researcher/7191d467d9b3497f80212ff402c8f9cd.json"}}, {"family": "Yang", "given": "Chentao", "initials": "C", "orcid": "0000-0003-3447-2316", "researcher": {"href": "https://publications.scilifelab.se/researcher/62ca43a2664c43c3a3e5e6377399ca50.json"}}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Moodley", "given": "Yoshan", "initials": "Y", "orcid": "0000-0003-4216-2924", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de66994605d4a809f28b04c8dcf91c6.json"}}, {"family": "Rookmaaker", "given": "Kees", "initials": "K", "orcid": "0000-0003-3121-5197", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc8b2d6563f84ad9bf8118836b5e470b.json"}}, {"family": "Bruford", "given": "Michael W", "initials": "MW"}, {"family": "Ryder", "given": "Oliver", "initials": "O"}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Bruins-van Sonsbeek", "given": "Linda G R", "initials": "LGR"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Cooper", "given": "Alan", "initials": "A"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Dunn", "given": "Robert R", "initials": "RR"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Antoine", "given": "Pierre-Olivier", "initials": "PO"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2021-09-16", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "184", "issue": "19", "pages": "4874-4885.e16", "issn-l": "0092-8674"}, "abstract": "Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (\u223c16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.", "doi": "10.1016/j.cell.2021.07.032", "pmid": "34433011", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(21)00891-6"}], "notes": [], "created": "2021-10-01T09:03:51.039Z", "modified": "2024-01-16T13:48:38.478Z"}, {"entity": "publication", "iuid": "6f70e1a8af3e47a5a3fa4fba74483b35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f70e1a8af3e47a5a3fa4fba74483b35"}}, "title": "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio M", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Blommaert", "given": "Julie", "initials": "J", "orcid": "0000-0003-1411-2313", "researcher": {"href": "https://publications.scilifelab.se/researcher/761067515ad240c9b82f0ea7625b1320.json"}}, {"family": "Liu", "given": "Jing", "initials": "J"}, {"family": "Haryoko", "given": "Tri", "initials": "T", "orcid": "0000-0002-8549-3662", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e409936447e49ef9cb6fe1c75417fb0.json"}}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA", "orcid": "0000-0002-1875-9504", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca007307f40c49d2baa3420c3fc61d02.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-09-13", "journal": {"title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn": "1471-2970", "issn-l": "0962-8436", "volume": "376", "issue": "1833", "pages": "20200186"}, "abstract": "It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.", "doi": "10.1098/rstb.2020.0186", "pmid": "34304594", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8310711"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5450746"}], "notes": [], "created": "2021-10-01T09:03:22.481Z", "modified": "2024-01-16T13:48:38.503Z"}, {"entity": "publication", "iuid": "960433d0e9d14c7baf59a3e9a519d1db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/960433d0e9d14c7baf59a3e9a519d1db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/960433d0e9d14c7baf59a3e9a519d1db"}}, "title": "A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.", "authors": [{"family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}}, {"family": "Gro\u03b2e-Wilde", "given": "Ewald", "initials": "E"}, {"family": "Krokene", "given": "Paal", "initials": "P"}, {"family": "Roy", "given": "Amit", "initials": "A"}, {"family": "Chakraborty", "given": "Amrita", "initials": "A"}, {"family": "L\u00f6fstedt", "given": "Christer", "initials": "C", "orcid": "0000-0002-3116-6922", "researcher": {"href": "https://publications.scilifelab.se/researcher/68150ac5a3d44f26af3fa81a5209c535.json"}}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Andersson", "given": "Martin N", "initials": "MN", "orcid": "0000-0001-9807-8524", "researcher": {"href": "https://publications.scilifelab.se/researcher/42bc7f90fad040c292fceed405df5ac3.json"}}, {"family": "Schlyter", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-1244-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/38df140cdd0e4a1693da808131833114.json"}}], "type": "journal article", "published": "2021-09-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "1059", "issn-l": "2399-3642"}, "abstract": "Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species complete their life cycle in nutritionally poor substrates and some can kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) can destroy >100 million m3 of spruce in a single year. We report a 236.8 Mb I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly has a contig N50 of 6.65 Mb in 272 contigs and is predicted to contain 23,923 protein-coding genes. We reveal expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This genome sequence from the genus Ips provides timely resources to address questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. In forests of today, increasingly stressed by global warming, this draft genome may assist in developing pest control strategies to mitigate outbreaks.", "doi": "10.1038/s42003-021-02602-3", "pmid": "34504275", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02602-3"}, {"db": "pmc", "key": "PMC8429705"}, {"db": "figshare", "key": "10.6084/m9.figshare.14503065"}], "notes": [], "created": "2021-09-22T15:33:20.295Z", "modified": "2024-01-16T13:48:38.511Z"}, {"entity": "publication", "iuid": "183750a1213e40eab8d3343e3823bee1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/183750a1213e40eab8d3343e3823bee1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/183750a1213e40eab8d3343e3823bee1"}}, "title": "Selection on accessible chromatin regions in Capsella grandiflora.", "authors": [{"family": "Horvath", "given": "Robert", "initials": "R", "orcid": "0000-0002-3221-8835", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd1f411c815a49bf91ada0eac39dee8b.json"}}, {"family": "Josephs", "given": "Emily B", "initials": "EB"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Stinchcombe", "given": "John R", "initials": "JR"}, {"family": "Wright", "given": "Stephen I", "initials": "SI", "orcid": "0000-0001-9973-9697", "researcher": {"href": "https://publications.scilifelab.se/researcher/31879f06b29d4e919c6dbcc55a7d4318.json"}}, {"family": "Scofield", "given": "Douglas", "initials": "D"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2021-09-08", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038"}, "abstract": "Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large non-coding fraction, functional non-coding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional non-coding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favourable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (\u03b1) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element (TE) insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on non-coding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.", "doi": "10.1093/molbev/msab270", "pmid": "34498072", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6366554"}], "notes": [], "created": "2021-10-01T09:09:08.357Z", "modified": "2024-01-16T13:48:38.533Z"}, {"entity": "publication", "iuid": "ec623039cd0c40c394cf4f1508fea79d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec623039cd0c40c394cf4f1508fea79d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec623039cd0c40c394cf4f1508fea79d"}}, "title": "Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin.", "authors": [{"family": "B\u00e4ckdahl", "given": "Jesper", "initials": "J"}, {"family": "Franz\u00e9n", "given": "Lovisa", "initials": "L"}, {"family": "Massier", "given": "Lucas", "initials": "L"}, {"family": "Li", "given": "Qian", "initials": "Q"}, {"family": "Jalkanen", "given": "Jutta", "initials": "J"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Bhalla", "given": "Nayanika", "initials": "N"}, {"family": "Thorell", "given": "Anders", "initials": "A"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Mejhert", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2021-09-07", "journal": {"title": "Cell Metab.", "issn": "1932-7420", "volume": "33", "issue": "9", "pages": "1869-1882.e6", "issn-l": "1550-4131"}, "abstract": "The contribution of cellular heterogeneity and architecture to white adipose tissue (WAT) function is poorly understood. Herein, we combined spatially resolved transcriptional profiling with single-cell RNA sequencing and image analyses to map human WAT composition and structure. This identified 18 cell classes with unique propensities to form spatially organized homo- and heterotypic clusters. Of these, three constituted mature adipocytes that were similar in size, but distinct in their spatial arrangements and transcriptional profiles. Based on marker genes, we termed these AdipoLEP, AdipoPLIN, and AdipoSAA. We confirmed, in independent datasets, that their respective gene profiles associated differently with both adipocyte and whole-body insulin sensitivity. Corroborating our observations, insulin stimulation in vivo by hyperinsulinemic-euglycemic clamp showed that only AdipoPLIN displayed a transcriptional response to insulin. Altogether, by mining this multimodal resource we identify that human WAT is composed of three classes of mature adipocytes, only one of which is insulin responsive.", "doi": "10.1016/j.cmet.2021.07.018", "pmid": "34380013", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S1550-4131(21)00363-6"}], "notes": [], "created": "2021-10-01T09:03:13.654Z", "modified": "2021-12-06T13:47:29.609Z"}, {"entity": "publication", "iuid": "d0afbf6a0f22480dacd378fbb39437db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0afbf6a0f22480dacd378fbb39437db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0afbf6a0f22480dacd378fbb39437db"}}, "title": "Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.", "authors": [{"family": "Bedoya-Reina", "given": "O C", "initials": "OC"}, {"family": "Li", "given": "W", "initials": "W"}, {"family": "Arceo", "given": "M", "initials": "M"}, {"family": "Plescher", "given": "M", "initials": "M"}, {"family": "Bullova", "given": "P", "initials": "P", "orcid": "0000-0002-5411-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9fa1a447d749f09e98b2d7b39ce499.json"}}, {"family": "Pui", "given": "H", "initials": "H"}, {"family": "Kaucka", "given": "M", "initials": "M"}, {"family": "Kharchenko", "given": "P", "initials": "P", "orcid": "0000-0002-6036-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67002dec1264bf2865da0017405ee9b.json"}}, {"family": "Martinsson", "given": "T", "initials": "T", "orcid": "0000-0002-9403-3123", "researcher": {"href": "https://publications.scilifelab.se/researcher/90deb3f5dd5446e5853da797411dfd5d.json"}}, {"family": "Holmberg", "given": "J", "initials": "J"}, {"family": "Adameyko", "given": "I", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}, {"family": "Deng", "given": "Q", "initials": "Q", "orcid": "0000-0001-5934-7816", "researcher": {"href": "https://publications.scilifelab.se/researcher/b74efaba0fab49acb7164a45beca5cd9.json"}}, {"family": "Larsson", "given": "C", "initials": "C"}, {"family": "Juhlin", "given": "C C", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}, {"family": "Kogner", "given": "P", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications.scilifelab.se/researcher/e963274b921a4a2c8263f509334d4e22.json"}}, {"family": "Schlisio", "given": "S", "initials": "S", "orcid": "0000-0002-2605-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8c1128e0d54cfe80758282ef94809b.json"}}], "type": "journal article", "published": "2021-09-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "5309"}, "abstract": "Childhood neuroblastoma has a remarkable variability in outcome. Age at diagnosis is one of the most important prognostic factors, with children less than 1 year old having favorable outcomes. Here we study single-cell and single-nuclei transcriptomes of neuroblastoma with different clinical risk groups and stages, including healthy adrenal gland. We compare tumor cell populations with embryonic mouse sympatho-adrenal derivatives, and post-natal human adrenal gland. We provide evidence that low and high-risk neuroblastoma have different cell identities, representing two disease entities. Low-risk neuroblastoma presents a transcriptome that resembles sympatho- and chromaffin cells, whereas malignant cells enriched in high-risk neuroblastoma resembles a subtype of TRKB+ cholinergic progenitor population identified in human post-natal gland. Analyses of these populations reveal different gene expression programs for worst and better survival in correlation with age at diagnosis. Our findings reveal two cellular identities and a composition of human neuroblastoma tumors reflecting clinical heterogeneity and outcome.", "doi": "10.1038/s41467-021-24870-7", "pmid": "34493726", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24870-7"}, {"db": "pmc", "key": "PMC8423786"}], "notes": [], "created": "2021-09-08T09:33:10.810Z", "modified": "2024-01-16T13:48:38.541Z"}, {"entity": "publication", "iuid": "396c371ed9e749c6847d3514834ff337", "links": {"self": {"href": "https://publications.scilifelab.se/publication/396c371ed9e749c6847d3514834ff337.json"}, "display": {"href": "https://publications.scilifelab.se/publication/396c371ed9e749c6847d3514834ff337"}}, "title": "Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.", "authors": [{"family": "Zhao", "given": "Yunpo", "initials": "Y"}, {"family": "Lindberg", "given": "Bo Gustav", "initials": "BG"}, {"family": "Esfahani", "given": "Shiva Seyedoleslami", "initials": "SS"}, {"family": "Tang", "given": "Xiongzhuo", "initials": "X"}, {"family": "Piazza", "given": "Stefano", "initials": "S"}, {"family": "Engstr\u00f6m", "given": "Ylva", "initials": "Y", "orcid": "0000-0002-8731-4613", "researcher": {"href": "https://publications.scilifelab.se/researcher/bce6a0618be14db6988a8c1dc2f0d97d.json"}}], "type": "journal article", "published": "2021-09-03", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "19", "issue": "1", "pages": "185", "issn-l": "1741-7007"}, "abstract": "A number of cellular processes have evolved in metazoans that increase the proteome repertoire in relation to the genome, such as alternative splicing and translation recoding. Another such process, translational stop codon readthrough (SCR), generates C-terminally extended protein isoforms in many eukaryotes, including yeast, plants, insects, and humans. While comparative genome analyses have predicted the existence of programmed SCR in many species including humans, experimental proof of its functional consequences are scarce.\n\nWe show that SCR of the Drosophila POU/Oct transcription factor Ventral veins lacking/Drifter (Vvl/Dfr) mRNA is prevalent in certain tissues in vivo, reaching a rate of 50% in the larval prothoracic gland. Phylogenetically, the C-terminal extension is conserved and harbors intrinsically disordered regions and amino acid stretches implied in transcriptional activation. Elimination of Vvl/Dfr translational readthrough by CRISPR/Cas9 mutagenesis changed the expression of a large number of downstream genes involved in processes such as chromatin regulation, neurogenesis, development, and immune response. As a proof-of-principle, we demonstrate that the C-terminal extension of Vvl/Dfr is necessary for correct timing of pupariation, by increasing the capacity to regulate its target genes. The extended Vvl/Dfr isoform acts in synergy with the transcription factor Molting defective (Mld) to increase the expression and biosynthesis of the steroid hormone ecdysone, thereby advancing pupariation. Consequently, late-stage larval development was prolonged and metamorphosis delayed in vvl/dfr readthrough mutants.\n\nWe demonstrate that translational recoding of a POU/Oct transcription factor takes place in a highly tissue-specific and temporally controlled manner. This dynamic and regulated recoding is necessary for normal expression of a large number of genes involved in many cellular and developmental processes. Loss of Vvl/Dfr translational readthrough negatively affects steroid hormone biosynthesis and delays larval development and progression into metamorphosis. Thus, this study demonstrates how SCR of a transcription factor can act as a developmental switch in a spatiotemporal manner, feeding into the timing of developmental transitions between different life-cycle stages.", "doi": "10.1186/s12915-021-01106-0", "pmid": "34479564", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-021-01106-0"}, {"db": "pmc", "key": "PMC8417969"}], "notes": [], "created": "2021-10-01T09:09:04.086Z", "modified": "2024-01-16T13:48:38.549Z"}, {"entity": "publication", "iuid": "624a2be52ba54010964648ca3858cbdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/624a2be52ba54010964648ca3858cbdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/624a2be52ba54010964648ca3858cbdb"}}, "title": "Regulatory T cells reduce endothelial neutral sphingomyelinase 2 to prevent T-cell migration into tumors.", "authors": [{"family": "Akeus", "given": "Paulina", "initials": "P"}, {"family": "Szeponik", "given": "Louis", "initials": "L"}, {"family": "Langenes", "given": "Veronica", "initials": "V"}, {"family": "Karlsson", "given": "Viktoria", "initials": "V"}, {"family": "Sundstr\u00f6m", "given": "Patrik", "initials": "P"}, {"family": "Bexe-Lindskog", "given": "Elinor", "initials": "E"}, {"family": "Tallon", "given": "Carolyn", "initials": "C"}, {"family": "Slusher", "given": "Barbara S", "initials": "BS"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Eur. J. Immunol.", "issn": "1521-4141", "volume": "51", "issue": "9", "pages": "2317-2329", "issn-l": "0014-2980"}, "abstract": "Endothelial cells are key regulators of transendothelial migration and their secretion of chemokines and expression of adhesion molecules facilitates lymphocyte entry into tissues. Previously, we demonstrated that Tregs can reduce transendothelial migration of T cells into tumors by decreasing endothelial CXCL10 secretion, but the mechanism by which this occurs is still not known. In this study, we aimed to define how Tregs decrease transendothelial migration into tumors. mRNA sequencing of intestinal tumor endothelial cells from Treg depleted mice identified neutral sphingomyelinase 2 (nSMase2) as a gene downregulated in the presence of Tregs. nSMase2 is expressed in human umbilical vein endothelial cells (HUVECs) and was decreased after coculture with Tregs. Furthermore, blocking of nSMase2 activity in vitro decreased VCAM1, CX3CL1, and CXCL10 expression in HUVECs, mirroring the same decrease found in Treg cocultures. In the APCmin/+ mouse model of intestinal cancer, nSMase2 is lower in tumor endothelial cells than in unaffected small intestine and chronic treatment with a nSMase2 inhibitor suppressed the increased migration that is otherwise seen in the absence of Tregs. We conclude that nSMase2 is an important mediator in endothelial cells supporting transendothelial migration, which may be targeted by Tregs to reduce T-cell migration into tumors.", "doi": "10.1002/eji.202149208", "pmid": "34272885", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:02:35.660Z", "modified": "2021-12-06T13:47:27.157Z"}, {"entity": "publication", "iuid": "61f78255d44b4e7c86dffd3216d74c85", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61f78255d44b4e7c86dffd3216d74c85.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61f78255d44b4e7c86dffd3216d74c85"}}, "title": "Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change.", "authors": [{"family": "Chattopadhyay", "given": "Balaji", "initials": "B"}, {"family": "Forcina", "given": "Giovanni", "initials": "G"}, {"family": "Garg", "given": "Kritika M", "initials": "KM"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Guerrini", "given": "Monica", "initials": "M"}, {"family": "Barbanera", "given": "Filippo", "initials": "F"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Genomics", "issn": "1089-8646", "volume": "113", "issue": "5", "pages": "3430-3438", "issn-l": "0888-7543"}, "abstract": "We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10\u00d7 Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.", "doi": "10.1016/j.ygeno.2021.08.010", "pmid": "34400239", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0888-7543(21)00317-7"}], "notes": [], "created": "2021-10-01T09:03:19.823Z", "modified": "2021-12-06T13:48:00.974Z"}, {"entity": "publication", "iuid": "f04ae85417c5408ebe1f3ec31464321c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f04ae85417c5408ebe1f3ec31464321c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f04ae85417c5408ebe1f3ec31464321c"}}, "title": "Exploring the \u03b2-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.", "authors": [{"family": "Martin", "given": "Frida", "initials": "F", "orcid": "0000-0002-3149-3835", "researcher": {"href": "https://publications.scilifelab.se/researcher/eacd9c056fb1451994bf6ab3289bbeb1.json"}}, {"family": "Halvarsson", "given": "Peter", "initials": "P"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "H\u00f6glund", "given": "Johan", "initials": "J"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2021-08-26", "journal": {"title": "International Journal for Parasitology: Drugs and Drug Resistance", "issn": "2211-3207", "volume": "17", "pages": "84-91", "issn-l": "2211-3207"}, "abstract": "Benzimidazole (BZ) drugs are frequently used to treat infections with the equine ascarid Parascaris univalens due to increasing resistance to macrocyclic lactones and pyrantel. Benzimidazole resistance is rare in ascarids in contrast to strongyle parasites where this resistance is widespread. In strongyles, single nucleotide polymorphisms (SNPs) at codons 167, 198 and 200 in a \u03b2-tubulin gene have been correlated to BZ resistance, but little is known about the \u03b2-tubulin genes and their possible involvement in BZ resistance in P. univalens and other ascarids. Previously two \u03b2-tubulin genes have been identified in P. univalens. In this study, we present five additional \u03b2-tubulin genes as well as the phylogenetic relationship of all seven genes to \u03b2-tubulins of other clade III and V nematodes. In addition, the efficacy of fenbendazole for treatment of P. univalens on a Swedish stud farm was studied in 2019 and 2020 using faecal egg count reduction test. Reductions varied from 73% to 88%, indicating the presence of a resistant P. univalens population on the farm. The emergence of BZ resistance emphasizes the need for development of molecular markers for rapid and more sensitive detection of resistant populations. We therefore investigated whether possible SNPs at positions 167, 198 or 200 in any of the \u03b2-tubulin genes could be used to distinguish between resistant and susceptible P. univalens populations. Amplicon sequencing covering the mutation sites 167, 198 and 200 in all seven \u03b2-tubulin genes revealed an absence of SNPs in both resistant and susceptible populations, suggesting that the mechanism behind BZ resistance in ascarids is different from that in strongyle nematodes and the search for a molecular marker for BZ resistance in P. univalens needs to continue.", "doi": "10.1016/j.ijpddr.2021.08.004", "pmid": "34467878", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-3207(21)00040-3"}, {"db": "pmc", "key": "PMC8406161"}], "notes": [], "created": "2021-09-22T15:36:40.621Z", "modified": "2024-01-16T13:48:38.626Z"}, {"entity": "publication", "iuid": "d75f05793daf405a9a5f56529ea04248", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d75f05793daf405a9a5f56529ea04248.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d75f05793daf405a9a5f56529ea04248"}}, "title": "Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.", "authors": [{"family": "Grochowski", "given": "Christopher M", "initials": "CM"}, {"family": "Krepischi", "given": "Ana C V", "initials": "ACV"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Du", "given": "Haowei", "initials": "H"}, {"family": "Bertola", "given": "Debora R", "initials": "DR"}, {"family": "Oliveira", "given": "Danyllo", "initials": "D"}, {"family": "Costa", "given": "Silvia S", "initials": "SS"}, {"family": "Lupski", "given": "James R", "initials": "JR"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB"}], "type": "journal article", "published": "2021-08-26", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "12", "pages": "708348", "issn-l": "1664-8021"}, "abstract": "Chromoanagenesis is a descriptive term that encompasses classes of catastrophic mutagenic processes that generate localized and complex chromosome rearrangements in both somatic and germline genomes. Herein, we describe a 5-year-old female presenting with a constellation of clinical features consistent with a clinical diagnosis of Coffin-Siris syndrome 1 (CSS1). Initial G-banded karyotyping detected a 90-Mb pericentric and a 47-Mb paracentric inversion on a single chromosome. Subsequent analysis of short-read whole-genome sequencing data and genomic optical mapping revealed additional inversions, all clustered on chromosome 6, one of them disrupting ARID1B for which haploinsufficiency leads to the CSS1 disease trait (MIM:135900). The aggregate structural variant data show that the resolved, the resolved derivative chromosome architecture presents four de novo inversions, one pericentric and three paracentric, involving six breakpoint junctions in what appears to be a shuffling of genomic material on this chromosome. Each junction was resolved to nucleotide-level resolution with mutational signatures suggestive of non-homologous end joining. The disruption of the gene ARID1B is shown to occur between the fourth and fifth exon of the canonical transcript with subsequent qPCR studies confirming a decrease in ARID1B expression in the patient versus healthy controls. Deciphering the underlying genomic architecture of chromosomal rearrangements and complex structural variants may require multiple technologies and can be critical to elucidating the molecular etiology of a patient's clinical phenotype or resolving unsolved Mendelian disease cases.", "doi": "10.3389/fgene.2021.708348", "pmid": "34512724", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8427664"}], "notes": [], "created": "2021-10-01T09:09:06.984Z", "modified": "2024-01-16T13:48:38.647Z"}, {"entity": "publication", "iuid": "d113d0c37b074a75b7a8dfb5c565524f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d113d0c37b074a75b7a8dfb5c565524f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d113d0c37b074a75b7a8dfb5c565524f"}}, "title": "Amnion signals are essential for mesoderm formation in primates.", "authors": [{"family": "Yang", "given": "Ran", "initials": "R"}, {"family": "Goedel", "given": "Alexander", "initials": "A", "orcid": "0000-0002-5980-2257", "researcher": {"href": "https://publications.scilifelab.se/researcher/866e8580c3d8462da0f3ee3b8909ea6f.json"}}, {"family": "Kang", "given": "Yu", "initials": "Y"}, {"family": "Si", "given": "Chenyang", "initials": "C"}, {"family": "Chu", "given": "Chu", "initials": "C"}, {"family": "Zheng", "given": "Yi", "initials": "Y"}, {"family": "Chen", "given": "Zhenzhen", "initials": "Z"}, {"family": "Gruber", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-7356-905X", "researcher": {"href": "https://publications.scilifelab.se/researcher/623bc96d071d410c8199b178a1e31808.json"}}, {"family": "Xiao", "given": "Yao", "initials": "Y"}, {"family": "Zhou", "given": "Chikai", "initials": "C", "orcid": "0000-0001-9653-3466", "researcher": {"href": "https://publications.scilifelab.se/researcher/05559fcfc7724eb1bf06305a907b58d4.json"}}, {"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Eroglu", "given": "Elif", "initials": "E"}, {"family": "Leung", "given": "Chuen-Yan", "initials": "CY"}, {"family": "Chen", "given": "Yongchang", "initials": "Y"}, {"family": "Fu", "given": "Jianping", "initials": "J", "orcid": "0000-0001-9629-6739", "researcher": {"href": "https://publications.scilifelab.se/researcher/127bba88c5534146ae9ba1b10929bb4b.json"}}, {"family": "Ji", "given": "Weizhi", "initials": "W", "orcid": "0000-0003-2550-4224", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e1228641df34f3fa2f8b961d414233b.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}, {"family": "Niu", "given": "Yuyu", "initials": "Y"}, {"family": "Chien", "given": "Kenneth R", "initials": "KR", "orcid": "0000-0002-2759-8378", "researcher": {"href": "https://publications.scilifelab.se/researcher/971382878b474966bbe58acaa1585999.json"}}], "type": "journal article", "published": "2021-08-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "5126", "issn-l": "2041-1723"}, "abstract": "Embryonic development is largely conserved among mammals. However, certain genes show divergent functions. By generating a transcriptional atlas containing >30,000 cells from post-implantation non-human primate embryos, we uncover that ISL1, a gene with a well-established role in cardiogenesis, controls a gene regulatory network in primate amnion. CRISPR/Cas9-targeting of ISL1 results in non-human primate embryos which do not yield viable offspring, demonstrating that ISL1 is critically required in primate embryogenesis. On a cellular level, mutant ISL1 embryos display a failure in mesoderm formation due to reduced BMP4 signaling from the amnion. Via loss of function and rescue studies in human embryonic stem cells we confirm a similar role of ISL1 in human in vitro derived amnion. This study highlights the importance of the amnion as a signaling center during primate mesoderm formation and demonstrates the potential of in vitro primate model systems to dissect the genetics of early human embryonic development.", "doi": "10.1038/s41467-021-25186-2", "pmid": "34446705", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8390679"}, {"db": "pii", "key": "10.1038/s41467-021-25186-2"}], "notes": [], "created": "2021-08-30T07:44:40.804Z", "modified": "2024-01-16T13:48:38.655Z"}, {"entity": "publication", "iuid": "e22e5204289044ba857e37082c88d678", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e22e5204289044ba857e37082c88d678.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e22e5204289044ba857e37082c88d678"}}, "title": "Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.", "authors": [{"family": "Mahboubi", "given": "Amir", "initials": "A"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Hanson", "given": "Johannes", "initials": "J", "orcid": "0000-0002-5605-7984", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d9c9973ca994461ad9f5c27b4341ddb.json"}}], "type": "journal article", "published": "2021-08-24", "journal": {"title": "Plant Methods", "issn": "1746-4811", "volume": "17", "issue": "1", "pages": "92", "issn-l": "1746-4811"}, "abstract": "Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.\n\nHere we developed a platform for Ribo-Seq library construction and data analysis to enable rapid quality assessment of Ribo-Seq libraries with the help of a small-scale sequencer. Our data show that several qualitative features of a Ribo-Seq library, such as read length distribution, P-site distribution, reading frame and triplet periodicity, can be effectively evaluated using only the data generated by a benchtop sequencer with a very limited number of reads.\n\nOur pipeline enables rapid evaluation of Ribo-Seq libraries, opening up possibilities for optimization of Ribo-Seq library construction from difficult samples, and leading to better decision making prior to more costly deep sequencing.", "doi": "10.1186/s13007-021-00791-w", "pmid": "34429136", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13007-021-00791-w"}, {"db": "pmc", "key": "PMC8386038"}], "notes": [], "created": "2021-10-01T09:03:54.651Z", "modified": "2024-01-16T13:48:38.670Z"}, {"entity": "publication", "iuid": "84400c672468497a95dad6c02d07bc4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84400c672468497a95dad6c02d07bc4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84400c672468497a95dad6c02d07bc4e"}}, "title": "Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.", "authors": [{"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Le Duc", "given": "Diana", "initials": "D"}, {"family": "Duch\u00eane", "given": "David A", "initials": "DA"}, {"family": "Krishnan", "given": "Arunkumar", "initials": "A"}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Rutschmann", "given": "Sereina", "initials": "S"}, {"family": "Grau", "given": "Jose H", "initials": "JH"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Weyrich", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-6944-1854", "researcher": {"href": "https://publications.scilifelab.se/researcher/681593466a04416591a1bfeaafcf7adc.json"}}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Werdelin", "given": "Lars", "initials": "L"}, {"family": "Dalerum", "given": "Fredrik", "initials": "F"}, {"family": "Sch\u00f6neberg", "given": "Torsten", "initials": "T"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2021-08-23", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "38", "issue": "9", "pages": "3884-3897", "issn-l": "0737-4038"}, "abstract": "During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last \u223c2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.", "doi": "10.1093/molbev/msab055", "pmid": "34426844", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "6149117"}, {"db": "pmc", "key": "PMC8382907"}], "notes": [], "created": "2021-10-01T09:03:52.309Z", "modified": "2021-12-06T13:48:34.820Z"}, {"entity": "publication", "iuid": "6e36deedea8441929da5b46f6fd59241", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e36deedea8441929da5b46f6fd59241.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e36deedea8441929da5b46f6fd59241"}}, "title": "Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.", "authors": [{"family": "Ma", "given": "Junjie", "initials": "J", "orcid": "0000-0002-8449-6917", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6026d070e7e4e9dac2171b255ee68f5.json"}}, {"family": "Tibbitt", "given": "Christopher A", "initials": "CA", "orcid": "0000-0002-7730-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d8a6804b0be4aba9a9256dd2df71656.json"}}, {"family": "Geor\u00e9n", "given": "Susanna Kumlien", "initials": "SK"}, {"family": "Christian", "given": "Murray", "initials": "M", "orcid": "0000-0001-8998-1367", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb1873d4fdf441d584119e8ef3f65fdb.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B"}, {"family": "Cardell", "given": "Lars-Olaf", "initials": "LO", "orcid": "0000-0003-0538-9580", "researcher": {"href": "https://publications.scilifelab.se/researcher/54051709c86b4dae91c536ab56318894.json"}}, {"family": "Bachert", "given": "Claus", "initials": "C", "orcid": "0000-0003-4742-1665", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4d0ea7f36744ff1b83f5cd3525d4310.json"}}, {"family": "Coquet", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0002-5967-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b74959951024d6ea9712b55f115652e.json"}}], "type": "journal article", "published": "2021-08-13", "journal": {"title": "Sci Immunol", "issn": "2470-9468", "volume": "6", "issue": "62", "issn-l": null}, "abstract": "Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by a chronic inflammatory process often associated with comorbid asthma. In this study, we analyzed the transcriptomes of single T helper (TH) cells from nasal polyps of patients with CRSwNP and validated these findings using multiparameter flow cytometry. Polyp tissue contained suppressive T regulatory (Treg) cells, TH2 cells, type 2 innate lymphoid cells, and three transcriptionally distinct subsets of cytotoxic CD4+ T cells (CD4+ CTL). GATA3 expression was a feature of polyp Treg cells, whereas TH2 cells highly expressed TCN1, CD200R, and HPGDS and were enriched for genes involved in lipid metabolism. Only a portion of polyp TH2 cells expressed the prostaglandin D2 receptor CRTH2, whereas a subpopulation of CD109+CRTH2- TH2 cells expressed mRNA for common inhibitor receptors including LAG3 and TIM3 and produced IL-10. Together, we resolved the complexity of TH cells in patients with CRSwNP, identifying several distinct clusters of CD4+ CTL and a population of CD109+CRTH2- TH2 cells with putative regulatory potential.", "doi": "10.1126/sciimmunol.abg6356", "pmid": "34389612", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6/62/eabg6356"}], "notes": [], "created": "2021-12-02T13:03:20.260Z", "modified": "2024-01-16T13:48:38.775Z"}, {"entity": "publication", "iuid": "8d1b160b1ba145ce952fadcba56d41a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d1b160b1ba145ce952fadcba56d41a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d1b160b1ba145ce952fadcba56d41a6"}}, "title": "Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.", "authors": [{"family": "Martin", "given": "Ga\u00ebtan", "initials": "G"}, {"family": "Rissanen", "given": "Antti J", "initials": "AJ"}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL"}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Peura", "given": "Sari", "initials": "S"}], "type": "journal article", "published": "2021-08-12", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "669937", "issn-l": "1664-302X"}, "abstract": "Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50\u00b0 North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.", "doi": "10.3389/fmicb.2021.669937", "pmid": "34456882", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8397446"}], "notes": [], "created": "2021-10-01T09:03:57.031Z", "modified": "2024-01-16T13:48:38.782Z"}, {"entity": "publication", "iuid": "49d7f88a4b4a46af8d50dbdab7de9479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49d7f88a4b4a46af8d50dbdab7de9479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49d7f88a4b4a46af8d50dbdab7de9479"}}, "title": "Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.", "authors": [{"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Salas", "given": "Beatriz", "initials": "B"}, {"family": "Ganji", "given": "Suresh", "initials": "S"}, {"family": "Jorquera-Rom\u00e1n", "given": "Cristian", "initials": "C"}, {"family": "Valenzuela", "given": "Maria Luisa", "initials": "ML"}, {"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Unelius", "given": "C Rikard", "initials": "CR"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Vera", "given": "Mario", "initials": "M"}], "type": "journal article", "published": "2021-08-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "11", "issue": "1", "pages": "16275", "issn-l": "2045-2322"}, "abstract": "Bioleaching of metal sulfide ores involves acidophilic microbes that catalyze the chemical dissolution of the metal sulfide bond that is enhanced by attached and planktonic cell mediated oxidation of iron(II)-ions and inorganic sulfur compounds. Leptospirillum spp. often predominate in sulfide mineral-containing environments, including bioheaps for copper recovery from chalcopyrite, as they are effective primary mineral colonizers and oxidize iron(II)-ions efficiently. In this study, we demonstrated a functional diffusible signal factor interspecies quorum sensing signaling mechanism in Leptospirillum ferriphilum and Leptospirillum ferrooxidans that produces (Z)-11-methyl-2-dodecenoic acid when grown with pyrite as energy source. In addition, pure diffusible signal factor and extracts from supernatants of pyrite grown Leptospirillum spp. inhibited biological iron oxidation in various species, and that pyrite grown Leptospirillum cells were less affected than iron grown cells to self inhibition. Finally, transcriptional analyses for the inhibition of iron-grown L. ferriphilum cells due to diffusible signal factor was compared with the response to exposure of cells to N- acyl-homoserine-lactone type quorum sensing signal compounds. The data suggested that Leptospirillum spp. diffusible signal factor production is a strategy for niche protection and defense against other microbes and it is proposed that this may be exploited to inhibit unwanted acidophile species.", "doi": "10.1038/s41598-021-95324-9", "pmid": "34381075", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-021-95324-9"}, {"db": "pmc", "key": "PMC8357829"}], "notes": [], "created": "2021-10-01T09:03:16.277Z", "modified": "2024-01-16T13:48:38.805Z"}, {"entity": "publication", "iuid": "6963712d5ff441bc82d154cba4a54fbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6963712d5ff441bc82d154cba4a54fbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6963712d5ff441bc82d154cba4a54fbb"}}, "title": "PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.", "authors": [{"family": "Seyfferth", "given": "Carolin", "initials": "C", "orcid": "0000-0002-8962-3778", "researcher": {"href": "https://publications.scilifelab.se/researcher/2237d285735b40eea838eedfe54a4454.json"}}, {"family": "Wessels", "given": "Bernard A", "initials": "BA", "orcid": "0000-0003-0717-1630", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c8a7ef9a3e64345b2be703fb991cf41.json"}}, {"family": "Vahala", "given": "Jorma", "initials": "J"}, {"family": "Kangasj\u00e4rvi", "given": "Jaakko", "initials": "J"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Lundberg-Felten", "given": "Judith", "initials": "J"}], "type": "journal article", "published": "2021-08-03", "journal": {"title": "Cells", "issn": "2073-4409", "volume": "10", "issue": "8", "pages": "1971", "issn-l": "2073-4409"}, "abstract": "Secondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identified a novel role for the ethylene-induced Populus Ethylene Response Factor PtERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of PtERF85 is high in phloem and cambium cells and during the expansion of xylem cells, while it is low in maturing xylem tissue. Extending PtERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation, and growth. The expression of genes associated with plant vascular development and the biosynthesis of SCW chemical components such as xylan and lignin, was down-regulated in the transgenic trees. Our results suggest that PtERF85 activates genes related to xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of PtERF85 during wood development together with the observed phenotypes in response to ectopic PtERF85 expression suggests that PtERF85 contributes to the transition of fiber cells from elongation to secondary cell wall deposition.", "doi": "10.3390/cells10081971", "pmid": "34440740", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "cells10081971"}, {"db": "pmc", "key": "PMC8393460"}], "notes": [], "created": "2021-10-01T09:03:49.871Z", "modified": "2024-01-16T13:48:38.888Z"}, {"entity": "publication", "iuid": "a0c7031690744d69bd94427f6d63b73c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c7031690744d69bd94427f6d63b73c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c7031690744d69bd94427f6d63b73c"}}, "title": "Genome-wide estrogen receptor \u03b2 chromatin binding in human colon cancer cells reveals its tumor suppressor activity.", "authors": [{"family": "Indukuri", "given": "Rajitha", "initials": "R", "orcid": "0000-0001-6570-842X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94148ec0ffb74f9bb0243c18a1256c22.json"}}, {"family": "Jafferali", "given": "Mohammed Hakim", "initials": "MH"}, {"family": "Song", "given": "Dandan", "initials": "D"}, {"family": "Damdimopoulos", "given": "Anastasios", "initials": "A"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Zhao", "given": "Chunyan", "initials": "C"}, {"family": "Archer", "given": "Amena", "initials": "A", "orcid": "0000-0002-0400-4151", "researcher": {"href": "https://publications.scilifelab.se/researcher/4502538fe3e84cb6a6618c972fa10b08.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2021-08-01", "journal": {"title": "Int. J. Cancer", "issn": "1097-0215", "volume": "149", "issue": "3", "pages": "692-706", "issn-l": "0020-7136"}, "abstract": "Colorectal cancer (CRC) is the third leading cause of cancer death in the western world. In women, menopausal hormone therapy has been shown to reduce CRC incidence by 20%. Studies demonstrate that estrogen activating estrogen receptor beta (ER\u03b2) protects against CRC. ER\u03b2 is a nuclear receptor that regulates gene expression through interactions with the chromatin. This molecular mechanism is, however, not well characterized in colon. Here, we present for the first time, the cistrome of ER\u03b2 in different colon cancer cell lines. We use cell lines engineered to express ER\u03b2, optimize and validate an ER\u03b2 antibody for chromatin-immunoprecipitation (ChIP), and perform ChIP-Seq. We identify key binding motifs, including ERE, AP-1, and TCF sites, and we determine enrichment of binding to cis-regulatory chromatin sites of genes involved in tumor development, cell migration, cell adhesion, apoptosis, and Wnt signaling pathways. We compare the corresponding cistromes of colon and breast cancer and find that they are conserved for about a third of genes, including GREB1, but that ER\u03b2 tethering to TCF and KLF family motifs is characteristic for colon. We exemplify upregulation of putative CRC tumor suppressor gene CST5 where ER\u03b2 in colon cells binds to cis-regulatory regions nearby (-351 bp) the transcriptional start site. Our work provides a foundation for understanding the mechanism of action of ER\u03b2 in CRC prevention.", "doi": "10.1002/ijc.33573", "pmid": "33754337", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-06-09T12:16:18.247Z", "modified": "2024-01-16T13:48:38.912Z"}, {"entity": "publication", "iuid": "f18d7672bbbb4e5dbcd524fde4fbc995", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f18d7672bbbb4e5dbcd524fde4fbc995.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f18d7672bbbb4e5dbcd524fde4fbc995"}}, "title": "The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.", "authors": [{"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Zisi", "given": "Asimina", "initials": "A", "orcid": "0000-0002-4253-0275", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf82380ca6e4cd1985bc9dd23789539.json"}}, {"family": "Sakkas", "given": "Elpidoforos", "initials": "E"}, {"family": "Bartkova", "given": "Jirina", "initials": "J"}, {"family": "Katsori", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0001-5252-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af59464d2c74c27af7a43fb5d1a670e.json"}}, {"family": "Dyrskj\u00f8t", "given": "Lars", "initials": "L"}, {"family": "Broholm", "given": "Helle", "initials": "H", "orcid": "0000-0002-6029-822X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6d1ef8a71f24d1694aee57b47c22198.json"}}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "32", "issn-l": "2375-2548"}, "abstract": "Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.", "doi": "10.1126/sciadv.abf7561", "pmid": "34348895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "7/32/eabf7561"}, {"db": "pmc", "key": "PMC8336962"}], "notes": [], "created": "2021-10-01T09:03:24.915Z", "modified": "2023-06-19T11:42:22.695Z"}, {"entity": "publication", "iuid": "1112006ac1ac48f59879095ea00312d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1112006ac1ac48f59879095ea00312d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1112006ac1ac48f59879095ea00312d3"}}, "title": "Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).", "authors": [{"family": "Figueroa", "given": "Daniela", "initials": "D"}, {"family": "Capo", "given": "Eric", "initials": "E", "orcid": "0000-0001-9143-7061", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4017e9c8167487b882ee2d045d96494.json"}}, {"family": "Lindh", "given": "Markus V", "initials": "MV", "orcid": "0000-0002-7120-4145", "researcher": {"href": "https://publications.scilifelab.se/researcher/a190553c9e95454aafbe8a7b5ee1967e.json"}}, {"family": "Rowe", "given": "Owen F", "initials": "OF"}, {"family": "Paczkowska", "given": "Joanna", "initials": "J", "orcid": "0000-0003-3568-7968", "researcher": {"href": "https://publications.scilifelab.se/researcher/439421721c7c46e98c787198713a6503.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-7819-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/812b8d6654af4482a308367f052f64c7.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "23", "issue": "8", "pages": "4200-4213", "issn-l": "1462-2912"}, "abstract": "Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting ~ 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.", "doi": "10.1111/1462-2920.15597", "pmid": "33998121", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:00:23.090Z", "modified": "2024-01-16T13:48:38.945Z"}, {"entity": "publication", "iuid": "028827c58bea4f14bbedb8ef627db6fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/028827c58bea4f14bbedb8ef627db6fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/028827c58bea4f14bbedb8ef627db6fc"}}, "title": "SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.", "authors": [{"family": "Guo", "given": "Min", "initials": "M", "orcid": "0000-0002-2291-1230", "researcher": {"href": "https://publications.scilifelab.se/researcher/b31e97bd7c2b4cb49b173189d515c2dc.json"}}, {"family": "Goudarzi", "given": "Kaveh M", "initials": "KM"}, {"family": "Abedi", "given": "Shiva", "initials": "S"}, {"family": "Pieber", "given": "Melanie", "initials": "M"}, {"family": "Sj\u00f6berg", "given": "Elin", "initials": "E", "orcid": "0000-0002-8799-4874", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd51131ccec248aea0bcf013a7da3296.json"}}, {"family": "Behnan", "given": "Jinan", "initials": "J", "orcid": "0000-0001-5780-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fbacfae35ad4364b5058e432aa6e6df.json"}}, {"family": "Zhang", "given": "Xing-Mei", "initials": "XM"}, {"family": "Harris", "given": "Robert A", "initials": "RA"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Oncogene", "issn": "1476-5594", "volume": "40", "issue": "32", "pages": "5066-5080", "issn-l": "0950-9232"}, "abstract": "Intratumoral heterogeneity is a characteristic of glioblastomas that contain an intermixture of cell populations displaying different glioblastoma subtype gene expression signatures. Proportions of these populations change during tumor evolution, but the occurrence and regulation of glioblastoma subtype transition is not well described. To identify regulators of glioblastoma subtypes we utilized a combination of in vitro experiments and in silico analyses, using experimentally generated as well as publicly available data. Through this combined approach SOX2 was identified to confer a proneural glioblastoma subtype gene expression signature. SFRP2 was subsequently identified as a SOX2-antagonist, able to induce a mesenchymal glioblastoma subtype signature. A subset of patient glioblastoma samples with high SFRP2 and low SOX2 expression was particularly enriched with mesenchymal subtype samples. Phenotypically, SFRP2 decreased tumor sphere formation, stemness as assessed by limiting dilution assay, and overall cell proliferation but increased cell motility, whereas SOX2 induced the opposite effects. Furthermore, an SFRP2/non-canonical-WNT/KLF4/PDGFR/phospho-AKT/SOX2 signaling axis was found to be involved in the mesenchymal transition. Analysis of human tumor tissue spatial gene expression patterns showed distinct expression of SFRP2- and SOX2-correlated genes in vascular and cellular areas, respectively. Finally, conditioned media from SFRP2 overexpressing cells increased CD206 on macrophages. Together, these findings present SFRP2 as a SOX2-antagonist with the capacity to induce a mesenchymal subtype transition in glioma cells located in vascular tumor areas, highlighting its role in glioblastoma tumor evolution and intratumoral heterogeneity.", "doi": "10.1038/s41388-021-01825-2", "pmid": "34021259", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41388-021-01825-2"}, {"db": "pmc", "key": "PMC8363098"}], "notes": [], "created": "2021-10-01T09:01:02.317Z", "modified": "2022-03-29T11:45:30.466Z"}, {"entity": "publication", "iuid": "aac00ea44cb647ffb44382c885f897a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aac00ea44cb647ffb44382c885f897a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aac00ea44cb647ffb44382c885f897a2"}}, "title": "Molecular architecture of the developing mouse brain.", "authors": [{"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Siletti", "given": "Kimberly", "initials": "K"}, {"family": "Furlan", "given": "Alessandro", "initials": "A"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1429-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/a5c0db7c1c9b474b8726fbd44d530330.json"}}, {"family": "Vinsland", "given": "Elin", "initials": "E"}, {"family": "Mossi Albiach", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-7009-4901", "researcher": {"href": "https://publications.scilifelab.se/researcher/71fd1a6c4e174f27b2e25a24732838d0.json"}}, {"family": "Mattsson Langseth", "given": "Christoffer", "initials": "C", "orcid": "0000-0003-2230-8594", "researcher": {"href": "https://publications.scilifelab.se/researcher/df19aaf2ad714a63aa40dc6b18a06229.json"}}, {"family": "Khven", "given": "Irina", "initials": "I"}, {"family": "Lederer", "given": "Alex R", "initials": "AR"}, {"family": "Dratva", "given": "Lisa M", "initials": "LM", "orcid": "0000-0002-2873-6787", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ff74c24d9a4f71b6684d2eb3d177db.json"}}, {"family": "Johnsson", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Linnarsson", "given": "Sten", "initials": "S", "orcid": "0000-0002-3491-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c0d35942ce042688ea07f23902a8d46.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "596", "issue": "7870", "pages": "92-96", "issn-l": "0028-0836"}, "abstract": "The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of this process requires a systematic characterization of cell states over the entire spatiotemporal range of brain development. The ability of single-cell RNA sequencing and spatial transcriptomics to reveal the molecular heterogeneity of complex tissues has therefore been particularly powerful in the nervous system. Previous studies have explored development in specific brain regions1-8, the whole adult brain9 and even entire embryos10. Here we report a comprehensive single-cell transcriptomic atlas of the embryonic mouse brain between gastrulation and birth. We identified almost eight hundred cellular states that describe a developmental program for the functional elements of the brain and its enclosing membranes, including the early neuroepithelium, region-specific secondary organizers, and both neurogenic and gliogenic progenitors. We also used in situ mRNA sequencing to map the spatial expression patterns of key developmental genes. Integrating the in situ data with our single-cell clusters revealed the precise spatial organization of neural progenitors during the patterning of the nervous system.", "doi": "10.1038/s41586-021-03775-x", "pmid": "34321664", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03775-x"}], "notes": [], "created": "2021-10-01T09:03:14.935Z", "modified": "2025-10-17T13:02:17.936Z"}, {"entity": "publication", "iuid": "e61a5dfc16b449178d8a242d4f877960", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e61a5dfc16b449178d8a242d4f877960.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e61a5dfc16b449178d8a242d4f877960"}}, "title": "Dynamics of Baltic Sea phages driven by environmental changes.", "authors": [{"family": "Hoetzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-1932-6479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6324668ed1db48a787d75bd996d5358c.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Arabi", "given": "Rahaf", "initials": "R"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Hutinet", "given": "Geoffrey", "initials": "G"}, {"family": "Bayfield", "given": "Oliver W", "initials": "OW"}, {"family": "Traving", "given": "Sachia", "initials": "S"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Middelboe", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9587-9171", "researcher": {"href": "https://publications.scilifelab.se/researcher/319059b849c144d8883950f014279c59.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "23", "issue": "8", "pages": "4576-4594", "issn-l": "1462-2912"}, "abstract": "Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.", "doi": "10.1111/1462-2920.15651", "pmid": "34190387", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:01:12.767Z", "modified": "2024-01-16T13:48:39.004Z"}, {"entity": "publication", "iuid": "b7eea19211a243ea8425fff9af2dc589", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7eea19211a243ea8425fff9af2dc589.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7eea19211a243ea8425fff9af2dc589"}}, "title": "Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Kierczak", "given": "Marcin", "initials": "M"}, {"family": "Peona", "given": "Valentina", "initials": "V"}, {"family": "Whitley", "given": "Kaitlyn M", "initials": "KM"}, {"family": "Larva", "given": "Tuuli", "initials": "T"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Miller-Struttmann", "given": "Nicole E", "initials": "NE"}, {"family": "Geib", "given": "Jennifer C", "initials": "JC"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "comparative study", "published": "2021-07-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "8", "pages": "3126-3143"}, "abstract": "Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (dXY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.", "doi": "10.1093/molbev/msab086", "pmid": "33823537", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6199435"}, {"db": "pmc", "key": "PMC8321533"}], "notes": [], "created": "2021-04-12T09:33:02.825Z", "modified": "2024-01-16T13:48:39.049Z"}, {"entity": "publication", "iuid": "e0aeef535c474932927ea3ec20227770", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0aeef535c474932927ea3ec20227770.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0aeef535c474932927ea3ec20227770"}}, "title": "Complex population structure of the Atlantic puffin revealed by whole genome analyses.", "authors": [{"family": "Kersten", "given": "Oliver", "initials": "O", "orcid": "0000-0001-9304-2493", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b317e145ab940a2a612b38ddb698e79.json"}}, {"family": "Star", "given": "Bastiaan", "initials": "B", "orcid": "0000-0003-0235-9810", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4edcdfadd284a8e9b6b474ff34fd424.json"}}, {"family": "Leigh", "given": "Deborah M", "initials": "DM", "orcid": "0000-0003-3902-2568", "researcher": {"href": "https://publications.scilifelab.se/researcher/48b5deef5a7444109a5e490e267e8c72.json"}}, {"family": "Anker-Nilssen", "given": "Tycho", "initials": "T", "orcid": "0000-0002-1030-5524", "researcher": {"href": "https://publications.scilifelab.se/researcher/35855a3c33304060ba5c3f660079e484.json"}}, {"family": "Str\u00f8m", "given": "Hallvard", "initials": "H"}, {"family": "Danielsen", "given": "J\u00f3hannis", "initials": "J", "orcid": "0000-0002-9775-4786", "researcher": {"href": "https://publications.scilifelab.se/researcher/2074ae819cd84f839fed587ae95807a3.json"}}, {"family": "Descamps", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0003-0590-9013", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf274a4bdbac47cca89bd922c977b1e0.json"}}, {"family": "Erikstad", "given": "Kjell E", "initials": "KE"}, {"family": "Fitzsimmons", "given": "Michelle G", "initials": "MG", "orcid": "0000-0002-1749-3695", "researcher": {"href": "https://publications.scilifelab.se/researcher/572fce1630a9444684e3080555907207.json"}}, {"family": "Fort", "given": "J\u00e9r\u00f4me", "initials": "J", "orcid": "0000-0002-0860-6707", "researcher": {"href": "https://publications.scilifelab.se/researcher/232a039a62754c6dbcc98497a243e92a.json"}}, {"family": "Hansen", "given": "Erpur S", "initials": "ES", "orcid": "0000-0001-6899-2817", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c3158ad44124231804b993ce046fbb4.json"}}, {"family": "Harris", "given": "Mike P", "initials": "MP"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Kleven", "given": "Oddmund", "initials": "O", "orcid": "0000-0003-0267-6795", "researcher": {"href": "https://publications.scilifelab.se/researcher/77abc47074084d85af635520a118143e.json"}}, {"family": "Mallory", "given": "Mark L", "initials": "ML", "orcid": "0000-0003-2744-3437", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8fda3f16774feeb99eb4209a18f013.json"}}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce6b0ca9c5224a26947b5f941d75f039.json"}}, {"family": "Boessenkool", "given": "Sanne", "initials": "S", "orcid": "0000-0001-8033-1165", "researcher": {"href": "https://publications.scilifelab.se/researcher/49f2aaa706b446bca8e44c639fcbd0a8.json"}}], "type": "journal article", "published": "2021-07-29", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "922", "issn-l": "2399-3642"}, "abstract": "The factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.", "doi": "10.1038/s42003-021-02415-4", "pmid": "34326442", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-02415-4"}, {"db": "pmc", "key": "PMC8322098"}], "notes": [], "created": "2021-10-01T09:03:20.955Z", "modified": "2024-01-16T13:48:39.060Z"}, {"entity": "publication", "iuid": "9582fbb5d0864897a3b6e0fd249a194b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9582fbb5d0864897a3b6e0fd249a194b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9582fbb5d0864897a3b6e0fd249a194b"}}, "title": "Unraveling negative biotic interactions determining soil microbial community assembly and functioning.", "authors": [{"family": "Romdhane", "given": "Sana", "initials": "S"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A", "orcid": "0000-0002-4707-9559", "researcher": {"href": "https://publications.scilifelab.se/researcher/38996366bf744d2e89398d9f5195c0c1.json"}}, {"family": "Aubert", "given": "Julie", "initials": "J", "orcid": "0000-0001-5203-5748", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ebb159d634b4e52bc684668009ce33c.json"}}, {"family": "Bru", "given": "David", "initials": "D"}, {"family": "Breuil", "given": "Marie-Christine", "initials": "MC"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}, {"family": "Mounier", "given": "Arnaud", "initials": "A"}, {"family": "Ouadah", "given": "Sarah", "initials": "S"}, {"family": "Tsiknia", "given": "Myrto", "initials": "M", "orcid": "0000-0002-0924-4509", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab7fd9f77f824b3196b57cc1d86d0636.json"}}, {"family": "Philippot", "given": "Laurent", "initials": "L", "orcid": "0000-0003-3461-4492", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ef457126a748aebd40ff834d20085c.json"}}], "type": "journal article", "published": "2021-07-28", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362"}, "abstract": "Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.", "doi": "10.1038/s41396-021-01076-9", "pmid": "34321619", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-021-01076-9"}], "notes": [], "created": "2021-10-01T09:03:46.208Z", "modified": "2021-12-06T13:48:07.440Z"}, {"entity": "publication", "iuid": "3f21e66476504fa2a202d18dd4ab1a25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f21e66476504fa2a202d18dd4ab1a25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f21e66476504fa2a202d18dd4ab1a25"}}, "title": "Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.", "authors": [{"family": "Kwon", "given": "Hyeogsun", "initials": "H", "orcid": "0000-0002-4141-4061", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd140ccd75dd4d80badb163dc7b569ab.json"}}, {"family": "Mohammed", "given": "Mubasher", "initials": "M"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O", "orcid": "0000-0002-7573-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9f587e682f433dbcdbe932861d1a69.json"}}, {"family": "Ankarklev", "given": "Johan", "initials": "J"}, {"family": "Smith", "given": "Ryan C", "initials": "RC", "orcid": "0000-0003-0245-2265", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8748dad26d043e9bdb52a2cf3a8f6c5.json"}}], "type": "journal article", "published": "2021-07-28", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "10", "issn-l": "2050-084X"}, "abstract": "Mosquito immune cells, known as hemocytes, are integral to cellular and humoral responses that limit pathogen survival and mediate immune priming. However, without reliable cell markers and genetic tools, studies of mosquito immune cells have been limited to morphological observations, leaving several aspects of their biology uncharacterized. Here, we use single-cell RNA sequencing (scRNA-seq) to characterize mosquito immune cells, demonstrating an increased complexity to previously defined prohemocyte, oenocytoid, and granulocyte subtypes. Through functional assays relying on phagocytosis, phagocyte depletion, and RNA-FISH experiments, we define markers to accurately distinguish immune cell subtypes and provide evidence for immune cell maturation and differentiation. In addition, gene-silencing experiments demonstrate the importance of lozenge in defining the mosquito oenocytoid cell fate. Together, our scRNA-seq analysis provides an important foundation for future studies of mosquito immune cell biology and a valuable resource for comparative invertebrate immunology.", "doi": "10.7554/eLife.66192", "pmid": "34318744", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Microbial Single Cell Genomics": null, "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "66192"}, {"db": "pmc", "key": "PMC8376254"}], "notes": [], "created": "2021-10-01T09:03:55.828Z", "modified": "2024-01-16T13:48:39.067Z"}, {"entity": "publication", "iuid": "d3750af0071a4ba1ad310809381e3fe7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3750af0071a4ba1ad310809381e3fe7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3750af0071a4ba1ad310809381e3fe7"}}, "title": "Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.", "authors": [{"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M", "orcid": "0000-0003-3588-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c5d5c765980461997541605f7512623.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bell", "given": "Emma", "initials": "E", "orcid": "0000-0002-2064-6496", "researcher": {"href": "https://publications.scilifelab.se/researcher/d81b7088d61947dd823b9a6faff49f31.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D", "orcid": "0000-0003-2858-9809", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cd65b63aec74d7b9375568306d26dce.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Bernier-Latmani", "given": "Rizlan", "initials": "R", "orcid": "0000-0001-6547-722X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba86cb9b29a426fa98fb70ad2c634e5.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2021-07-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "4253", "issn-l": "2041-1723"}, "abstract": "While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.", "doi": "10.1038/s41467-021-24549-z", "pmid": "34253732", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24549-z"}, {"db": "pmc", "key": "PMC8275790"}], "notes": [], "created": "2021-08-09T12:22:57.037Z", "modified": "2024-01-16T13:48:39.118Z"}, {"entity": "publication", "iuid": "d48dec0c5acd4c628f8923ae5339eb5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d48dec0c5acd4c628f8923ae5339eb5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d48dec0c5acd4c628f8923ae5339eb5d"}}, "title": "Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.", "authors": [{"family": "Calleja-Rodriguez", "given": "Ainhoa", "initials": "A"}, {"family": "Chen", "given": "ZhiQiang", "initials": "Z"}, {"family": "Suontama", "given": "Mari", "initials": "M"}, {"family": "Pan", "given": "Jin", "initials": "J"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2021-07-07", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "volume": "12", "pages": "666820", "issn-l": "1664-462X"}, "abstract": "Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive \u00d7 additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.", "doi": "10.3389/fpls.2021.666820", "pmid": "34305966", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8294091"}], "notes": [], "created": "2021-10-01T09:03:48.743Z", "modified": "2024-01-16T13:48:39.125Z"}, {"entity": "publication", "iuid": "cd197346a3404e49b2b51b03e1b7f753", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd197346a3404e49b2b51b03e1b7f753.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd197346a3404e49b2b51b03e1b7f753"}}, "title": "High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.", "authors": [{"family": "Zhang", "given": "Linlin", "initials": "L", "orcid": "0000-0003-0247-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a9f542614414a63a2435f1e0790be58.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Reed", "given": "Robert D", "initials": "RD"}], "type": "journal article", "published": "2021-07-06", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "7", "issn-l": "1759-6653"}, "abstract": "The painted lady butterfly, Vanessa cardui, has the longest migration routes, the widest hostplant diversity, and one of the most complex wing patterns of any insect. Due to minimal culturing requirements, easily characterized wing pattern elements, and technical feasibility of CRISPR/Cas9 genome editing, V. cardui is emerging as a functional genomics model for diverse research programs. Here, we report a high-quality, annotated genome assembly of the V. cardui genome, generated using 84\u00d7 coverage of PacBio long-read data, which we assembled into 205 contigs with a total length of 425.4 Mb (N50 = 10.3 Mb). The genome was very complete (single-copy complete Benchmarking Universal Single-Copy Orthologs [BUSCO] 97%), with contigs assembled into presumptive chromosomes using synteny analyses. Our annotation used embryonic, larval, and pupal transcriptomes, and 20 transcriptomes across five different wing developmental stages. Gene annotations showed a high level of accuracy and completeness, with 14,437 predicted protein-coding genes. This annotated genome assembly constitutes an important resource for diverse functional genomic studies ranging from the developmental genetic basis of butterfly color pattern, to coevolution with diverse hostplants.", "doi": "10.1093/gbe/evab145", "pmid": "34282459", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6310739"}, {"db": "pmc", "key": "PMC8290113"}], "notes": [], "created": "2021-10-01T09:02:33.146Z", "modified": "2024-01-16T13:48:39.151Z"}, {"entity": "publication", "iuid": "2de2b799b9a14b1d8a6da54b92f723f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2de2b799b9a14b1d8a6da54b92f723f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2de2b799b9a14b1d8a6da54b92f723f2"}}, "title": "Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.", "authors": [{"family": "Haas", "given": "Julia C", "initials": "JC"}, {"family": "Vergara", "given": "Alexander", "initials": "A"}, {"family": "Serrano", "given": "Alonso R", "initials": "AR", "orcid": "0000-0002-1635-6410", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbb5a3f8e00542adb782f0671294f746.json"}}, {"family": "Mishra", "given": "Sanatkumar", "initials": "S"}, {"family": "Hurry", "given": "Vaughan", "initials": "V"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}], "type": "journal article", "published": "2021-07-05", "journal": {"title": "Tree Physiol", "issn": "1758-4469", "volume": "41", "issue": "7", "pages": "1230-1246", "issn-l": "0829-318X"}, "abstract": "Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.", "doi": "10.1093/treephys/tpaa178", "pmid": "33416078", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6069261"}, {"db": "pmc", "key": "PMC8271197"}], "notes": [], "created": "2021-06-09T12:14:31.283Z", "modified": "2024-01-16T13:48:39.166Z"}, {"entity": "publication", "iuid": "ecf3b621ca47491aba1186ac4de7cb14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecf3b621ca47491aba1186ac4de7cb14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecf3b621ca47491aba1186ac4de7cb14"}}, "title": "Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.", "authors": [{"family": "\u00c9li\u00e1s", "given": "Szabolcs", "initials": "S", "orcid": "0000-0003-0223-1251", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4763bc3947c9b6d05195bb01703b.json"}}, {"family": "Schmidt", "given": "Angelika", "initials": "A", "orcid": "0000-0002-1185-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3708b225fbae4c239bdc3bea34beff17.json"}}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J", "orcid": "0000-0002-9568-5588", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc6bb8ee30064dd4bc275d0ee8edb158.json"}}], "type": "journal article", "published": "2021-07-03", "journal": {"title": "J Immunol Res", "issn": "2314-7156", "volume": "2021", "pages": "8880585", "issn-l": null}, "abstract": "GM-CSF produced by autoreactive CD4-positive T helper cells is involved in the pathogenesis of autoimmune diseases, such as multiple sclerosis. However, the molecular regulators that establish and maintain the features of GM-CSF-positive CD4 T cells are unknown. In order to identify these regulators, we isolated human GM-CSF-producing CD4 T cells from human peripheral blood by using a cytokine capture assay. We compared these cells to the corresponding GM-CSF-negative fraction, and furthermore, we studied na\u00efve CD4 T cells, memory CD4 T cells, and bulk CD4 T cells from the same individuals as additional control cell populations. As a result, we provide a rich resource of integrated chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from these primary human CD4 T cell subsets and we show that the identified signatures are associated with human autoimmune diseases, especially multiple sclerosis. By combining information about mRNA expression, DNA accessibility, and predicted transcription factor binding, we reconstructed directed gene regulatory networks connecting transcription factors to their targets, which comprise putative key regulators of human GM-CSF-positive CD4 T cells as well as memory CD4 T cells. Our results suggest potential therapeutic targets to be investigated in the future in human autoimmune disease.", "doi": "10.1155/2021/8880585", "pmid": "34285924", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8275380"}], "notes": [], "created": "2021-10-01T09:03:23.726Z", "modified": "2021-12-06T13:48:04.927Z"}, {"entity": "publication", "iuid": "9249d1bd183c4a2dbece43a7d7e1db47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9249d1bd183c4a2dbece43a7d7e1db47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9249d1bd183c4a2dbece43a7d7e1db47"}}, "title": "The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.", "authors": [{"family": "Bakovic", "given": "Vid", "initials": "V", "orcid": "0000-0001-9506-5816", "researcher": {"href": "https://publications.scilifelab.se/researcher/613026a563c543c794e0094c0239920b.json"}}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Hargeby", "given": "Anders", "initials": "A"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "14", "pages": "3530-3547", "issn-l": "0962-1083"}, "abstract": "Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented \"reed\" and light-pigmented \"stonewort\" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F2 and F4 cave \u00d7 surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.", "doi": "10.1111/mec.15987", "pmid": "34002902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.2547d7wqj"}], "notes": [], "created": "2021-10-01T09:01:08.974Z", "modified": "2024-01-16T13:48:39.201Z"}, {"entity": "publication", "iuid": "52e365acd12b4c318e05d09da7818e98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52e365acd12b4c318e05d09da7818e98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52e365acd12b4c318e05d09da7818e98"}}, "title": "Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.", "authors": [{"family": "Bartosovic", "given": "Marek", "initials": "M", "orcid": "0000-0003-2057-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce3c36916eb844e7bc10f73b95f6494a.json"}}, {"family": "Kabbe", "given": "Mukund", "initials": "M"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "39", "issue": "7", "pages": "825-835"}, "abstract": "In contrast to single-cell approaches for measuring gene expression and DNA accessibility, single-cell methods for analyzing histone modifications are limited by low sensitivity and throughput. Here, we combine the CUT&Tag technology, developed to measure bulk histone modifications, with droplet-based single-cell library preparation to produce high-quality single-cell data on chromatin modifications. We apply single-cell CUT&Tag (scCUT&Tag) to tens of thousands of cells of the mouse central nervous system and probe histone modifications characteristic of active promoters, enhancers and gene bodies (H3K4me3, H3K27ac and H3K36me3) and inactive regions (H3K27me3). These scCUT&Tag profiles were sufficient to determine cell identity and deconvolute regulatory principles such as promoter bivalency, spreading of H3K4me3 and promoter-enhancer connectivity. We also used scCUT&Tag to investigate the single-cell chromatin occupancy of transcription factor OLIG2 and the cohesin complex component RAD21. Our results indicate that analysis of histone modifications and transcription factor occupancy at single-cell resolution provides unique insights into epigenomic landscapes in the central nervous system.", "doi": "10.1038/s41587-021-00869-9", "pmid": "33846645", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-021-00869-9"}, {"db": "pmc", "key": "PMC7611252"}, {"db": "mid", "key": "EMS118412"}], "notes": [], "created": "2021-04-13T13:18:06.127Z", "modified": "2024-01-16T13:48:39.210Z"}, {"entity": "publication", "iuid": "bf7e976078d04040bcd472b4d8d7c795", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf7e976078d04040bcd472b4d8d7c795.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf7e976078d04040bcd472b4d8d7c795"}}, "title": "Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.", "authors": [{"family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "researcher": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}}, {"family": "Albert", "given": "S\u00e9r\u00e9na", "initials": "S", "orcid": "0000-0002-7299-7263", "researcher": {"href": "https://publications.scilifelab.se/researcher/32b48bc190fa4bd189e0b9a2f2bad8ef.json"}}, {"family": "Winder", "given": "Monika", "initials": "M", "orcid": "0000-0001-9467-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b09dfb6b68445249b8a93c655433189.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "14", "pages": "3515-3529", "issn-l": "0962-1083"}, "abstract": "Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial \u03b1-diversity was not affected by POM addition, while bacterial \u03b2-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.", "doi": "10.1111/mec.15984", "pmid": "33993575", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:01:06.266Z", "modified": "2024-01-16T13:48:39.232Z"}, {"entity": "publication", "iuid": "ddf03b5f1f1c47209a97f015b429d9c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddf03b5f1f1c47209a97f015b429d9c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddf03b5f1f1c47209a97f015b429d9c4"}}, "title": "On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA", "orcid": "0000-0002-7212-813X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dadd1300e85443d8ee98a2d58d08a4b.json"}}, {"family": "Tedder", "given": "Andrew", "initials": "A", "orcid": "0000-0002-7378-4673", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a29b3c1160f46bf8b21e331268eb4b1.json"}}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C"}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "issn-l": "0018-067X", "volume": "127", "issue": "1", "pages": "124-134"}, "abstract": "Polyploidy, or whole-genome duplication, is a common speciation mechanism in plants. An important barrier to polyploid establishment is a lack of compatible mates. Because self-compatibility alleviates this problem, it has long been hypothesized that there should be an association between polyploidy and self-compatibility (SC), but empirical support for this prediction is mixed. Here, we investigate whether the molecular makeup of the Brassicaceae self-incompatibility (SI) system, and specifically dominance relationships among S-haplotypes mediated by small RNAs, could facilitate loss of SI in allopolyploid crucifers. We focus on the allotetraploid species Capsella bursa-pastoris, which formed ~300 kya by hybridization and whole-genome duplication involving progenitors from the lineages of Capsella orientalis and Capsella grandiflora. We conduct targeted long-read sequencing to assemble and analyze eight full-length S-locus haplotypes, representing both homeologous subgenomes of C. bursa-pastoris. We further analyze small RNA (sRNA) sequencing data from flower buds to identify candidate dominance modifiers. We find that C. orientalis-derived S-haplotypes of C. bursa-pastoris harbor truncated versions of the male SI specificity gene SCR and express a conserved sRNA-based candidate dominance modifier with a target in the C. grandiflora-derived S-haplotype. These results suggest that pollen-level dominance may have facilitated loss of SI in C. bursa-pastoris. Finally, we demonstrate that spontaneous somatic tetraploidization after a wide cross between C. orientalis and C. grandiflora can result in production of self-compatible tetraploid offspring. We discuss the implications of this finding on the mode of formation of this widespread weed.", "doi": "10.1038/s41437-021-00434-9", "pmid": "33875831", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-021-00434-9"}, {"db": "pmc", "key": "PMC8249383"}], "notes": [], "created": "2021-09-02T09:52:09.038Z", "modified": "2024-01-16T13:48:39.247Z"}, {"entity": "publication", "iuid": "a2d409c477d843b68f024873b1ebc0eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2d409c477d843b68f024873b1ebc0eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2d409c477d843b68f024873b1ebc0eb"}}, "title": "Mammuthus sp. (Early and Middle Pleistocene Mammoths).", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Trends Genet.", "issn": "0168-9525", "volume": "37", "issue": "7", "pages": "682-683", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tig.2021.04.006", "pmid": "33985817", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0168-9525(21)00102-5"}], "notes": [], "created": "2021-06-09T12:16:52.282Z", "modified": "2024-01-16T13:48:39.270Z"}, {"entity": "publication", "iuid": "f6f8f0ee5824415a8d8a54f6d2553b53", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6f8f0ee5824415a8d8a54f6d2553b53.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6f8f0ee5824415a8d8a54f6d2553b53"}}, "title": "High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Norkko", "given": "Alf", "initials": "A"}, {"family": "Creer", "given": "Simon", "initials": "S"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "13", "pages": "3023-3039", "issn-l": "0962-1083"}, "abstract": "Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates < 1 mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematode Sabatieria and foraminifera Elphidium in high OC, and Cryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.", "doi": "10.1111/mec.15561", "pmid": "32706485", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-07T16:32:27.480Z", "modified": "2024-01-16T13:48:39.277Z"}, {"entity": "publication", "iuid": "8cbc18de608b493d87efccfa5a1ae454", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cbc18de608b493d87efccfa5a1ae454.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cbc18de608b493d87efccfa5a1ae454"}}, "title": "Genomic signatures of rapid adaptive divergence in a tropical montane species.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "She", "given": "Huishang", "initials": "H"}, {"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Biol. Lett.", "issn": "1744-957X", "volume": "17", "issue": "7", "pages": "20210089", "issn-l": "1744-9561"}, "abstract": "Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird (Amblyornis papuensis). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.", "doi": "10.1098/rsbl.2021.0089", "pmid": "34314643", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8315830"}, {"db": "Dryad", "key": "10.5061/dryad.37pvmcvjr"}], "notes": [], "created": "2021-10-01T09:03:17.400Z", "modified": "2024-01-16T13:48:39.285Z"}, {"entity": "publication", "iuid": "a10ef57139814fb299f0fd7187b6b2d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a10ef57139814fb299f0fd7187b6b2d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a10ef57139814fb299f0fd7187b6b2d3"}}, "title": "FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response.", "authors": [{"family": "Bogatyrova", "given": "Olga", "initials": "O"}, {"family": "Mattsson", "given": "Johanna S M", "initials": "JSM", "orcid": "0000-0002-5294-7808", "researcher": {"href": "https://publications.scilifelab.se/researcher/894626ea67fd459eb08e4a9c4768fb09.json"}}, {"family": "Ross", "given": "Edith M", "initials": "EM"}, {"family": "Sanderson", "given": "Michael P", "initials": "MP"}, {"family": "Backman", "given": "Max", "initials": "M"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H", "orcid": "0000-0001-7402-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/618b52d539ee4e36ba7f9ce3b23f9d7f.json"}}, {"family": "Kurppa", "given": "Pinja", "initials": "P", "orcid": "0000-0003-3790-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f5b2c06aade428490f10e5eaf015d51.json"}}, {"family": "La Fleur", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Wilm", "given": "Claudia", "initials": "C"}, {"family": "Zimmermann", "given": "Astrid", "initials": "A"}, {"family": "Esdar", "given": "Christina", "initials": "C"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Eur. J. Cancer", "issn": "1879-0852", "volume": "151", "issue": null, "pages": "136-149", "issn-l": "0959-8049"}, "abstract": "Amplification of fibroblast growth factor receptor 1 (FGFR1) in non-small cell lung cancer (NSCLC) has been considered as an actionable drug target. However, pan-FGFR tyrosine kinase inhibitors did not demonstrate convincing clinical efficacy in FGFR1-amplified NSCLC patients. This study aimed to characterise the molecular context of FGFR1 expression and to define biomarkers predictive of FGFR1 inhibitor response. In this study, 635 NSCLC samples were characterised for FGFR1 protein expression by immunohistochemistry and copy number gain (CNG) by in situ hybridisation (n = 298) or DNA microarray (n = 189). FGFR1 gene expression (n = 369) and immune cell profiles (n = 309) were also examined. Furthermore, gene expression, methylation and microRNA data from The Cancer Genome Atlas (TCGA) were compared. A panel of FGFR1-amplified NSCLC patient-derived xenograft (PDX) models were tested for response to the selective FGFR1 antagonist M6123. A minority of patients demonstrated FGFR1 CNG (10.5%) or increased FGFR1 mRNA (8.7%) and protein expression (4.4%). FGFR1 CNG correlated weakly with FGFR1 gene and protein expression. Tumours overexpressing FGFR1 protein were typically devoid of driver alterations (e.g. EGFR, KRAS) and showed reduced infiltration of T-lymphocytes and lower PD-L1 expression. Promoter methylation and microRNA were identified as regulators of FGFR1 expression in NSCLC and other cancers. Finally, NSCLC PDX models demonstrating FGFR1 amplification and FGFR1 protein overexpression were sensitive to M6123. The unique molecular and immune features of tumours with high FGFR1 expression provide a rationale to stratify patients in future clinical trials of FGFR1 pathway-targeting agents.", "doi": "10.1016/j.ejca.2021.04.005", "pmid": "33984662", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "S0959-8049(21)00226-4"}], "notes": [], "created": "2021-06-09T12:16:54.718Z", "modified": "2021-11-10T12:23:43.669Z"}, {"entity": "publication", "iuid": "83d87735b99145889c0e1ebe02901133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83d87735b99145889c0e1ebe02901133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83d87735b99145889c0e1ebe02901133"}}, "title": "Bifidobacteria-mediated immune system imprinting early in life", "authors": [{"family": "Henrick", "given": "Bethany M", "initials": "BM"}, {"family": "Rodriguez", "given": "Lucie", "initials": "L"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Henckel", "given": "Ewa", "initials": "E"}, {"family": "Arzoomand", "given": "Aron", "initials": "A"}, {"family": "Olin", "given": "Axel", "initials": "A"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Tan", "given": "Ziyang", "initials": "Z"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Ehrlich", "given": "Amy M", "initials": "AM"}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Mugabo", "given": "Constantin Habimana", "initials": "CH"}, {"family": "Ambrosiani", "given": "Ylva", "initials": "Y"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Chew", "given": "Stephanie", "initials": "S"}, {"family": "Brown", "given": "Heather K", "initials": "HK"}, {"family": "Prambs", "given": "Johann", "initials": "J"}, {"family": "Bohlin", "given": "Kajsa", "initials": "K"}, {"family": "Mitchell", "given": "Ryan D", "initials": "RD"}, {"family": "Underwood", "given": "Mark A", "initials": "MA"}, {"family": "Smilowitz", "given": "Jennifer T", "initials": "JT"}, {"family": "German", "given": "J Bruce", "initials": "JB"}, {"family": "Frese", "given": "Steven A", "initials": "SA"}, {"family": "Brodin", "given": "Petter", "initials": "P"}], "type": "journal-article", "published": "2021-07-00", "journal": {"title": "Cell", "issn": "0092-8674", "issn-l": null, "volume": "184", "issue": "15", "pages": "3884-3898.e11"}, "abstract": "Immune-microbe interactions early in life influence the risk of allergies, asthma, and other inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by providing nutrients to specialized microbes that in turn benefit the host's immune system. Such bacteria have co-evolved with humans but are now increasingly rare in modern societies. Here we show that a lack of bifidobacteria, and in particular depletion of genes required for human milk oligosaccharide (HMO) utilization from the metagenome, is associated with systemic inflammation and immune dysregulation early in life. In breastfed infants given Bifidobacterium infantis EVC001, which expresses all HMO-utilization genes, intestinal T helper 2 (Th2) and Th17 cytokines were silenced and interferon \u03b2 (IFN\u03b2) was induced. Fecal water from EVC001-supplemented infants contains abundant indolelactate and B. infantis-derived indole-3-lactic acid (ILA) upregulated immunoregulatory galectin-1 in Th2 and Th17 cells during polarization, providing a functional link between beneficial microbes and immunoregulation during the first months of life.", "doi": "10.1016/j.cell.2021.05.030", "pmid": "34143954", "labels": {"Cellular Immunomonitoring": "Technology development", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(21)00660-7"}], "notes": [], "created": "2021-11-24T09:22:22.336Z", "modified": "2024-01-16T13:48:39.293Z"}, {"entity": "publication", "iuid": "54c9837ba01344a59254e070a33987d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54c9837ba01344a59254e070a33987d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54c9837ba01344a59254e070a33987d1"}}, "title": "Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.", "authors": [{"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Seidel", "given": "Laura", "initials": "L"}, {"family": "van Wyk", "given": "Nathan", "initials": "N"}, {"family": "Zhang", "given": "Ruichi", "initials": "R"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Embile", "given": "Rodrigo F", "initials": "RF"}, {"family": "Walder", "given": "Ingar", "initials": "I"}, {"family": "Leivisk\u00e4", "given": "Tiina", "initials": "T"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2021-06-30", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "pages": "693615", "issn-l": "1664-302X"}, "abstract": "Vanadium - a transition metal - is found in the ferrous-ferric mineral, magnetite. Vanadium has many industrial applications, such as in the production of high-strength low-alloy steels, and its increasing global industrial consumption requires new primary sources. Bioleaching is a biotechnological process for microbially catalyzed dissolution of minerals and wastes for metal recovery such as biogenic organic acid dissolution of bauxite residues. In this study, 16S rRNA gene amplicon sequencing was used to identify microorganisms in Nordic mining environments influenced by vanadium containing sources. These data identified gene sequences that aligned to the Gluconobacter genus that produce gluconic acid. Several strategies for magnetite dissolution were tested including oxidative and reductive bioleaching by acidophilic microbes along with dissimilatory reduction by Shewanella spp. that did not yield significant metal release. In addition, abiotic dissolution of the magnetite was tested with gluconic and oxalic acids, and yielded 3.99 and 81.31% iron release as a proxy for vanadium release, respectively. As a proof of principle, leaching via gluconic acid production by Gluconobacter oxydans resulted in a maximum yield of 9.8% of the available iron and 3.3% of the vanadium. Addition of an increased concentration of glucose as electron donor for gluconic acid production alone, or in combination with calcium carbonate to buffer the pH, increased the rate of iron dissolution and final vanadium recoveries. These data suggest a strategy of biogenic organic acid mediated vanadium recovery from magnetite and point the way to testing additional microbial species to optimize the recovery.", "doi": "10.3389/fmicb.2021.693615", "pmid": "34276626", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8278310"}], "notes": [], "created": "2021-10-01T09:02:34.422Z", "modified": "2024-01-16T13:48:39.394Z"}, {"entity": "publication", "iuid": "236e229a33f94e5cbbd5fca21439b072", "links": {"self": {"href": "https://publications.scilifelab.se/publication/236e229a33f94e5cbbd5fca21439b072.json"}, "display": {"href": "https://publications.scilifelab.se/publication/236e229a33f94e5cbbd5fca21439b072"}}, "title": "DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.", "authors": [{"family": "Novotny", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8910-6183", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c63db5be95c40e49940affadc958928.json"}}, {"family": "Zamora-Terol", "given": "Sara", "initials": "S", "orcid": "0000-0002-7822-3197", "researcher": {"href": "https://publications.scilifelab.se/researcher/25e1b401fc9a49c5b6f89eaa18f89a57.json"}}, {"family": "Winder", "given": "Monika", "initials": "M"}], "type": "journal article", "published": "2021-06-30", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "288", "issue": "1953", "pages": "20210908", "issn-l": "0962-8452"}, "abstract": "Alternative pathways of energy transfer guarantee the functionality and productivity in marine food webs that experience strong seasonality. Nevertheless, the complexity of zooplankton interactions is rarely considered in trophic studies because of the lack of detailed information about feeding interactions in nature. In this study, we used DNA metabarcoding to highlight the diversity of trophic niches in a wide range of micro- and mesozooplankton, including ciliates, rotifers, cladocerans, copepods and their prey, by sequencing 16- and 18S rRNA genes. Our study demonstrates that the zooplankton trophic niche partitioning goes beyond both phylogeny and size and reinforces the importance of diversity in resource use for stabilizing food web efficiency by allowing for several different pathways of energy transfer. We further highlight that small, rarely studied zooplankton (rotifers and ciliates) fill an important role in the Baltic Sea pelagic primary production pathways and the potential of ciliates, rotifers and crustaceans in the utilization of filamentous and picocyanobacteria within the pelagic food web. The approach used in this study is a suitable entry point to ecosystem-wide food web modelling considering species-specific resource use of key consumers.", "doi": "10.1098/rspb.2021.0908", "pmid": "34130506", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8206686"}, {"db": "Dryad", "key": "10.5061/dryad.gb5mkkwpw"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.5448706"}], "notes": [], "created": "2021-10-01T09:02:29.362Z", "modified": "2024-01-16T13:48:39.416Z"}, {"entity": "publication", "iuid": "e18b31942e41465999c590cac3365408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e18b31942e41465999c590cac3365408"}}, "title": "COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.", "authors": [{"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/839bf10741044782aecdc77b3f06fc88.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3fdde99294d422694c7a8a00c9811ed.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcd83e58cd74addbbcbf0ed6e1d6db7.json"}}, {"family": "Milia", "given": "Maria Grazia", "initials": "MG"}, {"family": "Brossa", "given": "Silvia", "initials": "S"}, {"family": "Huong Nguyen", "given": "Thi Thu", "initials": "TT", "orcid": "0000-0002-9089-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/57451410c8ac4547a4b09111a020e396.json"}}, {"family": "Cerutti", "given": "Francesco", "initials": "F", "orcid": "0000-0003-0480-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a243dc846624a8a8292dde5416fa402.json"}}, {"family": "Berrino", "given": "Enrico", "initials": "E"}, {"family": "Sapino", "given": "Anna", "initials": "A"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "Sottile", "given": "Antonino", "initials": "A"}, {"family": "Ghisetti", "given": "Valeria", "initials": "V", "orcid": "0000-0002-4698-598X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75237266d0b1496f909cb0c53ff87920.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb66f0013e954d99a2be4df7309b7ae3.json"}}], "type": "journal article", "published": "2021-06-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3903", "issn-l": "2041-1723"}, "abstract": "While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.", "doi": "10.1038/s41467-021-24078-9", "pmid": "34162869", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-24078-9"}, {"db": "pmc", "key": "PMC8222401"}], "notes": [], "created": "2021-10-01T09:02:30.491Z", "modified": "2024-01-16T13:48:39.472Z"}, {"entity": "publication", "iuid": "3377e2c5a59a446fbd1b6fce70a197e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3377e2c5a59a446fbd1b6fce70a197e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3377e2c5a59a446fbd1b6fce70a197e4"}}, "title": "Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.", "authors": [{"family": "Chen", "given": "Zhi-Qiang", "initials": "ZQ"}, {"family": "Zan", "given": "Yanjun", "initials": "Y"}, {"family": "Milesi", "given": "Pascal", "initials": "P"}, {"family": "Zhou", "given": "Linghua", "initials": "L"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Li", "given": "Lili", "initials": "L"}, {"family": "Cui", "given": "BinBin", "initials": "B"}, {"family": "Niu", "given": "Shihui", "initials": "S"}, {"family": "Westin", "given": "Johan", "initials": "J"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Garc\u00eda-Gil", "given": "Maria Rosario", "initials": "MR"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}, {"family": "Wu", "given": "Harry X", "initials": "HX", "orcid": "0000-0002-7072-4704", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d1a037ab43842b081d239c90bb30636.json"}}], "type": "journal article", "published": "2021-06-13", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "22", "issue": "1", "pages": "179", "issn-l": "1474-7596"}, "abstract": "Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.\n\nWe identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.\n\nSeveral important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.", "doi": "10.1186/s13059-021-02392-1", "pmid": "34120648", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-021-02392-1"}, {"db": "pmc", "key": "PMC8201819"}], "notes": [], "created": "2021-10-01T09:02:31.873Z", "modified": "2024-01-16T13:48:39.509Z"}, {"entity": "publication", "iuid": "edd45af5bed64d469fc62f7ac60e5176", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edd45af5bed64d469fc62f7ac60e5176.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edd45af5bed64d469fc62f7ac60e5176"}}, "title": "Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.", "authors": [{"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "Mapelli", "given": "Igor", "initials": "I"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Do\u011fu", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Erdal", "given": "\u00d6m\u00fcr Dilek", "initials": "\u00d6D"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB"}, {"family": "Bayliss", "given": "Alex", "initials": "A"}, {"family": "Mazzucato", "given": "Camilla", "initials": "C"}, {"family": "Fer", "given": "Evrim", "initials": "E"}, {"family": "\u00c7oko\u011flu", "given": "Sevim Seda", "initials": "SS"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Karamurat", "given": "Cansu", "initials": "C"}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC"}, {"family": "Sevkar", "given": "Arda", "initials": "A"}, {"family": "Da\u011fta\u015f", "given": "Nihan Dil\u015fad", "initials": "ND"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM"}, {"family": "Adams", "given": "Donovan", "initials": "D"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E"}, {"family": "Milella", "given": "Marco", "initials": "M"}, {"family": "Schotsmans", "given": "Eline M J", "initials": "EMJ"}, {"family": "Yurtman", "given": "Erin\u00e7", "initials": "E"}, {"family": "\u00c7etin", "given": "Mehmet", "initials": "M"}, {"family": "Yorulmaz", "given": "Sevgi", "initials": "S"}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE"}, {"family": "Ghalichi", "given": "Ayshin", "initials": "A"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Bilgin", "given": "C Can", "initials": "CC"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "de Kleijn", "given": "Maurice", "initials": "M"}, {"family": "Mustafao\u011flu", "given": "G\u00f6khan", "initials": "G"}, {"family": "Fairbairn", "given": "Andrew", "initials": "A"}, {"family": "Pearson", "given": "Jessica", "initials": "J"}, {"family": "Togan", "given": "\u0130nci", "initials": "\u0130"}, {"family": "Kayacan", "given": "Nurcan", "initials": "N"}, {"family": "Marciniak", "given": "Arkadiusz", "initials": "A"}, {"family": "Larsen", "given": "Clark Spencer", "initials": "CS"}, {"family": "Hodder", "given": "Ian", "initials": "I"}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7"}, {"family": "Pilloud", "given": "Marin", "initials": "M"}, {"family": "S\u00fcrer", "given": "Elif", "initials": "E"}, {"family": "Gerritsen", "given": "Fokke", "initials": "F"}, {"family": "\u00d6zbal", "given": "Rana", "initials": "R"}, {"family": "Baird", "given": "Douglas", "initials": "D"}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS"}, {"family": "Duru", "given": "G\u00fcne\u015f", "initials": "G"}, {"family": "\u00d6zba\u015faran", "given": "Mihriban", "initials": "M"}, {"family": "Haddow", "given": "Scott D", "initials": "SD"}, {"family": "Kn\u00fcsel", "given": "Christopher J", "initials": "CJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}], "type": "journal article", "published": "2021-06-07", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "11", "pages": "2455-2468.e18", "issn-l": "0960-9822"}, "abstract": "The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from A\u015f\u0131kl\u0131 H\u00f6y\u00fck and \u00c7atalh\u00f6y\u00fck. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, A\u015f\u0131kl\u0131 H\u00f6y\u00fck and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of \u00c7atalh\u00f6y\u00fck and Barc\u0131n, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in \u00c7atalh\u00f6y\u00fck,3-5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.", "doi": "10.1016/j.cub.2021.03.050", "pmid": "33857427", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00423-1"}, {"db": "pmc", "key": "PMC8210650"}], "notes": [], "created": "2021-06-09T12:15:46.749Z", "modified": "2024-01-16T13:48:39.527Z"}, {"entity": "publication", "iuid": "ad3b96b9f1e04610964e663761b2ac63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad3b96b9f1e04610964e663761b2ac63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad3b96b9f1e04610964e663761b2ac63"}}, "title": "Reinforcing one-carbon metabolism via folic acid/Folr1 promotes \u03b2-cell differentiation.", "authors": [{"family": "Karampelias", "given": "Christos", "initials": "C", "orcid": "0000-0002-9990-5760", "researcher": {"href": "https://publications.scilifelab.se/researcher/509894ee3f0e41eeaf57eb2febc18c70.json"}}, {"family": "Rezanejad", "given": "Habib", "initials": "H", "orcid": "0000-0003-3067-6602", "researcher": {"href": "https://publications.scilifelab.se/researcher/8759a9d7c6654216b6336f9fb3d0fb92.json"}}, {"family": "Rosko", "given": "Mandy", "initials": "M"}, {"family": "Duan", "given": "Likun", "initials": "L", "orcid": "0000-0003-3293-6682", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ab937d463cc4fc29a5d31eb9e75ac54.json"}}, {"family": "Lu", "given": "Jing", "initials": "J"}, {"family": "Pazzagli", "given": "Laura", "initials": "L", "orcid": "0000-0002-1908-6073", "researcher": {"href": "https://publications.scilifelab.se/researcher/06de06fae02a4de28dbda5456129fc18.json"}}, {"family": "Bertolino", "given": "Philippe", "initials": "P", "orcid": "0000-0001-8064-8269", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fddf1c144e04b80893cdf2c00a7e85b.json"}}, {"family": "Cesta", "given": "Carolyn E", "initials": "CE", "orcid": "0000-0001-5759-9366", "researcher": {"href": "https://publications.scilifelab.se/researcher/804a85a43f0e42e9ba01f7b77a0e02fb.json"}}, {"family": "Liu", "given": "Xiaojing", "initials": "X", "orcid": "0000-0002-4231-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/550389a9d42447f6a93b0eb67c9ab119.json"}}, {"family": "Korbutt", "given": "Gregory S", "initials": "GS"}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f796ff515c95491e9cd47018e02220c0.json"}}], "type": "journal article", "published": "2021-06-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3362", "issn-l": "2041-1723"}, "abstract": "Diabetes can be caused by an insufficiency in \u03b2-cell mass. Here, we performed a genetic screen in a zebrafish model of \u03b2-cell loss to identify pathways promoting \u03b2-cell regeneration. We found that both folate receptor 1 (folr1) overexpression and treatment with folinic acid, stimulated \u03b2-cell differentiation in zebrafish. Treatment with folinic acid also stimulated \u03b2-cell differentiation in cultures of neonatal pig islets, showing that the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets, the increased \u03b2-cell differentiation originated from ductal cells. Mechanistically, comparative metabolomic analysis of zebrafish with/without \u03b2-cell ablation and with/without folinic acid treatment indicated \u03b2-cell regeneration could be attributed to changes in the pyrimidine, carnitine, and serine pathways. Overall, our results suggest evolutionarily conserved and previously unknown roles for folic acid and one-carbon metabolism in the generation of \u03b2-cells.", "doi": "10.1038/s41467-021-23673-0", "pmid": "34099692", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23673-0"}, {"db": "pmc", "key": "PMC8184927"}], "notes": [], "created": "2021-10-01T09:01:03.656Z", "modified": "2024-01-16T13:48:39.535Z"}, {"entity": "publication", "iuid": "b86cf71475ae4738bc321ea00e52164a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b86cf71475ae4738bc321ea00e52164a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b86cf71475ae4738bc321ea00e52164a"}}, "title": "Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing.", "authors": [{"family": "Walcher", "given": "Lia", "initials": "L"}, {"family": "Kistenmacher", "given": "Ann-Kathrin", "initials": "AK"}, {"family": "Sommer", "given": "Charline", "initials": "C"}, {"family": "B\u00f6hlen", "given": "Sebastian", "initials": "S"}, {"family": "Ziemann", "given": "Christina", "initials": "C"}, {"family": "Dehmel", "given": "Susann", "initials": "S"}, {"family": "Braun", "given": "Armin", "initials": "A"}, {"family": "Tretbar", "given": "Uta Sandy", "initials": "US"}, {"family": "Kl\u00f6\u00df", "given": "Stephan", "initials": "S"}, {"family": "Schambach", "given": "Axel", "initials": "A"}, {"family": "Morgan", "given": "Michael", "initials": "M"}, {"family": "L\u00f6ffler", "given": "Dennis", "initials": "D"}, {"family": "K\u00e4mpf", "given": "Christoph", "initials": "C"}, {"family": "Blumert", "given": "Conny", "initials": "C"}, {"family": "Reiche", "given": "Kristin", "initials": "K"}, {"family": "Beckmann", "given": "Jana", "initials": "J"}, {"family": "K\u00f6nig", "given": "Ulla", "initials": "U"}, {"family": "Standfest", "given": "Bastian", "initials": "B"}, {"family": "Thoma", "given": "Martin", "initials": "M"}, {"family": "Makert", "given": "Gustavo R", "initials": "GR"}, {"family": "Ulbert", "given": "Sebastian", "initials": "S"}, {"family": "Kossatz-B\u00f6hlert", "given": "Uta", "initials": "U"}, {"family": "K\u00f6hl", "given": "Ulrike", "initials": "U"}, {"family": "D\u00fcnkel", "given": "Anna", "initials": "A"}, {"family": "Fricke", "given": "Stephan", "initials": "S"}], "type": "journal article", "published": "2021-06-04", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "12", "pages": "684052", "issn-l": "1664-3224"}, "abstract": "With increasing clinical use of NK-92 cells and their CAR-modified derivatives in cancer immunotherapy, there is a growing demand for efficient production processes of these \"off-the-shelf\" therapeutics. In order to ensure safety and prevent the occurrence of secondary tumors, (CAR-)NK-92 cell proliferation has to be inactivated before transfusion. This is commonly achieved by gamma irradiation. Recently, we showed proof of concept that low energy electron irradiation (LEEI) is a new method for NK-92 inactivation. LEEI has several advantages over gamma irradiation, including a faster reaction time, a more reproducible dose rate and much less requirements on radiation shielding. Here, LEEI was further evaluated as a promising alternative to gamma irradiation yielding cells with highly maintained cytotoxic effector function.\n\nEffectiveness and efficiency of LEEI and gamma irradiation were analyzed using NK-92 and CD123-directed CAR-NK-92 cells. LEE-irradiated cells were extensively characterized and compared to gamma-irradiated cells via flow cytometry, cytotoxicity assays, and comet assays, amongst others.\n\nOur results show that both irradiation methods caused a progressive decrease in cell viability and are, therefore, suitable for inhibition of cell proliferation. Notably, the NK-mediated specific lysis of tumor cells was maintained at stable levels for three days post-irradiation, with a trend towards higher activities after LEEI treatment as compared to gamma irradiation. Both gamma irradiation as well as LEEI led to substantial DNA damage and an accumulation of irradiated cells in the G2/M cell cycle phases. In addition, transcriptomic analysis of irradiated cells revealed approximately 12-fold more differentially expressed genes two hours after gamma irradiation, compared to LEEI. Analysis of surface molecules revealed an irradiation-induced decrease in surface expression of CD56, but no changes in the levels of the activating receptors NKp46, NKG2D, or NKp30.\n\nThe presented data show that LEEI inactivates (CAR-)NK-92 cells as efficiently as gamma irradiation, but with less impact on the overall gene expression. Due to logistic advantages, LEEI might provide a superior alternative for the manufacture of (CAR-)NK-92 cells for clinical application.", "doi": "10.3389/fimmu.2021.684052", "pmid": "34149724", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8212864"}], "notes": [], "created": "2021-10-01T09:02:28.231Z", "modified": "2021-12-06T13:46:55.990Z"}, {"entity": "publication", "iuid": "fef0390426a644b68ba591fd96bd94e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fef0390426a644b68ba591fd96bd94e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fef0390426a644b68ba591fd96bd94e0"}}, "title": "Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.", "authors": [{"family": "Friess", "given": "Lara", "initials": "L"}, {"family": "Cheray", "given": "Mathilde", "initials": "M"}, {"family": "Keane", "given": "Lily", "initials": "L"}, {"family": "Grabert", "given": "Kathleen", "initials": "K"}, {"family": "Joseph", "given": "Bertrand", "initials": "B", "orcid": "0000-0001-5655-9979", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cbb8902d726446fa0a3b25b649f82aa.json"}}], "type": "journal article", "published": "2021-06-03", "journal": {"title": "Mol Brain", "issn": "1756-6606", "volume": "14", "issue": "1", "pages": "87", "issn-l": null}, "abstract": "Microglia, resident immunocompetent cells of the central nervous system, can display a range of reaction states and thereby exhibit distinct biological functions across development, adulthood and under disease conditions. Distinct gene expression profiles are reported to define each of these microglial reaction states. Hence, the identification of modulators of selective microglial transcriptomic signature, which have the potential to regulate unique microglial function has gained interest. Here, we report the identification of ATG7 (Autophagy-related 7) as a selective modulator of an NF-\u03baB-dependent transcriptional program controlling the pro-inflammatory response of microglia. We also uncover that microglial Atg7-deficiency was associated with reduced microglia-mediated neurotoxicity, and thus a loss of biological function associated with the pro-inflammatory microglial reactive state. Further, we show that Atg7-deficiency in microglia did not impact on their ability to respond to alternative stimulus, such as one driving them towards an anti-inflammatory/tumor supportive phenotype. The identification of distinct regulators, such as Atg7, controlling specific microglial transcriptional programs could lead to developing novel therapeutic strategies aiming to manipulate selected microglial phenotypes, instead of the whole microglial population with is associated with several pitfalls.", "doi": "10.1186/s13041-021-00794-7", "pmid": "34082793", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13041-021-00794-7"}, {"db": "pmc", "key": "PMC8173846"}], "notes": [], "created": "2021-10-01T09:01:11.502Z", "modified": "2024-01-16T13:48:39.543Z"}, {"entity": "publication", "iuid": "4d45ed3127e14888bfb30d089ff84763", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d45ed3127e14888bfb30d089ff84763.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d45ed3127e14888bfb30d089ff84763"}}, "title": "RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.", "authors": [{"family": "Avican", "given": "Kemal", "initials": "K", "orcid": "0000-0003-0707-2050", "researcher": {"href": "https://publications.scilifelab.se/researcher/84631a1299084ea695653c961e906ff3.json"}}, {"family": "Aldahdooh", "given": "Jehad", "initials": "J"}, {"family": "Togninalli", "given": "Matteo", "initials": "M"}, {"family": "Mahmud", "given": "A K M Firoj", "initials": "AKMF", "orcid": "0000-0002-6541-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6eb0bf023f343359be1914cb9100c0e.json"}}, {"family": "Tang", "given": "Jing", "initials": "J", "orcid": "0000-0001-7480-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1219a45cf6a428c87b6d99369e5f726.json"}}, {"family": "Borgwardt", "given": "Karsten M", "initials": "KM"}, {"family": "Rhen", "given": "Mikael", "initials": "M"}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}], "type": "comparative study", "published": "2021-06-02", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "3282", "issn-l": "2041-1723"}, "abstract": "Bacterial processes necessary for adaption to stressful host environments are potential targets for new antimicrobials. Here, we report large-scale transcriptomic analyses of 32 human bacterial pathogens grown under 11 stress conditions mimicking human host environments. The potential relevance of the in vitro stress conditions and responses is supported by comparisons with available in vivo transcriptomes of clinically important pathogens. Calculation of a probability score enables comparative cross-microbial analyses of the stress responses, revealing common and unique regulatory responses to different stresses, as well as overlapping processes participating in different stress responses. We identify conserved and species-specific 'universal stress responders', that is, genes showing altered expression in multiple stress conditions. Non-coding RNAs are involved in a substantial proportion of the responses. The data are collected in a freely available, interactive online resource (PATHOgenex).", "doi": "10.1038/s41467-021-23588-w", "pmid": "34078900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23588-w"}, {"db": "pmc", "key": "PMC8172932"}], "notes": [], "created": "2021-10-01T09:00:20.445Z", "modified": "2021-12-06T13:46:14.370Z"}, {"entity": "publication", "iuid": "2561d68da0bd4709abff07531e1c6b60", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2561d68da0bd4709abff07531e1c6b60.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2561d68da0bd4709abff07531e1c6b60"}}, "title": "Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).", "authors": [{"family": "Eriksson", "given": "J S", "initials": "JS", "orcid": "0000-0002-1303-730X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0df5892d479444caadecbc155894ad2.json"}}, {"family": "Bacon", "given": "C D", "initials": "CD"}, {"family": "Bennett", "given": "D J", "initials": "DJ"}, {"family": "Pfeil", "given": "B E", "initials": "BE"}, {"family": "Oxelman", "given": "B", "initials": "B"}, {"family": "Antonelli", "given": "A", "initials": "A"}], "type": "journal article", "published": "2021-06-02", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "21", "issue": "1", "pages": "107", "issn-l": null}, "abstract": "The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events.\n\nUsing target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in > 54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus.\n\nHere, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.", "doi": "10.1186/s12862-021-01751-7", "pmid": "34078291", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-021-01751-7"}, {"db": "pmc", "key": "PMC8170824"}, {"db": "Dryad", "key": "10.5061/dryad.hqbzkh1fc"}], "notes": [], "created": "2021-10-01T09:00:24.434Z", "modified": "2021-12-06T13:46:16.831Z"}, {"entity": "publication", "iuid": "9efe05ebc70c4c4693210baba690ef94", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9efe05ebc70c4c4693210baba690ef94.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9efe05ebc70c4c4693210baba690ef94"}}, "title": "Genomic and fitness consequences of inbreeding in an endangered carnivore.", "authors": [{"family": "Hasselgren", "given": "Malin", "initials": "M", "orcid": "0000-0002-4875-4413", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e7f1368a98040f4a683c3d082483079.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K", "orcid": "0000-0002-9707-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/40450a7e8cda45ba8292b9a677b3fb29.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "12", "pages": "2790-2799", "issn-l": "0962-1083"}, "abstract": "Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.", "doi": "10.1111/mec.15943", "pmid": "33955096", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.gmsbcc2mn"}], "notes": [], "created": "2021-06-09T12:16:53.553Z", "modified": "2024-01-16T13:48:39.611Z"}, {"entity": "publication", "iuid": "ef91de67722040beadef03c2bedd39f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef91de67722040beadef03c2bedd39f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef91de67722040beadef03c2bedd39f1"}}, "title": "Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.", "authors": [{"family": "Alm Rosenblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4077-7821", "researcher": {"href": "https://publications.scilifelab.se/researcher/1db3e7106016494bb4365e099a8493ef.json"}}, {"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "\u00d3lason", "given": "P\u00e1ll", "initials": "P"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Blomberg", "given": "Anders", "initials": "A", "orcid": "0000-0002-1260-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/5eec83537e954ff49431042e168a5f20.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Mar Biotechnol (NY)", "issn": "1436-2236", "volume": "23", "issue": "3", "pages": "402-416", "issn-l": null}, "abstract": "Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (\u03c0) in coding regions (average \u03c0 \u2248 5% and average \u03c0 in fourfold degenerate sites \u2248 20%), and an overall high repeat content (at least 40%). We also report on high variation in the \u03b1-octopamine receptor OctA (average \u03c0 = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.", "doi": "10.1007/s10126-021-10033-8", "pmid": "33931810", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s10126-021-10033-8"}, {"db": "pmc", "key": "PMC8270832"}], "notes": [], "created": "2021-05-06T15:00:04.738Z", "modified": "2024-01-16T13:48:39.618Z"}, {"entity": "publication", "iuid": "b745a82ad93842d789d695d24818b5b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b745a82ad93842d789d695d24818b5b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b745a82ad93842d789d695d24818b5b0"}}, "title": "Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.", "authors": [{"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Modolo", "given": "Laurent", "initials": "L", "orcid": "0000-0002-7606-4110", "researcher": {"href": "https://publications.scilifelab.se/researcher/5570d99d8a5c4622a43609209072c9bc.json"}}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Zamboni", "given": "Margherita", "initials": "M"}, {"family": "Larsson", "given": "Anton J M", "initials": "AJM", "orcid": "0000-0001-5876-7763", "researcher": {"href": "https://publications.scilifelab.se/researcher/556d55c077674448ad3b7043a6ed5d6c.json"}}, {"family": "Stenudd", "given": "Moa", "initials": "M"}, {"family": "Eriksson", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0003-3050-2039", "researcher": {"href": "https://publications.scilifelab.se/researcher/95bee9e2ef704a418e73aa73f71968c4.json"}}, {"family": "Durif", "given": "Ghislain", "initials": "G"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Picelli", "given": "Simone", "initials": "S"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sandberg", "given": "Rickard", "initials": "R"}, {"family": "R\u00e9u", "given": "Pedro", "initials": "P"}, {"family": "Talavera-Lopez", "given": "Carlos", "initials": "C", "orcid": "0000-0001-8590-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/3194c2d9e8a84e18a62744bd3c1912d0.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Blom", "given": "Kim", "initials": "K"}, {"family": "Sandberg", "given": "Johan K", "initials": "JK", "orcid": "0000-0002-6275-0750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7468c415a46645a3a4c3d28badcff954.json"}}, {"family": "Picard", "given": "Franck", "initials": "F"}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J", "orcid": "0000-0001-6948-7281", "researcher": {"href": "https://publications.scilifelab.se/researcher/75b05fc1689e4d6c9ec0ecd513905a36.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2021-05-25", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "35", "issue": "8", "pages": "109174", "issn-l": null}, "abstract": "The CD8+ T cell response to an antigen is composed of many T cell clones with unique T cell receptors, together forming a heterogeneous repertoire of effector and memory cells. How individual T cell clones contribute to this heterogeneity throughout immune responses remains largely unknown. In this study, we longitudinally track human CD8+ T cell clones expanding in response to yellow fever virus (YFV) vaccination at the single-cell level. We observed a drop in clonal diversity in blood from the acute to memory phase, suggesting that clonal selection shapes the circulating memory repertoire. Clones in the memory phase display biased differentiation trajectories along a gradient from stem cell to terminally differentiated effector memory fates. In secondary responses, YFV- and influenza-specific CD8+ T cell clones are poised to recapitulate skewed differentiation trajectories. Collectively, we show that the sum of distinct clonal phenotypes results in the multifaceted human T cell response to acute viral infections.", "doi": "10.1016/j.celrep.2021.109174", "pmid": "34038736", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(21)00519-2"}], "notes": [], "created": "2021-10-01T09:00:19.310Z", "modified": "2024-01-16T13:48:39.656Z"}, {"entity": "publication", "iuid": "d4fea5c68ca349b3b177908157d63c66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4fea5c68ca349b3b177908157d63c66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4fea5c68ca349b3b177908157d63c66"}}, "title": "Phage Biocontrol of Pseudomonas aeruginosa in Water.", "authors": [{"family": "Kauppinen", "given": "Ari", "initials": "A", "orcid": "0000-0001-7354-5595", "researcher": {"href": "https://publications.scilifelab.se/researcher/a964ecc2db484ad6939da041c8abdad9.json"}}, {"family": "Siponen", "given": "Sallamaari", "initials": "S", "orcid": "0000-0002-9206-7979", "researcher": {"href": "https://publications.scilifelab.se/researcher/59731d8093794f81ad530ffbd87c2a7a.json"}}, {"family": "Pitk\u00e4nen", "given": "Tarja", "initials": "T", "orcid": "0000-0002-7591-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7145dda3b464397bd84dfd21f1523f8.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}, {"family": "Pursiainen", "given": "Anna", "initials": "A"}, {"family": "Torvinen", "given": "Eila", "initials": "E"}, {"family": "Miettinen", "given": "Ilkka T", "initials": "IT", "orcid": "0000-0002-6729-5507", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff6de31f6b6343d68bbc7e37b43d139f.json"}}], "type": "journal article", "published": "2021-05-17", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "13", "issue": "5", "pages": "928", "issn-l": "1999-4915"}, "abstract": "Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two P. aeruginosa bacteriophages (vB_PaeM_V523 and vB_PaeM_V524) were isolated from wastewater and characterized physically and functionally. Genomic and morphological characterization showed that both were myoviruses within the Pbunavirus genus. Both had a similar latent period (50-55 min) and burst size (124-134 PFU/infected cell), whereas there was variation in the host range. In addition to these environmental phages, a commercial Pseudomonas phage, JG003 (DSM 19870), was also used in the biocontrol experiments. The biocontrol potential of the three phages in water was tested separately and together as a cocktail against two P. aeruginosa strains; PAO1 and the environmental strain 17V1507. With PAO1, all phages initially reduced the numbers of the bacterial host, with phage V523 being the most efficient (>2.4 log10 reduction). For the environmental P. aeruginosa strain (17V1507), only the phage JG003 caused a reduction (1.2 log10) compared to the control. The cocktail of three phages showed a slightly higher decrease in the level of the hosts compared to the use of individual phages. Although no synergistic effect was observed in the host reduction with the use of the phage cocktail, the cocktail-treated hosts did not appear to acquire resistance as rapidly as hosts treated with a single phage. The results of this study provide a significant step in the development of bacteriophage preparations for the control of pathogens and harmful microbes in water environments.", "doi": "10.3390/v13050928", "pmid": "34067885", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "v13050928"}, {"db": "pmc", "key": "PMC8156286"}], "notes": [], "created": "2021-10-01T09:01:07.571Z", "modified": "2024-01-16T13:48:39.742Z"}, {"entity": "publication", "iuid": "d033a5c5278c4463ad6a2a211e4b46ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d033a5c5278c4463ad6a2a211e4b46ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d033a5c5278c4463ad6a2a211e4b46ea"}}, "title": "Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.", "authors": [{"family": "Wojewodzic", "given": "Marcin W", "initials": "MW", "orcid": "0000-0003-2501-5201", "researcher": {"href": "https://publications.scilifelab.se/researcher/d838d8f26e2843579500d5500d2400e4.json"}}, {"family": "Leithaug", "given": "Magnus", "initials": "M"}, {"family": "Lauritzen", "given": "Marianne", "initials": "M"}, {"family": "Lyle", "given": "Robert", "initials": "R"}, {"family": "Haglund", "given": "Sofia", "initials": "S"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Ewels", "given": "Philip A", "initials": "PA"}, {"family": "Grotmol", "given": "Tom", "initials": "T"}, {"family": "Rounge", "given": "Trine B", "initials": "TB", "orcid": "0000-0003-2677-2722", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d490ad51ac640c688fe5d457efb7ada.json"}}], "type": "journal article", "published": "2021-05-12", "journal": {"title": "Clin Epigenetics", "issn": "1868-7083", "volume": "13", "issue": "1", "pages": "107", "issn-l": "1868-7075"}, "abstract": "Long-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments and storage might introduce biases and fragmentation to the DNA. In particular, starting with low-input DNA can result in low-diversity libraries. However, successful whole-genome bisulphite sequencing (WGBS) of such serum samples has the potential to open biobanks for epigenetic analyses and deliver novel prediagnostic biomarkers. Here, we perform WGBS using the Accel-NGS library preparation kit on ultralow amounts of DNA from long-term archived samples with diverse pretreatments from the Janus Serum Bank.\n\nNinety-four of the 96 samples produced satisfactory methylation calls; an average of 578 M reads per sample generated a mean coverage of 17\u00d7 and mean duplication level of 35%. Failed samples were related to poor bisulphite conversion rather than to sequencing or library preparation. We demonstrate the feasibility of WGBS on ultralow DNA yields from serum samples stored up to 48 years.\n\nOur results show the potential of large serum biobank collections for future epigenomic studies and biomarker discovery.", "doi": "10.1186/s13148-021-01097-3", "pmid": "33980276", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "10.1186/s13148-021-01097-3"}, {"db": "pmc", "key": "PMC8114536"}], "notes": [], "created": "2021-06-09T12:17:09.585Z", "modified": "2021-11-10T12:24:51.271Z"}, {"entity": "publication", "iuid": "d1331317a1ad4eef8b35fbb9e6a4a2e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1331317a1ad4eef8b35fbb9e6a4a2e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1331317a1ad4eef8b35fbb9e6a4a2e3"}}, "title": "Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy.", "authors": [{"family": "Hellberg", "given": "Sandra", "initials": "S"}, {"family": "Raffetseder", "given": "Johanna", "initials": "J"}, {"family": "Rundquist", "given": "Olof", "initials": "O"}, {"family": "Magnusson", "given": "Rasmus", "initials": "R"}, {"family": "Papapavlou", "given": "Georgia", "initials": "G"}, {"family": "Jenmalm", "given": "Maria C", "initials": "MC"}, {"family": "Ernerudh", "given": "Jan", "initials": "J"}, {"family": "Gustafsson", "given": "Mika", "initials": "M"}], "type": "journal article", "published": "2021-05-12", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "12", "pages": "672168", "issn-l": "1664-3224"}, "abstract": "The changes in progesterone (P4) levels during and after pregnancy coincide with the temporary improvement and worsening of several autoimmune diseases like multiple sclerosis (MS) and rheumatoid arthritis (RA). Most likely immune-endocrine interactions play a major role in these pregnancy-induced effects. In this study, we used next generation sequencing to investigate the direct effects of P4 on CD4+ T cell activation, key event in pregnancy and disease. We report profound dampening effects of P4 on T cell activation, altering the gene and protein expression profile and reversing many of the changes induced during the activation. The transcriptomic changes induced by P4 were significantly enriched for genes associated with diseases known to be modulated during pregnancy such as MS, RA and psoriasis. STAT1 and STAT3 were significantly downregulated by P4 and their downstream targets were significantly enriched among the disease-associated genes. Several of these genes included well-known and disease-relevant cytokines, such as IL-12\u03b2, CXCL10 and OSM, which were further validated also at the protein level using proximity extension assay. Our results extend the previous knowledge of P4 as an immune regulatory hormone and support its importance during pregnancy for regulating potentially detrimental immune responses towards the semi-allogenic fetus. Further, our results also point toward a potential role for P4 in the pregnancy-induced disease immunomodulation and highlight the need for further studies evaluating P4 as a future treatment option.", "doi": "10.3389/fimmu.2021.672168", "pmid": "34054852", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8149943"}], "notes": [], "created": "2021-10-01T09:01:10.279Z", "modified": "2022-12-02T08:53:30.137Z"}, {"entity": "publication", "iuid": "503a270c509f483ba14d05ddc08c1626", "links": {"self": {"href": "https://publications.scilifelab.se/publication/503a270c509f483ba14d05ddc08c1626.json"}, "display": {"href": "https://publications.scilifelab.se/publication/503a270c509f483ba14d05ddc08c1626"}}, "title": "African and Asian leopards are highly differentiated at the genomic level.", "authors": [{"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Becker", "given": "Matthew S", "initials": "MS"}, {"family": "Cahill", "given": "James A", "initials": "JA"}, {"family": "Fickel", "given": "Joerns", "initials": "J", "orcid": "0000-0002-0593-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/40018134351a481ab2d00b4113404c47.json"}}, {"family": "F\u00f6rster", "given": "Daniel W G", "initials": "DWG", "orcid": "0000-0002-6934-0404", "researcher": {"href": "https://publications.scilifelab.se/researcher/71cd2161c82547d7a0bb7d4049a41473.json"}}, {"family": "Gries", "given": "Katrin", "initials": "K", "orcid": "0000-0001-9441-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95bd682636c4becb3e977da6b5f221e.json"}}, {"family": "Hartmann", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3476-0169", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ae4f0b70c4c33a7070830804670f8.json"}}, {"family": "Havm\u00f8ller", "given": "Rasmus Wors\u00f8e", "initials": "RW"}, {"family": "Henneberger", "given": "Kirstin", "initials": "K"}, {"family": "Kern", "given": "Christian", "initials": "C", "orcid": "0000-0003-0298-064X", "researcher": {"href": "https://publications.scilifelab.se/researcher/268334dc599142d0929293626d4d35c3.json"}}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Mayer", "given": "Frieder", "initials": "F"}, {"family": "OBrien", "given": "Stephen J", "initials": "SJ", "orcid": "0000-0001-7857-0757", "researcher": {"href": "https://publications.scilifelab.se/researcher/261799ba7d5b4989b5f0f7b0388e3f32.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Sinding", "given": "Mikkel-Holder S", "initials": "MS"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Uphyrkina", "given": "Olga", "initials": "O", "orcid": "0000-0002-4436-1647", "researcher": {"href": "https://publications.scilifelab.se/researcher/649667810d2849a4957d5d9f475eb225.json"}}, {"family": "Wachter", "given": "Bettina", "initials": "B", "orcid": "0000-0002-0414-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/a28e4139fcf84006a6b132d49edddbce.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bhak", "given": "Jong", "initials": "J"}, {"family": "Manica", "given": "Andrea", "initials": "A", "orcid": "0000-0003-1895-450X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9332f04a6854ba18fad50c5fca8891c.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2021-05-10", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "9", "pages": "1872-1882.e5", "issn-l": "0960-9822"}, "abstract": "Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.", "doi": "10.1016/j.cub.2021.03.084", "pmid": "33848458", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00457-7"}], "notes": [], "created": "2021-06-09T12:14:28.866Z", "modified": "2021-11-10T12:24:57.977Z"}, {"entity": "publication", "iuid": "84ed076056f343a9bbd9ab0dfa94e830", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84ed076056f343a9bbd9ab0dfa94e830.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84ed076056f343a9bbd9ab0dfa94e830"}}, "title": "The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "13", "issue": "5", "pages": null}, "abstract": "Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may-when balanced-promote genetic diversity. Here, we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 resequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.", "doi": "10.1093/gbe/evab064", "pmid": "33760095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "6184863"}, {"db": "pmc", "key": "PMC8175052"}, {"db": "Dryad", "key": "10.5061/dryad.fj6q573tr"}], "notes": [], "created": "2021-10-01T09:00:15.619Z", "modified": "2024-01-16T13:48:39.792Z"}, {"entity": "publication", "iuid": "7a887e2d751543cda0fd97112b70afe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a887e2d751543cda0fd97112b70afe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a887e2d751543cda0fd97112b70afe0"}}, "title": "Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).", "authors": [{"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MP", "orcid": "0000-0003-0296-0577", "researcher": {"href": "https://publications.scilifelab.se/researcher/2abfa65f99b44f1ba6f8f0e6f3d7d8a4.json"}}, {"family": "Rastas", "given": "Pasi", "initials": "P", "orcid": "0000-0003-2768-1339", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a8f5f2160154bdfa0b21dfc132d4871.json"}}, {"family": "Steward", "given": "Rachel A", "initials": "RA", "orcid": "0000-0001-8610-334X", "researcher": {"href": "https://publications.scilifelab.se/researcher/336dd53f21a84ed49d55be3623ee1b16.json"}}, {"family": "Nylin", "given": "Soren", "initials": "S", "orcid": "0000-0003-4195-8920", "researcher": {"href": "https://publications.scilifelab.se/researcher/68d7f780ed30472eb2af408b0762c14d.json"}}, {"family": "Wheat", "given": "Christopher W", "initials": "CW", "orcid": "0000-0003-1863-2340", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e498f04977a48c89ffcd0bae890d4cb.json"}}], "type": "journal article", "published": "2021-05-07", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "5", "issn-l": "1759-6653"}, "abstract": "The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.", "doi": "10.1093/gbe/evab054", "pmid": "33749729", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6179806"}, {"db": "pmc", "key": "PMC8140205"}], "notes": [], "created": "2021-06-09T12:14:35.404Z", "modified": "2024-01-16T13:48:39.799Z"}, {"entity": "publication", "iuid": "a38ee778ff164c3f81c0f75f0c598e62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a38ee778ff164c3f81c0f75f0c598e62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a38ee778ff164c3f81c0f75f0c598e62"}}, "title": "Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.", "authors": [{"family": "Mazzurana", "given": "Luca", "initials": "L"}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Wigge", "given": "Leif", "initials": "L"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Williams", "given": "Teresa C", "initials": "TC"}, {"family": "Ravindran", "given": "Avinash", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "S\u00e4fholm", "given": "Jesper", "initials": "J"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dahl\u00e9n", "given": "Sven-Erik", "initials": "SE"}, {"family": "Orre", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "H\u00f6\u00f6g", "given": "Charlotte", "initials": "C"}, {"family": "Hedin", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-4921-8516", "researcher": {"href": "https://publications.scilifelab.se/researcher/d451be670f7f456ebca935690af79076.json"}}, {"family": "Szczegielniak", "given": "Sylwester", "initials": "S"}, {"family": "Almer", "given": "Sven", "initials": "S", "orcid": "0000-0001-9334-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/b22467cf9a68465a93a27b11ace20713.json"}}, {"family": "Mj\u00f6sberg", "given": "Jenny", "initials": "J"}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Cell Res", "issn": "1001-0602", "issn-l": null, "volume": "31", "issue": "5", "pages": "554-568"}, "abstract": "The impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident na\u00efve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2+ and CRTH2- ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-\u03b4 rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease.", "doi": "10.1038/s41422-020-00445-x", "pmid": "33420427", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41422-020-00445-x"}, {"db": "pmc", "key": "PMC8089104"}], "notes": [], "created": "2021-01-11T12:39:39.962Z", "modified": "2024-01-16T13:48:39.843Z"}, {"entity": "publication", "iuid": "6a9f4e6154e740f9826bf888aa10b91a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a9f4e6154e740f9826bf888aa10b91a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a9f4e6154e740f9826bf888aa10b91a"}}, "title": "Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.", "authors": [{"family": "Ain", "given": "Noor Ul", "initials": "NU"}, {"family": "Baroncelli", "given": "Marta", "initials": "M"}, {"family": "Costantini", "given": "Alice", "initials": "A", "orcid": "0000-0003-1408-9272", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d1ec6874e0c41b8a22cb4c0f3275bec.json"}}, {"family": "Ishaq", "given": "Tayyaba", "initials": "T"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Nilsson", "given": "Ola", "initials": "O"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Naz", "given": "Sadaf", "initials": "S", "orcid": "0000-0002-1912-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/46d041b7b2ba483eb303cbe3164c2c98.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "J. Med. Genet.", "issn": "1468-6244", "volume": "58", "issue": "5", "pages": "351-356", "issn-l": "0022-2593"}, "abstract": "Studies exploring molecular mechanisms underlying congenital skeletal disorders have revealed novel regulators of skeletal homeostasis and shown protein glycosylation to play an important role.\n\nTo identify the genetic cause of rhizomelic skeletal dysplasia in a consanguineous Pakistani family.\n\nClinical investigations were carried out for four affected individuals in the recruited family. Whole genome sequencing (WGS) was completed using DNA from two affected and two unaffected individuals from the family. Sequencing data were processed, filtered and analysed. In silico analyses were performed to predict the effects of the candidate variant on the protein structure and function. Small interfering RNAs (siRNAs) were used to study the effect of Gnpnat1 gene knockdown in primary rat chondrocytes.\n\nThe patients presented with short stature due to extreme shortening of the proximal segments of the limbs. Radiographs of one individual showed hip dysplasia and severe platyspondyly. WGS data analyses identified a homozygous missense variant c.226G>A; p.(Glu76Lys) in GNPNAT1, segregating with the disease. Glucosamine 6-phosphate N-acetyltransferase, encoded by the highly conserved gene GNPNAT1, is one of the enzymes required for synthesis of uridine diphosphate N-acetylglucosamine, which participates in protein glycosylation. Knockdown of Gnpnat1 by siRNAs decreased cellular proliferation and expression of chondrocyte differentiation markers collagen type 2 and alkaline phosphatase, indicating that Gnpnat1 is important for growth plate chondrocyte proliferation and differentiation.\n\nThis study describes a novel severe skeletal dysplasia associated with a biallelic, variant in GNPNAT1. Our data suggest that GNPNAT1 is important for growth plate chondrogenesis.", "doi": "10.1136/jmedgenet-2020-106929", "pmid": "32591345", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "jmedgenet-2020-106929"}], "notes": [], "created": "2020-12-07T16:32:23.854Z", "modified": "2024-01-16T13:48:39.879Z"}, {"entity": "publication", "iuid": "8c474726bc6544628fbd78328d2a664b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c474726bc6544628fbd78328d2a664b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c474726bc6544628fbd78328d2a664b"}}, "title": "In vivo screen identifies a SIK inhibitor that induces \u03b2 cell proliferation through a transient UPR.", "authors": [{"family": "Charbord", "given": "J\u00e9r\u00e9mie", "initials": "J", "orcid": "0000-0002-8411-8182", "researcher": {"href": "https://publications.scilifelab.se/researcher/47b63a06b76d4de1843f570dc3b90f27.json"}}, {"family": "Ren", "given": "Lipeng", "initials": "L"}, {"family": "Sharma", "given": "Rohit B", "initials": "RB"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "\u00c5gren", "given": "Rasmus", "initials": "R"}, {"family": "Chu", "given": "Lianhe", "initials": "L"}, {"family": "Tworus", "given": "Dominika", "initials": "D"}, {"family": "Schulz", "given": "Nadja", "initials": "N"}, {"family": "Charbord", "given": "Pierre", "initials": "P"}, {"family": "Stewart", "given": "Andrew F", "initials": "AF", "orcid": "0000-0001-7866-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/8287ffc577bd4d63b4b3f556589ec799.json"}}, {"family": "Wang", "given": "Peng", "initials": "P"}, {"family": "Alonso", "given": "Laura C", "initials": "LC", "orcid": "0000-0001-5056-8970", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fc585e98f6b4fa6a765606003b48789.json"}}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f796ff515c95491e9cd47018e02220c0.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Nat Metab", "issn": "2522-5812", "volume": "3", "issue": "5", "pages": "682-700", "issn-l": "2522-5812"}, "abstract": "It is known that \u03b2 cell proliferation expands the \u03b2 cell mass during development and under certain hyperglycemic conditions in the adult, a process that may be used for \u03b2 cell regeneration in diabetes. Here, through a new high-throughput screen using a luminescence ubiquitination-based cell cycle indicator (LUCCI) in zebrafish, we identify HG-9-91-01 as a driver of proliferation and confirm this effect in mouse and human \u03b2 cells. HG-9-91-01 is an inhibitor of salt-inducible kinases (SIKs), and overexpression of Sik1 specifically in \u03b2 cells blocks the effect of HG-9-91-01 on \u03b2 cell proliferation. Single-cell transcriptomic analyses of mouse \u03b2 cells demonstrate that HG-9-91-01 induces a wave of activating transcription factor (ATF)6-dependent unfolded protein response (UPR) before cell cycle entry. Importantly, the UPR wave is not associated with an increase in insulin expression. Additional mechanistic studies indicate that HG-9-91-01 induces multiple signalling effectors downstream of SIK inhibition, including CRTC1, CRTC2, ATF6, IRE1 and mTOR, which integrate to collectively drive \u03b2 cell proliferation.", "doi": "10.1038/s42255-021-00391-x", "pmid": "34031592", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s42255-021-00391-x"}], "notes": [], "created": "2021-06-03T07:12:21.146Z", "modified": "2024-01-16T13:48:39.887Z"}, {"entity": "publication", "iuid": "3ae89e2aba6e4057b948605c5db0ef47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ae89e2aba6e4057b948605c5db0ef47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ae89e2aba6e4057b948605c5db0ef47"}}, "title": "Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "case reports", "published": "2021-05-00", "journal": {"title": "Hum. Genet.", "issn": "1432-1203", "issn-l": "0340-6717", "volume": "140", "issue": "5", "pages": "775-790"}, "abstract": "Chromoanagenesis is a genomic event responsible for the formation of complex structural chromosomal rearrangements (CCRs). Germline chromoanagenesis is rare and the majority of reported cases are associated with an affected phenotype. Here, we report a healthy female carrying two de novo CCRs involving chromosomes 4, 19, 21 and X and chromosomes 7 and 11, respectively, with a total of 137 breakpoint junctions (BPJs). We characterized the CCRs using a hybrid-sequencing approach, combining short-read sequencing, nanopore sequencing, and optical mapping. The results were validated using multiple cytogenetic methods, including fluorescence in situ hybridization, spectral karyotyping, and Sanger sequencing. We identified 137 BPJs, which to our knowledge is the highest number of reported breakpoint junctions in germline chromoanagenesis. We also performed a statistical assessment of the positioning of the breakpoints, revealing a significant enrichment of BPJ-affecting genes (96 intragenic BPJs, 26 genes, p < 0.0001), indicating that the CCRs formed during active transcription of these genes. In addition, we find that the DNA fragments are unevenly and non-randomly distributed across the derivative chromosomes indicating a multistep process of scattering and re-joining of DNA fragments. In summary, we report a new maximum number of BPJs (137) in germline chromoanagenesis. We also show that a hybrid sequencing approach is necessary for the correct characterization of complex CCRs. Through in-depth statistical assessment, it was found that the CCRs most likely was formed through an event resembling chromoplexy-a catastrophic event caused by erroneous transcription factor binding.", "doi": "10.1007/s00439-020-02242-3", "pmid": "33315133", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00439-020-02242-3"}, {"db": "pmc", "key": "PMC8052244"}], "notes": [], "created": "2021-01-08T16:30:24.743Z", "modified": "2024-01-16T13:48:39.901Z"}, {"entity": "publication", "iuid": "cb971709f76944139aa5a66027bd3da4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb971709f76944139aa5a66027bd3da4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb971709f76944139aa5a66027bd3da4"}}, "title": "Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.", "authors": [{"family": "Sandholt", "given": "Arnar K S", "initials": "AKS", "orcid": "0000-0001-8926-1052", "researcher": {"href": "https://publications.scilifelab.se/researcher/be881c7a0be44f878e9541b90899ea01.json"}}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "S\u00f6derlund", "given": "Robert", "initials": "R"}, {"family": "Lund\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Troell", "given": "Karin", "initials": "K"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}, {"family": "Wattrang", "given": "Eva", "initials": "E", "orcid": "0000-0002-9804-169X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ef4e114ca144741a46f15eecde0f3ec.json"}}], "type": "journal article", "published": "2021-05-00", "journal": {"title": "Parasitology", "issn": "1469-8161", "volume": "148", "issue": "6", "pages": "712-725", "issn-l": null}, "abstract": "The study aimed to monitor parasite and host gene expression during the early stages of Eimeria tenella infection of chicken cells using dual RNA-Seq analysis. For this, we used chicken macrophage-like cell line HD11 cultures infected in vitro with purified E. tenella sporozoites. Cultures were harvested between 2 and 72 h post-infection and mRNA was extracted and sequenced. Dual RNA-Seq analysis showed clear patterns of altered expression for both parasite and host genes during infection. For example, genes in the chicken immune system showed upregulation early (2\u20134 h), a strong downregulation of genes across the immune system at 24 h and a repetition of early patterns at 72 h, indicating that invasion by a second generation of parasites was occurring. The observed downregulation may be due to immune self-regulation or to immune evasive mechanisms exerted by E. tenella. Results also suggested pathogen recognition receptors involved in E. tenella innate recognition, MRC2, TLR15 and NLRC5 and showed distinct chemokine and cytokine induction patterns. Moreover, the expression of several functional categories of Eimeria genes, such as rhoptry kinase genes and microneme genes, were also examined, showing distinctive differences which were expressed in sporozoites and merozoites.", "doi": "10.1017/S0031182021000111", "pmid": "33536090", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0031182021000111"}, {"db": "pmc", "key": "PMC8056837"}], "notes": [], "created": "2021-06-09T12:15:36.974Z", "modified": "2024-01-16T13:48:39.926Z"}, {"entity": "publication", "iuid": "69df6028b26644dd926f5a42f24c5dff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69df6028b26644dd926f5a42f24c5dff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69df6028b26644dd926f5a42f24c5dff"}}, "title": "Cyanophage Diversity and Community Structure in Dead Zone Sediments.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Hall", "given": "Per O J", "initials": "POJ"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2021-04-28", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "6", "issue": "2", "issn-l": "2379-5042"}, "abstract": "Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N2 fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient-representing oxic, hypoxic, and anoxic conditions-in one of the world's largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N2 fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments.IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.", "doi": "10.1128/mSphere.00208-21", "pmid": "33910994", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6/2/e00208-21"}, {"db": "pmc", "key": "PMC8092138"}], "notes": [], "created": "2021-06-09T12:16:56.678Z", "modified": "2024-01-16T13:48:39.964Z"}, {"entity": "publication", "iuid": "4b1f601660114d06a6b095089773121c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b1f601660114d06a6b095089773121c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b1f601660114d06a6b095089773121c"}}, "title": "Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.", "authors": [{"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "Gasparyan", "given": "Boris", "initials": "B"}, {"family": "Bar-Oz", "given": "Guy", "initials": "G"}, {"family": "Pinhasi", "given": "Ron", "initials": "R"}, {"family": "Foronova", "given": "Irina", "initials": "I"}, {"family": "Puzachenko", "given": "Andrey Y", "initials": "AY"}, {"family": "Pacher", "given": "Martina", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Baryshnikov", "given": "Gennady", "initials": "G"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2021-04-26", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "8", "pages": "1771-1779.e7", "issn-l": "0960-9822"}, "abstract": "Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a \u223c360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.", "doi": "10.1016/j.cub.2021.01.073", "pmid": "33592193", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00138-X"}], "notes": [], "created": "2021-06-09T12:15:39.416Z", "modified": "2021-11-10T12:25:32.345Z"}, {"entity": "publication", "iuid": "735c9b9d0c6245a788a78a937efb44eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb"}}, "title": "Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Steiner", "given": "Cynthia C", "initials": "CC", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Brace", "given": "Selina", "initials": "S", "orcid": "0000-0003-2126-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/476fbd04aaaf453f943f5eea976c3cff.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "historical article", "published": "2021-04-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2393", "issn-l": "2041-1723"}, "abstract": "Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.", "doi": "10.1038/s41467-021-22386-8", "pmid": "33896938", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-22386-8"}, {"db": "pmc", "key": "PMC8071806"}], "notes": [], "created": "2021-04-30T07:55:37.656Z", "modified": "2024-01-16T13:48:39.991Z"}, {"entity": "publication", "iuid": "bde798548a684c14b9deef470c7ac140", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bde798548a684c14b9deef470c7ac140.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bde798548a684c14b9deef470c7ac140"}}, "title": "Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.", "authors": [{"family": "Mattsson", "given": "Lina", "initials": "L"}, {"family": "S\u00f6renson", "given": "Eva", "initials": "E"}, {"family": "Capo", "given": "Eric", "initials": "E"}, {"family": "Farnelid", "given": "Hanna Maria", "initials": "HM"}, {"family": "Hirwa", "given": "Maurice", "initials": "M"}, {"family": "Olofsson", "given": "Martin", "initials": "M"}, {"family": "Svensson", "given": "Fredrik", "initials": "F"}, {"family": "Lindehoff", "given": "Elin", "initials": "E"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}], "type": "journal article", "published": "2021-04-22", "journal": {"title": "Front Bioeng Biotechnol", "issn": "2296-4185", "volume": "9", "issue": null, "pages": "651895", "issn-l": null}, "abstract": "Functionally uniform monocultures have remained the paradigm in microalgal cultivation despite the apparent challenges to avoid invasions by other microorganisms. A mixed microbial consortium approach has the potential to optimize and maintain biomass production despite of seasonal changes and to be more resilient toward contaminations. Here we present a 3-year outdoor production of mixed consortia of locally adapted microalgae and bacteria in cold temperate latitude. Microalgal consortia were cultivated in flat panel photobioreactors using brackish Baltic Sea water and CO2 from a cement factory (Degerhamn, Cementa AB, Heidelberg Cement Group) as a sustainable CO2 source. To evaluate the ability of the microbial consortia to maintain stable biomass production while exposed to seasonal changes in both light and temperature, we tracked changes in the microbial community using molecular methods (16S and 18S rDNA amplicon sequencing) and monitored the biomass production and quality (lipid, protein, and carbohydrate content) over 3 years. Despite changes in environmental conditions, the mixed consortia maintained stable biomass production by alternating between two different predominant green microalgae (Monoraphidium and Mychonastes) with complementary tolerance to temperature. The bacterial population was few taxa co-occured over time and the composition did not have any connection to the shifts in microalgal taxa. We propose that a locally adapted and mixed microalgal consortia, with complementary traits, can be useful for optimizing yield of commercial scale microalgal cultivation.", "doi": "10.3389/fbioe.2021.651895", "pmid": "33968914", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8100445"}], "notes": [], "created": "2021-06-09T12:17:08.355Z", "modified": "2024-01-16T13:48:40.030Z"}, {"entity": "publication", "iuid": "339b41037abf480ba2f5edd28bb2d957", "links": {"self": {"href": "https://publications.scilifelab.se/publication/339b41037abf480ba2f5edd28bb2d957.json"}, "display": {"href": "https://publications.scilifelab.se/publication/339b41037abf480ba2f5edd28bb2d957"}}, "title": "Active DNRA and denitrification in oxic hypereutrophic waters.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Zilius", "given": "Mindaugas", "initials": "M"}, {"family": "Samuiloviene", "given": "Aurelija", "initials": "A"}, {"family": "Vybernaite-Lubiene", "given": "Irma", "initials": "I"}, {"family": "Politi", "given": "Tobia", "initials": "T", "orcid": "0000-0001-6894-4284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d09ff3f832f44b3b98057305232f1de3.json"}}, {"family": "Klawonn", "given": "Isabell", "initials": "I", "orcid": "0000-0002-0675-436X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b14674d3bf9e41778013389d53d5d03e.json"}}, {"family": "Voss", "given": "Maren", "initials": "M", "orcid": "0000-0002-5827-9062", "researcher": {"href": "https://publications.scilifelab.se/researcher/075550c2b339480d80bab95cd9be2668.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}], "type": "journal article", "published": "2021-04-15", "journal": {"title": "Water Res.", "issn": "1879-2448", "volume": "194", "issue": null, "pages": "116954", "issn-l": "0043-1354"}, "abstract": "Since the start of synthetic fertilizer production more than a hundred years ago, the coastal ocean has been exposed to increasing nutrient loading, which has led to eutrophication and extensive algal blooms. Such hypereutrophic waters might harbor anaerobic nitrogen (N) cycling processes due to low-oxygen microniches associated with abundant organic particles, but studies on nitrate reduction in coastal pelagic environments are scarce. Here, we report on 15N isotope-labeling experiments, metagenome, and RT-qPCR data from a large hypereutrophic lagoon indicating that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were active processes, even though the bulk water was fully oxygenated (> 224 \u00b5M O2). DNRA in the bottom water corresponded to 83% of whole-ecosystem DNRA (water + sediment), while denitrification was predominant in the sediment. Microbial taxa important for DNRA according to the metagenomic data were dominated by Bacteroidetes (genus Parabacteroides) and Proteobacteria (genus Wolinella), while denitrification was mainly associated with proteobacterial genera Pseudomonas, Achromobacter, and Brucella. The metagenomic and microscopy data suggest that these anaerobic processes were likely occurring in low-oxygen microniches related to extensive growth of filamentous cyanobacteria, including diazotrophic Dolichospermum and non-diazotrophic Planktothrix. By summing the total nitrate fluxes through DNRA and denitrification, it results that DNRA retains approximately one fifth (19%) of the fixed N that goes through the nitrate pool. This is noteworthy as DNRA represents thus a very important recycling mechanism for fixed N, which sustains algal proliferation and leads to further enhancement of eutrophication in these endangered ecosystems.", "doi": "10.1016/j.watres.2021.116954", "pmid": "33667950", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(21)00152-4"}], "notes": [], "created": "2021-06-09T12:16:13.325Z", "modified": "2024-01-16T13:48:40.074Z"}, {"entity": "publication", "iuid": "b4782cdfe6284e678b37e60ddf9f30c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4782cdfe6284e678b37e60ddf9f30c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4782cdfe6284e678b37e60ddf9f30c8"}}, "title": "A spinal organ of proprioception for integrated motor action feedback.", "authors": [{"family": "Picton", "given": "Laurence D", "initials": "LD"}, {"family": "Bertuzzi", "given": "Maria", "initials": "M"}, {"family": "Pallucchi", "given": "Irene", "initials": "I"}, {"family": "Fontanel", "given": "Pierre", "initials": "P"}, {"family": "Dahlberg", "given": "Elin", "initials": "E"}, {"family": "Bj\u00f6rnfors", "given": "E Rebecka", "initials": "ER"}, {"family": "Iacoviello", "given": "Francesco", "initials": "F"}, {"family": "Shearing", "given": "Paul R", "initials": "PR"}, {"family": "El Manira", "given": "Abdeljabbar", "initials": "A"}], "type": "journal article", "published": "2021-04-07", "journal": {"title": "Neuron", "issn": "1097-4199", "issn-l": "0896-6273", "volume": "109", "issue": "7", "pages": "1188-1201.e7"}, "abstract": "Proprioception is essential for behavior and provides a sense of our body movements in physical space. Proprioceptor organs are thought to be only in the periphery. Whether the central nervous system can intrinsically sense its own movement remains unclear. Here we identify a segmental organ of proprioception in the adult zebrafish spinal cord, which is embedded by intraspinal mechanosensory neurons expressing Piezo2 channels. These cells are late-born, inhibitory, commissural neurons with unique molecular and physiological profiles reflecting a dual sensory and motor function. The central proprioceptive organ locally detects lateral body movements during locomotion and provides direct inhibitory feedback onto rhythm-generating interneurons responsible for the central motor program. This dynamically aligns central pattern generation with movement outcome for efficient locomotion. Our results demonstrate that a central proprioceptive organ monitors self-movement using hybrid neurons that merge sensory and motor entities into a unified network.", "doi": "10.1016/j.neuron.2021.01.018", "pmid": "33577748", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0896-6273(21)00040-4"}], "notes": [], "created": "2021-02-17T12:00:56.937Z", "modified": "2024-01-16T13:48:40.100Z"}, {"entity": "publication", "iuid": "94cdf9ed17a340d9a18e9348cf2fb025", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94cdf9ed17a340d9a18e9348cf2fb025.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94cdf9ed17a340d9a18e9348cf2fb025"}}, "title": "Severe congenital lactic acidosis and hypertrophic cardiomyopathy caused by an intronic variant in NDUFB7.", "authors": [{"family": "Correia", "given": "Sandrina P", "initials": "SP"}, {"family": "Moedas", "given": "Marco F", "initials": "MF"}, {"family": "Naess", "given": "Karin", "initials": "K"}, {"family": "Bruhn", "given": "Helene", "initials": "H"}, {"family": "Maffezzini", "given": "Camilla", "initials": "C"}, {"family": "Calvo-Garrido", "given": "Javier", "initials": "J"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Schober", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Freyer", "given": "Christoph", "initials": "C", "orcid": "0000-0003-0418-1673", "researcher": {"href": "https://publications.scilifelab.se/researcher/888298d25fb94acca7639063d3592373.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "42", "issue": "4", "pages": "378-384", "issn-l": "1059-7794"}, "abstract": "Mutations in structural subunits and assembly factors of complex I of the oxidative phosphorylation system constitute the most common cause of mitochondrial respiratory chain defects. Such mutations can present a wide range of clinical manifestations, varying from mild deficiencies to severe, lethal disorders. We describe a patient presenting intrauterine growth restriction and anemia, which displayed postpartum hypertrophic cardiomyopathy, lactic acidosis, encephalopathy, and a severe complex I defect with fatal outcome. Whole genome sequencing revealed an intronic biallelic mutation in the NDUFB7 gene (c.113-10C>G) and splicing pattern alterations in NDUFB7 messenger RNA were confirmed by RNA Sequencing. The detected variant resulted in a significant reduction of the NDUFB7 protein and reduced complex I activity. Complementation studies with expression of wild-type NDUFB7 in patient fibroblasts normalized complex I function. Here we report a case with a primary complex I defect due to a homozygous mutation in an intron region of the NDUFB7 gene.", "doi": "10.1002/humu.24173", "pmid": "33502047", "labels": {"Clinical Genomics Stockholm": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2021-02-04T14:33:05.943Z", "modified": "2021-12-06T13:45:27.325Z"}, {"entity": "publication", "iuid": "a9bb9bef6fc64c3fa3daf8e0dc7a60e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9bb9bef6fc64c3fa3daf8e0dc7a60e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9bb9bef6fc64c3fa3daf8e0dc7a60e4"}}, "title": "Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.", "authors": [{"family": "Bruhn", "given": "Helene", "initials": "H"}, {"family": "Samuelsson", "given": "Kristin", "initials": "K"}, {"family": "Schober", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Engvall", "given": "Martin", "initials": "M"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Calvo-Garrido", "given": "Javier", "initials": "J"}, {"family": "Press", "given": "Rayomand", "initials": "R"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Neurol Genet", "issn": "2376-7839", "volume": "7", "issue": "2", "pages": "e566", "issn-l": "2376-7839"}, "abstract": "To investigate the pathogenicity of a novel MT-ND3 mutation identified in a patient with adult-onset sensorimotor axonal polyneuropathy and report the clinical, morphologic, and biochemical findings.\n\nClinical assessments and morphologic and biochemical investigations of skeletal muscle and cultured myoblasts from the patient were performed. Whole-genome sequencing (WGS) of DNA from skeletal muscle and Sanger sequencing of mitochondrial DNA (mtDNA) from both skeletal muscle and cultured myoblasts were performed. Heteroplasmic levels of mutated mtDNA in different tissues were quantified by last-cycle hot PCR.\n\nMuscle showed ragged red fibers, paracrystalline inclusions, a significant reduction in complex I (CI) respiratory chain (RC) activity, and decreased adenosine triphosphate (ATP) production for all substrates used by CI. Sanger sequencing of DNA from skeletal muscle detected a unique previously unreported heteroplasmic mutation in mtDNA encoded MT-ND3, coding for a subunit in CI. WGS confirmed the mtDNA mutation but did not detect any other mutation explaining the disease. Cultured myoblasts, however, did not carry the mutation, and RC activity measurements in myoblasts were normal.\n\nWe report a case with adult-onset sensorimotor axonal polyneuropathy caused by a novel mtDNA mutation in MT-ND3. Loss of heteroplasmy in blood, cultured fibroblasts and myoblasts from the patient, and normal measurement of RC activity of the myoblasts support pathogenicity of the mutation. These findings highlight the importance of mitochondrial investigations in patients presenting with seemingly idiopathic polyneuropathy, especially if muscle also is affected.", "doi": "10.1212/NXG.0000000000000566", "pmid": "33732874", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "NG2020014720"}, {"db": "pmc", "key": "PMC7962437"}], "notes": [], "created": "2021-10-01T09:00:13.290Z", "modified": "2024-01-16T13:48:40.270Z"}, {"entity": "publication", "iuid": "b586007ebb4542e18c827db7e108b219", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b586007ebb4542e18c827db7e108b219.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b586007ebb4542e18c827db7e108b219"}}, "title": "Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root.", "authors": [{"family": "Abdelfattah", "given": "Ahmed", "initials": "A", "orcid": "0000-0001-6090-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/4321fbf1b3b642daa6a4f285f00a192f.json"}}, {"family": "Wisniewski", "given": "Michael", "initials": "M", "orcid": "0000-0002-7481-5590", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f4d23b738e407587b8a4fc9be257e7.json"}}, {"family": "Schena", "given": "Leonardo", "initials": "L", "orcid": "0000-0002-9737-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ab8b4ee37da49cca668efd0edd95bb6.json"}}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM", "orcid": "0000-0002-3550-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9cf8fde705481281edab32bc9156e5.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "23", "issue": "4", "pages": "2199-2214", "issn-l": "1462-2912"}, "abstract": "While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.", "doi": "10.1111/1462-2920.15392", "pmid": "33427409", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:00:16.874Z", "modified": "2021-12-06T13:45:32.144Z"}, {"entity": "publication", "iuid": "0517893fa4ac4c84b326d9582a35f368", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0517893fa4ac4c84b326d9582a35f368.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0517893fa4ac4c84b326d9582a35f368"}}, "title": "Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.", "authors": [{"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Zan", "given": "Yanjun", "initials": "Y"}, {"family": "Chen", "given": "Zhiqiang", "initials": "Z"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}, {"family": "Wu", "given": "Harry X", "initials": "HX", "orcid": "0000-0002-7072-4704", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d1a037ab43842b081d239c90bb30636.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "21", "issue": "3", "pages": "880-896", "issn-l": "1755-098X"}, "abstract": "Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome-wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS-based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two-step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high-confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high-quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.", "doi": "10.1111/1755-0998.13292", "pmid": "33179386", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7984398"}], "notes": [], "created": "2021-01-08T16:29:49.695Z", "modified": "2024-01-16T13:48:40.310Z"}, {"entity": "publication", "iuid": "af1d860a40a54aff870af824f6fef807", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af1d860a40a54aff870af824f6fef807"}}, "title": "The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.", "authors": [{"family": "Qu", "given": "Yanhua", "initials": "Y", "orcid": "0000-0002-4590-7787", "researcher": {"href": "https://publications.scilifelab.se/researcher/0443a97c3d564c49bc9361368ea2e20a.json"}}, {"family": "Chen", "given": "Chunhai", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Chen", "given": "Xiumin", "initials": "X"}, {"family": "Hao", "given": "Yan", "initials": "Y", "orcid": "0000-0002-1415-7610", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c1a42ec6cf4f3f990220e6b4735bec.json"}}, {"family": "She", "given": "Huishang", "initials": "H", "orcid": "0000-0001-6259-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/a02a8db02a40437a87bd000b995d10c8.json"}}, {"family": "Wang", "given": "Mengxia", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP", "orcid": "0000-0002-4143-9998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c2c08919d6f4ad9a54dce2481f47cbc.json"}}, {"family": "Lin", "given": "Haiyan", "initials": "H", "orcid": "0000-0002-1623-9361", "researcher": {"href": "https://publications.scilifelab.se/researcher/e54d1bf82275458794a989de37b58480.json"}}, {"family": "Cai", "given": "Tianlong", "initials": "T"}, {"family": "Song", "given": "Gang", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Jia", "given": "Chenxi", "initials": "C"}, {"family": "Chen", "given": "Chunyan", "initials": "C", "orcid": "0000-0002-2882-4517", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dd523248fd54ae299c069b960312115.json"}}, {"family": "Zhang", "given": "Hailin", "initials": "H"}, {"family": "Li", "given": "Jiang", "initials": "J", "orcid": "0000-0003-2099-8165", "researcher": {"href": "https://publications.scilifelab.se/researcher/b64bd87a57e0468b879e6361e79e3000.json"}}, {"family": "Liang", "given": "Liping", "initials": "L"}, {"family": "Wu", "given": "Tianyu", "initials": "T"}, {"family": "Zhao", "given": "Jinyang", "initials": "J", "orcid": "0000-0002-8150-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d41f239fe612446194498f9e5ed06321.json"}}, {"family": "Gao", "given": "Qiang", "initials": "Q", "orcid": "0000-0001-9880-4944", "researcher": {"href": "https://publications.scilifelab.se/researcher/faf3d20ec8344174a8c001bac7464421.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Zhai", "given": "Weiwei", "initials": "W", "orcid": "0000-0001-7938-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/e33e2ebb818449b9b95ba2484fccaa86.json"}}, {"family": "Zhang", "given": "Chi", "initials": "C"}, {"family": "Zhang", "given": "Yong E", "initials": "YE", "orcid": "0000-0003-3770-2383", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c91998c67674b75891a4473451916d6.json"}}, {"family": "Lei", "given": "Fumin", "initials": "F", "orcid": "0000-0001-9920-8167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e9cc44c016c4d099f674d182c08fbaa.json"}}], "type": "journal article", "published": "2021-03-30", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "13", "pages": "e2012398118", "issn-l": "0027-8424"}, "abstract": "Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai-Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.", "doi": "10.1073/pnas.2012398118", "pmid": "33753478", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2012398118"}, {"db": "pmc", "key": "PMC8020664"}], "notes": [], "created": "2021-06-09T12:15:45.569Z", "modified": "2024-01-16T13:48:40.345Z"}, {"entity": "publication", "iuid": "0e1bbf61a53e4ca28df35e545999d271", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1bbf61a53e4ca28df35e545999d271.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1bbf61a53e4ca28df35e545999d271"}}, "title": "Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.", "authors": [{"family": "Indukuri", "given": "Rajitha", "initials": "R"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Archer", "given": "Amena", "initials": "A"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2021-03-30", "journal": {"title": "Front Endocrinol (Lausanne)", "issn": "1664-2392", "volume": "12", "issue": null, "pages": "650625", "issn-l": null}, "abstract": "Inflammation is a primary component of both initiation and promotion of colorectal cancer (CRC). Cytokines secreted by macrophages, including tumor necrosis factor alpha (TNF\u03b1), activates the pro-survival transcription factor complex NF\u03baB. The precise mechanism of NF\u03baB in CRC is not well studied, but we recently reported the genome-wide transcriptional impact of TNF\u03b1 in two CRC cell lines. Further, estrogen signaling influences inflammation in a complex manner and suppresses CRC development. CRC protective effects of estrogen have been shown to be mediated by estrogen receptor beta (ER\u03b2, ESR2), which also impacts inflammatory signaling of the colon. However, whether ER\u03b2 impacts the chromatin interaction (cistrome) of the main NF\u03baB subunit p65 (RELA) is not known. We used p65 chromatin immunoprecipitation followed by sequencing (ChIP-Seq) in two different CRC cell lines, HT29 and SW480, with and without expression of ER\u03b2. We here present the p65 colon cistrome of these two CRC cell lines. We identify that RELA and AP1 motifs are predominant in both cell lines, and additionally describe both common and cell line-specific p65 binding sites and correlate these to transcriptional changes related to inflammation, migration, apoptosis and circadian rhythm. Further, we determine that ER\u03b2 opposes a major fraction of p65 chromatin binding in HT29 cells, but enhances p65 binding in SW480 cells, thereby impacting the p65 cistrome differently in the two cell lines. However, the biological functions of the regulated genes appear to have similar roles in both cell lines. To our knowledge, this is the first time the p65 CRC cistrome is compared between different cell lines and the first time an influence by ER\u03b2 on the p65 cistrome is investigated. Our work provides a mechanistic foundation for a better understanding of how estrogen influences inflammatory signaling through NF\u03baB in CRC cells.", "doi": "10.3389/fendo.2021.650625", "pmid": "33859619", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8042384"}], "notes": [], "created": "2021-06-09T12:16:16.967Z", "modified": "2024-01-16T13:48:40.395Z"}, {"entity": "publication", "iuid": "9652d35801134a92a24c0e2f6a73c7eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9652d35801134a92a24c0e2f6a73c7eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9652d35801134a92a24c0e2f6a73c7eb"}}, "title": "PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.", "authors": [{"family": "He", "given": "Li", "initials": "L", "orcid": "0000-0002-4743-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6e2e4c7f88845bb895842e56a7622ae.json"}}, {"family": "Jones", "given": "Jennifer", "initials": "J"}, {"family": "He", "given": "Weiguo", "initials": "W", "orcid": "0000-0001-8929-7741", "researcher": {"href": "https://publications.scilifelab.se/researcher/66d5261aa3fa478b8efbd2ee645b18ac.json"}}, {"family": "Bjork", "given": "Bryan C", "initials": "BC", "orcid": "0000-0002-1245-091X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a26227e22d14f9a80d028859f8b9923.json"}}, {"family": "Wen", "given": "Jiayu", "initials": "J", "orcid": "0000-0003-1249-6456", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddd7475512db4109900e4a3c2e9e20f9.json"}}, {"family": "Dai", "given": "Qi", "initials": "Q", "orcid": "0000-0002-2082-0693", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b0dce19d67e4cdeb9d48a7e71a7028d.json"}}], "type": "journal article", "published": "2021-03-17", "journal": {"title": "Development", "issn": "1477-9129", "volume": "148", "issue": "6", "issn-l": "0950-1991"}, "abstract": "Radial glia (RG) in the neocortex sequentially generate distinct subtypes of projection neurons, accounting for the diversity and complex assembly of cortical neural circuits. Mechanisms that drive the rapid and precise temporal progression of RG are beginning to be elucidated. Here, we reveal that the RG-specific transcriptional regulator PRDM16 promotes the transition of early to late phase of neurogenesis in the mouse neocortex. Loss of Prdm16 delays the timely progression of RG, leading to defective cortical laminar organization. Our genomic analyses demonstrate that PRDM16 regulates a subset of genes that are dynamically expressed between early and late neurogenesis. We show that PRDM16 suppresses target gene expression through limiting chromatin accessibility of permissive enhancers. We further confirm that crucial target genes regulated by PRDM16 are neuronal specification genes, cell cycle regulators and molecules required for neuronal migration. These findings provide evidence to support the finding that neural progenitors temporally shift the gene expression program to achieve neural cell diversity.", "doi": "10.1242/dev.194670", "pmid": "33597191", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "dev.194670"}, {"db": "pmc", "key": "PMC7990860"}], "notes": [], "created": "2021-06-09T12:16:44.601Z", "modified": "2024-01-16T13:48:40.432Z"}, {"entity": "publication", "iuid": "7219d1caf1b64d9abaad5610b82fcaca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7219d1caf1b64d9abaad5610b82fcaca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7219d1caf1b64d9abaad5610b82fcaca"}}, "title": "Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.", "authors": [{"family": "Fellows Yates", "given": "James A", "initials": "JA"}, {"family": "Lamnidis", "given": "Thiseas C", "initials": "TC"}, {"family": "Borry", "given": "Maxime", "initials": "M"}, {"family": "Andrades Valtue\u00f1a", "given": "Aida", "initials": "A"}, {"family": "Fagern\u00e4s", "given": "Zandra", "initials": "Z"}, {"family": "Clayton", "given": "Stephen", "initials": "S"}, {"family": "Garcia", "given": "Maxime U", "initials": "MU"}, {"family": "Neukamm", "given": "Judith", "initials": "J"}, {"family": "Peltzer", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2021-03-16", "journal": {"title": "PeerJ", "issn": "2167-8359", "volume": "9", "pages": "e10947", "issn-l": "2167-8359"}, "abstract": "The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.", "doi": "10.7717/peerj.10947", "pmid": "33777521", "labels": {"NGI Stockholm (Genomics Applications)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10947"}, {"db": "pmc", "key": "PMC7977378"}], "notes": [], "created": "2021-11-30T13:55:19.333Z", "modified": "2021-11-30T13:55:19.339Z"}, {"entity": "publication", "iuid": "6ba3a0a503434b1d9709bdead1716425", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ba3a0a503434b1d9709bdead1716425.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ba3a0a503434b1d9709bdead1716425"}}, "title": "Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood.", "authors": [{"family": "Brownlie", "given": "Demi", "initials": "D", "orcid": "0000-0001-5932-6425", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e879a6ef8ff45bea049986707480e99.json"}}, {"family": "Scharenberg", "given": "Marlena", "initials": "M", "orcid": "0000-0002-7659-7216", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef22a304bdc429a81d7acf143f6295f.json"}}, {"family": "Mold", "given": "Jeff E", "initials": "JE", "orcid": "0000-0003-2195-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba167f912244d879746ed60a3c19568.json"}}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J", "orcid": "0000-0003-4575-5629", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c209a378be54ae699e7157892c3a709.json"}}, {"family": "Kek\u00e4l\u00e4inen", "given": "Eliisa", "initials": "E", "orcid": "0000-0001-6045-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/726903b084194aeb885b4cb42a8d33db.json"}}, {"family": "Buggert", "given": "Marcus", "initials": "M", "orcid": "0000-0003-0633-1719", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a54e4b5136642eeafa77ac5118a0c81.json"}}, {"family": "Nguyen", "given": "Son", "initials": "S"}, {"family": "Wilson", "given": "Jennifer N", "initials": "JN"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG", "orcid": "0000-0003-0908-7387", "researcher": {"href": "https://publications.scilifelab.se/researcher/54d696167bca4a389807143f84baeafe.json"}}, {"family": "Marquardt", "given": "Nicole", "initials": "N", "orcid": "0000-0003-3186-4752", "researcher": {"href": "https://publications.scilifelab.se/researcher/b87ccad53d354bdd80af490dc8a0c019.json"}}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}], "type": "journal article", "published": "2021-03-16", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "11", "pages": "e2016580118", "issn-l": "0027-8424"}, "abstract": "Human adaptive-like \"memory\" CD56dimCD16+ natural killer (NK) cells in peripheral blood from cytomegalovirus-seropositive individuals have been extensively investigated in recent years and are currently explored as a treatment strategy for hematological cancers. However, treatment of solid tumors remains limited due to insufficient NK cell tumor infiltration, and it is unknown whether large expansions of adaptive-like NK cells that are equipped for tissue residency and tumor homing exist in peripheral tissues. Here, we show that human lung and blood contains adaptive-like CD56brightCD16- NK cells with hallmarks of tissue residency, including expression of CD49a. Expansions of adaptive-like lung tissue-resident NK (trNK) cells were found to be present independently of adaptive-like CD56dimCD16+ NK cells and to be hyperresponsive toward target cells. Together, our data demonstrate that phenotypically, functionally, and developmentally distinct subsets of adaptive-like NK cells exist in human lung and blood. Given their tissue-related character and hyperresponsiveness, human lung adaptive-like trNK cells might represent a suitable alternative for therapies targeting solid tumors.", "doi": "10.1073/pnas.2016580118", "pmid": "33836578", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "2016580118"}, {"db": "pmc", "key": "PMC7980282"}], "notes": [], "created": "2021-06-09T12:16:15.739Z", "modified": "2021-11-10T12:26:18.872Z"}, {"entity": "publication", "iuid": "598bd6b5445f44679e26ebb6cb896fe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5"}}, "title": "The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.", "authors": [{"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "de Bruijn", "given": "Ino", "initials": "I", "orcid": "0000-0001-5427-4750", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c71c59a5f064f4c84150c7b5cd366ac.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2021-03-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "307", "issn-l": "2399-3642"}, "abstract": "The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.", "doi": "10.1038/s42003-021-01810-1", "pmid": "33686191", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01810-1"}, {"db": "pmc", "key": "PMC7940616"}], "notes": [], "created": "2021-06-09T12:14:33.814Z", "modified": "2024-01-16T13:48:40.474Z"}, {"entity": "publication", "iuid": "634a4941b9a3488cb12cafd4aab1d5e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/634a4941b9a3488cb12cafd4aab1d5e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/634a4941b9a3488cb12cafd4aab1d5e2"}}, "title": "Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.", "authors": [{"family": "Kupari", "given": "Jussi", "initials": "J", "orcid": "0000-0003-1540-5193", "researcher": {"href": "https://publications.scilifelab.se/researcher/96dfeacf7fe04bf099fbddf0c45ef693.json"}}, {"family": "Usoskin", "given": "Dmitry", "initials": "D"}, {"family": "Parisien", "given": "Marc", "initials": "M", "orcid": "0000-0003-2924-5960", "researcher": {"href": "https://publications.scilifelab.se/researcher/046deabca7484670a0c9f7378580d7f5.json"}}, {"family": "Lou", "given": "Daohua", "initials": "D"}, {"family": "Hu", "given": "Yizhou", "initials": "Y", "orcid": "0000-0002-2635-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b75010a59c243279eaf9ca7af75315b.json"}}, {"family": "Fatt", "given": "Michael", "initials": "M"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Sp\u00e5ngberg", "given": "Mats", "initials": "M"}, {"family": "Eriksson", "given": "Bengt", "initials": "B"}, {"family": "Barkas", "given": "Nikolaos", "initials": "N", "orcid": "0000-0002-4675-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/969cdbac84bb434d865b99c3d21be988.json"}}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Lor\u00e9", "given": "Karin", "initials": "K", "orcid": "0000-0001-7679-9494", "researcher": {"href": "https://publications.scilifelab.se/researcher/737245a5bc2144bd90be71487cbb3192.json"}}, {"family": "Khoury", "given": "Samar", "initials": "S"}, {"family": "Diatchenko", "given": "Luda", "initials": "L", "orcid": "0000-0002-1350-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ff8b8cc7d444732a4dfcb0c9e3d8507.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}], "type": "journal article", "published": "2021-03-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1510", "issn-l": "2041-1723"}, "abstract": "Distinct types of dorsal root ganglion sensory neurons may have unique contributions to chronic pain. Identification of primate sensory neuron types is critical for understanding the cellular origin and heritability of chronic pain. However, molecular insights into the primate sensory neurons are missing. Here we classify non-human primate dorsal root ganglion sensory neurons based on their transcriptome and map human pain heritability to neuronal types. First, we identified cell correlates between two major datasets for mouse sensory neuron types. Machine learning exposes an overall cross-species conservation of somatosensory neurons between primate and mouse, although with differences at individual gene level, highlighting the importance of primate data for clinical translation. We map genomic loci associated with chronic pain in human onto primate sensory neuron types to identify the cellular origin of chronic pain. Genome-wide associations for chronic pain converge on two different neuronal types distributed between pain disorders that display different genetic susceptibilities, suggesting both unique and shared mechanisms between different pain conditions.", "doi": "10.1038/s41467-021-21725-z", "pmid": "33686078", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21725-z"}, {"db": "pmc", "key": "PMC7940623"}], "notes": [], "created": "2021-06-09T12:16:22.425Z", "modified": "2024-01-16T13:48:40.539Z"}, {"entity": "publication", "iuid": "49087a366a2e44ad9a29b9b43f1b7ee2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49087a366a2e44ad9a29b9b43f1b7ee2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49087a366a2e44ad9a29b9b43f1b7ee2"}}, "title": "Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.", "authors": [{"family": "Seguin-Orlando", "given": "Andaine", "initials": "A", "orcid": "0000-0002-8265-3229", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f62251e48e34acdb3bea43f1f88c415.json"}}, {"family": "Donat", "given": "Richard", "initials": "R"}, {"family": "Der Sarkissian", "given": "Clio", "initials": "C"}, {"family": "Southon", "given": "John", "initials": "J"}, {"family": "Th\u00e8ves", "given": "Catherine", "initials": "C"}, {"family": "Manen", "given": "Claire", "initials": "C", "orcid": "0000-0002-7827-8876", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f2e0862b9bc42818c224fc1a9b5966f.json"}}, {"family": "Tch\u00e9r\u00e9missinoff", "given": "Yaramila", "initials": "Y"}, {"family": "Crub\u00e9zy", "given": "Eric", "initials": "E"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Deleuze", "given": "Jean-Fran\u00e7ois", "initials": "JF"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Guilaine", "given": "Jean", "initials": "J"}, {"family": "Orlando", "given": "Ludovic", "initials": "L", "orcid": "0000-0003-3936-1850", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca463500fb034711b6200d5b611e4c1d.json"}}], "type": "journal article", "published": "2021-03-08", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "5", "pages": "1072-1083.e10", "issn-l": "0960-9822"}, "abstract": "The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05\u00d7 coverage.16 This leaves the key transitional period covering \u223c3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning \u223c3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to \u223c63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as \u223c3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as \u223c2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.", "doi": "10.1016/j.cub.2020.12.015", "pmid": "33434506", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(20)31835-2"}], "notes": [], "created": "2021-06-09T12:15:40.686Z", "modified": "2021-11-10T12:26:26.443Z"}, {"entity": "publication", "iuid": "f9024c2fa0084cab8c1823079ad4453e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9024c2fa0084cab8c1823079ad4453e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9024c2fa0084cab8c1823079ad4453e"}}, "title": "Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.", "authors": [{"family": "Zhong", "given": "Xiuqin", "initials": "X"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2021-03-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "13", "issue": "3", "issn-l": "1759-6653"}, "abstract": "Differences in immune function between species could be a result of interspecific divergence in coding sequence and/or expression of immune genes. Here, we investigate how the degree of divergence in coding sequence and expression differs between functional categories of immune genes, and if differences between categories occur independently of other factors (expression level, pleiotropy). To this end, we compared spleen transcriptomes of wild-caught yellow-necked mice and bank voles. Immune genes expressed in the spleen were divided into four categories depending on the function of the encoded protein: pattern recognition receptors (PRR); signal transduction proteins; transcription factors; and cyto- and chemokines and their receptors. Genes encoding PRR and cyto-/chemokines had higher sequence divergence than genes encoding signal transduction proteins and transcription factors, even when controlling for potentially confounding factors. Genes encoding PRR also had higher expression divergence than genes encoding signal transduction proteins and transcription factors. There was a positive correlation between expression divergence and coding sequence divergence, in particular for PRR genes. We propose that this is a result of that divergence in PRR coding sequence leads to divergence in PRR expression through positive feedback of PRR ligand binding on PRR expression. When controlling for sequence divergence, expression divergence of PRR genes did not differ from other categories. Taken together, the results indicate that coding sequence divergence of PRR genes is a major cause of differences in immune function between species.", "doi": "10.1093/gbe/evab023", "pmid": "33565592", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6132239"}, {"db": "pmc", "key": "PMC7936018"}, {"db": "Dryad", "key": "10.5061/dryad.ncjsxkss3"}], "notes": [], "created": "2021-06-09T12:15:43.130Z", "modified": "2024-01-16T13:48:40.554Z"}, {"entity": "publication", "iuid": "54d66ea8cbd441738be55f5928034c3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54d66ea8cbd441738be55f5928034c3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54d66ea8cbd441738be55f5928034c3e"}}, "title": "Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.", "authors": [{"family": "Muus", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2779-0893", "researcher": {"href": "https://publications.scilifelab.se/researcher/64294a5aa1c14770bda4a82d1c3ad6e8.json"}}, {"family": "Luecken", "given": "Malte D", "initials": "MD", "orcid": "0000-0001-7464-7921", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b82068719d43448992741da54e00bd.json"}}, {"family": "Eraslan", "given": "G\u00f6kcen", "initials": "G"}, {"family": "Sikkema", "given": "Lisa", "initials": "L", "orcid": "0000-0001-9686-6295", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ac44fd17c99482685c93a121ff3f07f.json"}}, {"family": "Waghray", "given": "Avinash", "initials": "A"}, {"family": "Heimberg", "given": "Graham", "initials": "G"}, {"family": "Kobayashi", "given": "Yoshihiko", "initials": "Y"}, {"family": "Vaishnav", "given": "Eeshit Dhaval", "initials": "ED", "orcid": "0000-0003-3720-8051", "researcher": {"href": "https://publications.scilifelab.se/researcher/2053d240d2eb444c8f06063caa6b0ccb.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbf15f9b2bd447f49e0bbc5c8d4d3b21.json"}}, {"family": "Smillie", "given": "Christopher", "initials": "C"}, {"family": "Jagadeesh", "given": "Karthik A", "initials": "KA"}, {"family": "Duong", "given": "Elizabeth Thu", "initials": "ET", "orcid": "0000-0001-7122-4448", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c2bfca881e545d2879f8db22a828365.json"}}, {"family": "Fiskin", "given": "Evgenij", "initials": "E"}, {"family": "Torlai Triglia", "given": "Elena", "initials": "E", "orcid": "0000-0002-6059-0116", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cfcfff80e364607bb2f8d5ee04eb91a.json"}}, {"family": "Ansari", "given": "Meshal", "initials": "M", "orcid": "0000-0002-8819-7965", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea04d7f251e24f87a651ebbb826f3466.json"}}, {"family": "Cai", "given": "Peiwen", "initials": "P"}, {"family": "Lin", "given": "Brian", "initials": "B", "orcid": "0000-0002-8851-3534", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e5d51eb340f4dac86fb43f79367cff6.json"}}, {"family": "Buchanan", "given": "Justin", "initials": "J"}, {"family": "Chen", "given": "Sijia", "initials": "S"}, {"family": "Shu", "given": "Jian", "initials": "J"}, {"family": "Haber", "given": "Adam L", "initials": "AL"}, {"family": "Chung", "given": "Hattie", "initials": "H"}, {"family": "Montoro", "given": "Daniel T", "initials": "DT"}, {"family": "Adams", "given": "Taylor", "initials": "T"}, {"family": "Aliee", "given": "Hananeh", "initials": "H"}, {"family": "Allon", "given": "Samuel J", "initials": "SJ"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Angelidis", "given": "Ilias", "initials": "I"}, {"family": "Ashenberg", "given": "Orr", "initials": "O"}, {"family": "Bassler", "given": "Kevin", "initials": "K"}, {"family": "B\u00e9cavin", "given": "Christophe", "initials": "C"}, {"family": "Benhar", "given": "Inbal", "initials": "I"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L"}, {"family": "Bolt", "given": "Liam", "initials": "L"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Bui", "given": "Linh T", "initials": "LT"}, {"family": "Callori", "given": "Steven", "initials": "S"}, {"family": "Chaffin", "given": "Mark", "initials": "M"}, {"family": "Chichelnitskiy", "given": "Evgeny", "initials": "E"}, {"family": "Chiou", "given": "Joshua", "initials": "J"}, {"family": "Conlon", "given": "Thomas M", "initials": "TM"}, {"family": "Cuoco", "given": "Michael S", "initials": "MS"}, {"family": "Cuomo", "given": "Anna S E", "initials": "ASE"}, {"family": "Deprez", "given": "Marie", "initials": "M"}, {"family": "Duclos", "given": "Grant", "initials": "G"}, {"family": "Fine", "given": "Denise", "initials": "D"}, {"family": "Fischer", "given": "David S", "initials": "DS"}, {"family": "Ghazanfar", "given": "Shila", "initials": "S"}, {"family": "Gillich", "given": "Astrid", "initials": "A"}, {"family": "Giotti", "given": "Bruno", "initials": "B"}, {"family": "Gould", "given": "Joshua", "initials": "J"}, {"family": "Guo", "given": "Minzhe", "initials": "M"}, {"family": "Gutierrez", "given": "Austin J", "initials": "AJ"}, {"family": "Habermann", "given": "Arun C", "initials": "AC"}, {"family": "Harvey", "given": "Tyler", "initials": "T"}, {"family": "He", "given": "Peng", "initials": "P"}, {"family": "Hou", "given": "Xiaomeng", "initials": "X"}, {"family": "Hu", "given": "Lijuan", "initials": "L"}, {"family": "Hu", "given": "Yan", "initials": "Y"}, {"family": "Jaiswal", "given": "Alok", "initials": "A"}, {"family": "Ji", "given": "Lu", "initials": "L"}, {"family": "Jiang", "given": "Peiyong", "initials": "P"}, {"family": "Kapellos", "given": "Theodoros S", "initials": "TS"}, {"family": "Kuo", "given": "Christin S", "initials": "CS"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Leney-Greene", "given": "Michael A", "initials": "MA"}, {"family": "Lim", "given": "Kyungtae", "initials": "K"}, {"family": "Litvi\u0148ukov\u00e1", "given": "Monika", "initials": "M"}, {"family": "Ludwig", "given": "Leif S", "initials": "LS"}, {"family": "Lukassen", "given": "Soeren", "initials": "S"}, {"family": "Luo", "given": "Wendy", "initials": "W"}, {"family": "Maatz", "given": "Henrike", "initials": "H"}, {"family": "Madissoon", "given": "Elo", "initials": "E"}, {"family": "Mamanova", "given": "Lira", "initials": "L"}, {"family": "Manakongtreecheep", "given": "Kasidet", "initials": "K"}, {"family": "Leroy", "given": "Sylvie", "initials": "S"}, {"family": "Mayr", "given": "Christoph H", "initials": "CH"}, {"family": "Mbano", "given": "Ian M", "initials": "IM"}, {"family": "McAdams", "given": "Alexi M", "initials": "AM"}, {"family": "Nabhan", "given": "Ahmad N", "initials": "AN"}, {"family": "Nyquist", "given": "Sarah K", "initials": "SK"}, {"family": "Penland", "given": "Lolita", "initials": "L"}, {"family": "Poirion", "given": "Olivier B", "initials": "OB"}, {"family": "Poli", "given": "Sergio", "initials": "S"}, {"family": "Qi", "given": "CanCan", "initials": "C"}, {"family": "Queen", "given": "Rachel", "initials": "R"}, {"family": "Reichart", "given": "Daniel", "initials": "D"}, {"family": "Rosas", "given": "Ivan", "initials": "I"}, {"family": "Schupp", "given": "Jonas C", "initials": "JC"}, {"family": "Shea", "given": "Conor V", "initials": "CV"}, {"family": "Shi", "given": "Xingyi", "initials": "X"}, {"family": "Sinha", "given": "Rahul", "initials": "R"}, {"family": "Sit", "given": "Rene V", "initials": "RV"}, {"family": "Slowikowski", "given": "Kamil", "initials": "K"}, {"family": "Slyper", "given": "Michal", "initials": "M"}, {"family": "Smith", "given": "Neal P", "initials": "NP"}, {"family": "Sountoulidis", "given": "Alex", "initials": "A"}, {"family": "Strunz", "given": "Maximilian", "initials": "M"}, {"family": "Sullivan", "given": "Travis B", "initials": "TB"}, {"family": "Sun", "given": "Dawei", "initials": "D"}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Tan", "given": "Peng", "initials": "P"}, {"family": "Tantivit", "given": "Jessica", "initials": "J"}, {"family": "Travaglini", "given": "Kyle J", "initials": "KJ"}, {"family": "Tucker", "given": "Nathan R", "initials": "NR"}, {"family": "Vernon", "given": "Katherine A", "initials": "KA"}, {"family": "Wadsworth", "given": "Marc H", "initials": "MH"}, {"family": "Waldman", "given": "Julia", "initials": "J"}, {"family": "Wang", "given": "Xiuting", "initials": "X"}, {"family": "Xu", "given": "Ke", "initials": "K"}, {"family": "Yan", "given": "Wenjun", "initials": "W"}, {"family": "Zhao", "given": "William", "initials": "W"}, {"family": "Ziegler", "given": "Carly G K", "initials": "CGK"}, {"family": "NHLBI LungMap Consortium", "given": "", "initials": ""}, {"family": "Human Cell Atlas Lung Biological Network", "given": "", "initials": ""}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nat. Med.", "issn": "1546-170X", "volume": "27", "issue": "3", "pages": "546-559", "issn-l": "1078-8956"}, "abstract": "Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.", "doi": "10.1038/s41591-020-01227-z", "pmid": "33654293", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "mid", "key": "NIHMS1757283"}, {"db": "pmc", "key": "PMC9469728"}, {"db": "pii", "key": "10.1038/s41591-020-01227-z"}], "notes": [], "created": "2021-06-09T12:14:25.786Z", "modified": "2023-06-19T13:01:43.238Z"}, {"entity": "publication", "iuid": "2e7e49728505456faeaabd9b31cb95a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e7e49728505456faeaabd9b31cb95a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e7e49728505456faeaabd9b31cb95a3"}}, "title": "RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite.", "authors": [{"family": "Barrag\u00e1n", "given": "Carlos Eduardo", "initials": "CE"}, {"family": "M\u00e1rquez", "given": "Marco Antonio", "initials": "MA"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Montoya", "given": "Dolly", "initials": "D"}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Extremophiles", "issn": "1433-4909", "volume": "25", "issue": "2", "pages": "143-158", "issn-l": "1431-0651"}, "abstract": "Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.", "doi": "10.1007/s00792-021-01217-0", "pmid": "33616780", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00792-021-01217-0"}], "notes": [], "created": "2021-06-09T12:15:41.975Z", "modified": "2024-01-16T13:48:40.568Z"}, {"entity": "publication", "iuid": "a28f46bafc084df78efa91e2f3f049c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a28f46bafc084df78efa91e2f3f049c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a28f46bafc084df78efa91e2f3f049c7"}}, "title": "Million-year-old DNA sheds light on the genomic history of mammoths.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J"}, {"family": "Hartmann", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3476-0169", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ae4f0b70c4c33a7070830804670f8.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Thomas", "given": "Jessica A", "initials": "JA"}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b98a6e55a69644cda1e305da05c6838d.json"}}, {"family": "Fidan", "given": "Fatma Rabia", "initials": "FR", "orcid": "0000-0001-5877-7945", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d1cb5fb5754f25b1adbad44e9f4adf.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "591", "issue": "7849", "pages": "265-269"}, "abstract": "Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.", "doi": "10.1038/s41586-021-03224-9", "pmid": "33597750", "labels": {"NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03224-9"}, {"db": "pmc", "key": "PMC7116897"}, {"db": "mid", "key": "EMS114570"}], "notes": [], "created": "2021-02-22T13:16:35.556Z", "modified": "2024-01-16T13:48:40.588Z"}, {"entity": "publication", "iuid": "9935fbecc0e14408bf3d12dad0afc00c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9935fbecc0e14408bf3d12dad0afc00c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9935fbecc0e14408bf3d12dad0afc00c"}}, "title": "Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate PLK1.", "authors": [{"family": "Silva Cascales", "given": "Helena", "initials": "H", "orcid": "0000-0002-4320-6610", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b6d20c8593c461eabae8bcbdbfcfbaa.json"}}, {"family": "Burdova", "given": "Kamila", "initials": "K"}, {"family": "Middleton", "given": "Anna", "initials": "A", "orcid": "0000-0002-3351-4564", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b9b1ec878734578a23f6837bfec3077.json"}}, {"family": "Kuzin", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7139-1884", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fffd1dd85a049e6bd92b6c68b5f659f.json"}}, {"family": "M\u00fcllers", "given": "Erik", "initials": "E", "orcid": "0000-0002-2176-3248", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a060ead5074f1aa3c0e782665814a8.json"}}, {"family": "Stoy", "given": "Henriette", "initials": "H"}, {"family": "Baranello", "given": "Laura", "initials": "L", "orcid": "0000-0001-6039-1849", "researcher": {"href": "https://publications.scilifelab.se/researcher/a33e20ca8e284b5db1cca13e5e6d7940.json"}}, {"family": "Macurek", "given": "Libor", "initials": "L", "orcid": "0000-0002-0987-1238", "researcher": {"href": "https://publications.scilifelab.se/researcher/996ba2becfac43ad90a0480678c24964.json"}}, {"family": "Lindqvist", "given": "Arne", "initials": "A", "orcid": "0000-0002-0141-1579", "researcher": {"href": "https://publications.scilifelab.se/researcher/68e589e498e24d1c83e3256f28900189.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "4", "issue": "3", "pages": "e202000980", "issn-l": "2575-1077"}, "abstract": "Cyclin A2 is a key regulator of the cell cycle, implicated both in DNA replication and mitotic entry. Cyclin A2 participates in feedback loops that activate mitotic kinases in G2 phase, but why active Cyclin A2-CDK2 during the S phase does not trigger mitotic kinase activation remains unclear. Here, we describe a change in localisation of Cyclin A2 from being only nuclear to both nuclear and cytoplasmic at the S/G2 border. We find that Cyclin A2-CDK2 can activate the mitotic kinase PLK1 through phosphorylation of Bora, and that only cytoplasmic Cyclin A2 interacts with Bora and PLK1. Expression of predominately cytoplasmic Cyclin A2 or phospho-mimicking PLK1 T210D can partially rescue a G2 arrest caused by Cyclin A2 depletion. Cytoplasmic presence of Cyclin A2 is restricted by p21, in particular after DNA damage. Cyclin A2 chromatin association during DNA replication and additional mechanisms contribute to Cyclin A2 localisation change in the G2 phase. We find no evidence that such mechanisms involve G2 feedback loops and suggest that cytoplasmic appearance of Cyclin A2 at the S/G2 transition functions as a trigger for mitotic kinase activation.", "doi": "10.26508/lsa.202000980", "pmid": "33402344", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "4/3/e202000980"}, {"db": "pmc", "key": "PMC7812317"}], "notes": [], "created": "2021-01-08T16:30:28.613Z", "modified": "2021-11-10T12:26:43.353Z"}, {"entity": "publication", "iuid": "f56234dc807b4d78ab213054295f3f5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f56234dc807b4d78ab213054295f3f5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f56234dc807b4d78ab213054295f3f5d"}}, "title": "Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes.", "authors": [{"family": "Johansson", "given": "Helene", "initials": "H"}, {"family": "S\u00f8ndergaard", "given": "Jonas N\u00f8rskov", "initials": "JN"}, {"family": "Jorns", "given": "Carl", "initials": "C"}, {"family": "Kutter", "given": "Claudia", "initials": "C"}, {"family": "Ellis", "given": "Ewa C S", "initials": "ECS"}], "type": "journal article", "published": "2021-02-22", "journal": {"title": "Front Endocrinol (Lausanne)", "issn": "1664-2392", "volume": "11", "pages": "554922", "issn-l": null}, "abstract": "Bile acids (BAs) are detergents essential for intestinal absorption of lipids. Disruption of BA homeostasis can lead to severe liver damage. BA metabolism is therefore under strict regulation by sophisticated feedback mechanisms. The hormone-like protein Fibroblast growth factor 19 (FGF19) is essential for maintaining BA homeostasis by down regulating BA synthesis. Here, the impact of both FGF19 and chenodeoxycholic acid (CDCA) on primary human hepatocytes was investigated and a possible autocrine/paracrine function of FGF19 in regulation of BA synthesis evaluated. Primary human hepatocytes were treated with CDCA, recombinant FGF19 or conditioned medium containing endogenously produced FGF19. RNA sequencing revealed that treatment with CDCA causes deregulation of transcripts involved in BA metabolism, whereas treatment with FGF19 had minor effects. CDCA increased FGF19 mRNA expression within 1 h. We detected secretion of the resulting FGF19 protein into medium, mimicking in vivo observations. Furthermore, medium enriched with endogenously produced FGF19 reduced BA synthesis by down regulating CYP7A1 gene expression. However, following knockdown of FGF19, CDCA still independently decreased BA synthesis, presumably through the regulatory protein small heterodimer partner (SHP). In summary, we show that in primary human hepatocytes CDCA regulates BA synthesis in an FGF19-independent manner.", "doi": "10.3389/fendo.2020.554922", "pmid": "33692750", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7937932"}], "notes": [], "created": "2023-10-04T08:31:49.957Z", "modified": "2023-10-04T08:31:49.960Z"}, {"entity": "publication", "iuid": "efe6701f6ddd4dd5acaf8b1dfa7c3ec3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efe6701f6ddd4dd5acaf8b1dfa7c3ec3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efe6701f6ddd4dd5acaf8b1dfa7c3ec3"}}, "title": "Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.", "authors": [{"family": "Schneider", "given": "Andreas N", "initials": "AN", "orcid": "0000-0001-5431-955X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1859c02ba19541528bdfb9036119672c.json"}}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Richau", "given": "Kerstin", "initials": "K"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Hurry", "given": "Vaughan", "initials": "V"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}], "type": "journal article", "published": "2021-02-16", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "6", "issue": "1", "pages": null, "issn-l": "2379-5077"}, "abstract": "The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.", "doi": "10.1128/mSystems.00884-20", "pmid": "33594001", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6/1/e00884-20"}, {"db": "pmc", "key": "PMC8573963"}], "notes": [], "created": "2021-02-19T13:07:32.365Z", "modified": "2024-01-16T13:48:40.665Z"}, {"entity": "publication", "iuid": "a4bbbc6af47c4ff399e4ce88b4e2f840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4bbbc6af47c4ff399e4ce88b4e2f840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4bbbc6af47c4ff399e4ce88b4e2f840"}}, "title": "Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.", "authors": [{"family": "Wu", "given": "Haohao", "initials": "H", "orcid": "0000-0002-5511-7084", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bc2f62b53ce4aabb4db2508e7901228.json"}}, {"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Fontanet", "given": "Paula", "initials": "P", "orcid": "0000-0002-5324-6077", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe102480cb7458a941fc70fe7f5cb9b.json"}}, {"family": "Sharma", "given": "Anil", "initials": "A", "orcid": "0000-0002-7442-8494", "researcher": {"href": "https://publications.scilifelab.se/researcher/53eab132449648df8998ae6de526c99f.json"}}, {"family": "Bellardita", "given": "Carmelo", "initials": "C"}, {"family": "Quadros", "given": "Rolen M", "initials": "RM"}, {"family": "Jannig", "given": "Paulo R", "initials": "PR"}, {"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Heimel", "given": "J Alexander", "initials": "JA", "orcid": "0000-0002-5291-4184", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc34eb2a27f43c680a9198426041468.json"}}, {"family": "Cheung", "given": "Kylie K Y", "initials": "KKY"}, {"family": "Wanderoy", "given": "Simone", "initials": "S"}, {"family": "Xuan", "given": "Yang", "initials": "Y"}, {"family": "Meletis", "given": "Konstantinos", "initials": "K", "orcid": "0000-0001-5665-4781", "researcher": {"href": "https://publications.scilifelab.se/researcher/56822ffe0341444297c820580f52dfd0.json"}}, {"family": "Ruas", "given": "Jorge", "initials": "J", "orcid": "0000-0002-1110-2606", "researcher": {"href": "https://publications.scilifelab.se/researcher/b91c3fde15f7415aa1f6c9263ff913ff.json"}}, {"family": "Gurumurthy", "given": "Channabasavaiah B", "initials": "CB", "orcid": "0000-0002-8022-4033", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f30aa6db34f4d34b3bdb24ecb2069b4.json"}}, {"family": "Kiehn", "given": "Ole", "initials": "O"}, {"family": "Hadjab", "given": "Saida", "initials": "S", "orcid": "0000-0001-7953-8396", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79ab77088f43859e11b75dcae33d73.json"}}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0001-5484-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9494a8ea444facbf3b564670930ab5.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1026", "issn-l": "2041-1723"}, "abstract": "Proprioceptive neurons (PNs) are essential for the proper execution of all our movements by providing muscle sensory feedback to the central motor network. Here, using deep single cell RNAseq of adult PNs coupled with virus and genetic tracings, we molecularly identify three main types of PNs (Ia, Ib and II) and find that they segregate into eight distinct subgroups. Our data unveil a highly sophisticated organization of PNs into discrete sensory input channels with distinct spatial distribution, innervation patterns and molecular profiles. Altogether, these features contribute to finely regulate proprioception during complex motor behavior. Moreover, while Ib- and II-PN subtypes are specified around birth, Ia-PN subtypes diversify later in life along with increased motor activity. We also show Ia-PNs plasticity following exercise training, suggesting Ia-PNs are important players in adaptive proprioceptive function in adult mice.", "doi": "10.1038/s41467-021-21173-9", "pmid": "33589589", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21173-9"}, {"db": "pmc", "key": "PMC7884389"}], "notes": [], "created": "2021-06-09T12:14:37.963Z", "modified": "2024-01-16T13:48:40.686Z"}, {"entity": "publication", "iuid": "1ca0729f557a4cd3b8cb790b4a9d5961", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ca0729f557a4cd3b8cb790b4a9d5961.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ca0729f557a4cd3b8cb790b4a9d5961"}}, "title": "Asymmetric introgression reveals the genetic architecture of a plumage trait.", "authors": [{"family": "Semenov", "given": "Georgy A", "initials": "GA", "orcid": "0000-0002-7218-7885", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bb787f3be449299a263dcab28021b9.json"}}, {"family": "Linck", "given": "Ethan", "initials": "E"}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Harris", "given": "Rebecca B", "initials": "RB"}, {"family": "Khaydarov", "given": "David R", "initials": "DR"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P", "orcid": "0000-0001-7182-2763", "researcher": {"href": "https://publications.scilifelab.se/researcher/f426ea7151c546939b707d5ed71e7d04.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Taylor", "given": "Scott A", "initials": "SA", "orcid": "0000-0001-9580-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c6baa1b23242e0bfd586d7e42c0cb9.json"}}], "type": "journal article", "published": "2021-02-15", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1019", "issn-l": "2041-1723"}, "abstract": "Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.", "doi": "10.1038/s41467-021-21340-y", "pmid": "33589637", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-21340-y"}, {"db": "pmc", "key": "PMC7884433"}, {"db": "Dryad", "key": "10.5061/dryad.dv41ns1wv"}], "notes": [], "created": "2021-06-09T12:16:14.581Z", "modified": "2024-01-16T13:48:40.705Z"}, {"entity": "publication", "iuid": "4571d7f6b9ba472e8f2e5853ef6d82d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4571d7f6b9ba472e8f2e5853ef6d82d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4571d7f6b9ba472e8f2e5853ef6d82d8"}}, "title": "Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass.", "authors": [{"family": "S\u00f6renson", "given": "Eva", "initials": "E"}, {"family": "Capo", "given": "Eric", "initials": "E"}, {"family": "Farnelid", "given": "Hanna", "initials": "H"}, {"family": "Lindehoff", "given": "Elin", "initials": "E"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}], "type": "journal article", "published": "2021-02-11", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "12", "issue": null, "pages": "607601", "issn-l": "1664-302X"}, "abstract": "To better predict the consequences of environmental change on aquatic microbial ecosystems it is important to understand what enables community resilience. The mechanisms by which a microbial community maintain its overall function, for example, the cycling of carbon, when exposed to a stressor, can be explored by considering three concepts: biotic interactions, functional adaptations, and community structure. Interactions between species are traditionally considered as, e.g., mutualistic, parasitic, or neutral but are here broadly defined as either coexistence or competition, while functions relate to their metabolism (e.g., autotrophy or heterotrophy) and roles in ecosystem functioning (e.g., oxygen production, organic matter degradation). The term structure here align with species richness and diversity, where a more diverse community is though to exhibit a broader functional capacity than a less diverse community. These concepts have here been combined with ecological theories commonly used in resilience studies, i.e., adaptive cycles, panarchy, and cross-scale resilience, that describe how the status and behavior at one trophic level impact that of surrounding levels. This allows us to explore the resilience of a marine microbial community, cultivated in an outdoor photobioreactor, when exposed to a naturally occurring seasonal stress. The culture was monitored for 6weeks during which it was exposed to two different temperature regimes (21 \u00b1 2 and 11 \u00b1 1\u00b0C). Samples were taken for metatranscriptomic analysis, in order to assess the regulation of carbon uptake and utilization, and for amplicon (18S and 16S rRNA gene) sequencing, to characterize the community structure of both autotrophs (dominated by the green microalgae Mychonastes) and heterotrophs (associated bacterioplankton). Differential gene expression analyses suggested that community function at warm temperatures was based on concomitant utilization of inorganic and organic carbon assigned to autotrophs and heterotrophs, while at colder temperatures, the uptake of organic carbon was performed primarily by autotrophs. Upon the shift from high to low temperature, community interactions shifted from coexistence to competition for organic carbon. Network analysis indicated that the community structure showed opposite trends for autotrophs and heterotrophs in having either high or low diversity. Despite an abrupt change of temperature, the microbial community as a whole responded in a way that maintained the overall level of diversity and function within and across autotrophic and heterotrophic levels. This is in line with cross-scale resilience theory describing how ecosystems may balance functional overlaps within and functional redundancy between levels in order to be resilient to environmental change (such as temperature).", "doi": "10.3389/fmicb.2021.607601", "pmid": "33643237", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7905023"}], "notes": [], "created": "2021-06-09T12:16:23.703Z", "modified": "2024-01-16T13:48:40.725Z"}, {"entity": "publication", "iuid": "131283b276484c18b504aa4dc0115f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19"}}, "title": "The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.", "authors": [{"family": "Schober", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Moore", "given": "David", "initials": "D"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Moedas", "given": "Marco F", "initials": "MF", "orcid": "0000-0001-5461-0320", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a9cd9caaa014f4280544a243520e18c.json"}}, {"family": "Clemente", "given": "Paula", "initials": "P"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Fissi", "given": "Najla El", "initials": "NE", "orcid": "0000-0002-6631-4630", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec87cba920947028856aadb5892f7a6.json"}}, {"family": "Filograna", "given": "Roberta", "initials": "R"}, {"family": "Bucher", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0002-9391-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec4467fb36b44f0a0b1dfa056ec964d.json"}}, {"family": "Hinze", "given": "Yvonne", "initials": "Y", "orcid": "0000-0002-2966-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/a922a71f2fde43908945980353ed595a.json"}}, {"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e90cde879dc41eaade439bcf951a646.json"}}, {"family": "Hedman", "given": "Erik", "initials": "E", "orcid": "0000-0003-4017-9749", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffc752d50a6649248c6809ea5aec803d.json"}}, {"family": "Chernogubova", "given": "Ekaterina", "initials": "E"}, {"family": "Begzati", "given": "Arjana", "initials": "A", "orcid": "0000-0002-8770-8022", "researcher": {"href": "https://publications.scilifelab.se/researcher/a15af0dbd68445538bd92c89f6d901df.json"}}, {"family": "Wibom", "given": "Rolf", "initials": "R", "orcid": "0000-0001-6721-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d5fc666ef84a8784d8b28ecf233146.json"}}, {"family": "Jain", "given": "Mohit", "initials": "M"}, {"family": "Nilsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-6020-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c6d082934d818445fe0187dbb23e.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C", "orcid": "0000-0003-0418-1673", "researcher": {"href": "https://publications.scilifelab.se/researcher/888298d25fb94acca7639063d3592373.json"}}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "8", "issn-l": "2375-2548"}, "abstract": "Induction of the one-carbon cycle is an early hallmark of mitochondrial dysfunction and cancer metabolism. Vital intermediary steps are localized to mitochondria, but it remains unclear how one-carbon availability connects to mitochondrial function. Here, we show that the one-carbon metabolite and methyl group donor S-adenosylmethionine (SAM) is pivotal for energy metabolism. A gradual decline in mitochondrial SAM (mitoSAM) causes hierarchical defects in fly and mouse, comprising loss of mitoSAM-dependent metabolites and impaired assembly of the oxidative phosphorylation system. Complex I stability and iron-sulfur cluster biosynthesis are directly controlled by mitoSAM levels, while other protein targets are predominantly methylated outside of the organelle before import. The mitoSAM pool follows its cytosolic production, establishing mitochondria as responsive receivers of one-carbon units. Thus, we demonstrate that cellular methylation potential is required for energy metabolism, with direct relevance for pathophysiology, aging, and cancer.", "doi": "10.1126/sciadv.abf0717", "pmid": "33608280", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/8/eabf0717"}, {"db": "pmc", "key": "PMC7895438"}], "notes": [], "created": "2021-12-06T13:45:25.780Z", "modified": "2024-01-16T13:48:40.799Z"}, {"entity": "publication", "iuid": "9d68ff8c44864ab9b8cc705ce6dd407f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d68ff8c44864ab9b8cc705ce6dd407f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d68ff8c44864ab9b8cc705ce6dd407f"}}, "title": "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications.scilifelab.se/researcher/a08eb47d3b0f427da9402d89cee67df8.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Shutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a2b9ccd9ae84cdfbcb663591f39a77b.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "590", "issue": "7847", "pages": "649-654"}, "abstract": "The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.", "doi": "10.1038/s41586-021-03232-9", "pmid": "33627808", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Spatial Proteomics": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03232-9"}], "notes": [], "created": "2021-03-01T07:10:50.117Z", "modified": "2021-12-09T13:57:57.891Z"}, {"entity": "publication", "iuid": "8900950a1d67461cb627e4a31b553d07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8900950a1d67461cb627e4a31b553d07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8900950a1d67461cb627e4a31b553d07"}}, "title": "A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.", "authors": [{"family": "Kamal", "given": "Shady Mansour", "initials": "SM", "orcid": "0000-0002-7565-811X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ef64c5ead434175a8ebaf26a786a916.json"}}, {"family": "Cimdins-Ahne", "given": "Annika", "initials": "A", "orcid": "0000-0001-7414-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/e45bd6f6716e442aa9800ade4b2c9ccb.json"}}, {"family": "Lee", "given": "Changhan", "initials": "C", "orcid": "0000-0003-0327-4712", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c2596edd9c74f0abcdeea30a0c1a1dd.json"}}, {"family": "Li", "given": "Fengyang", "initials": "F", "orcid": "0000-0001-5102-6284", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df6d813f9c846288355fe6695f7e4ab.json"}}, {"family": "Mart\u00edn-Rodr\u00edguez", "given": "Alberto J", "initials": "AJ", "orcid": "0000-0003-2422-129X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65ffdf18851a414798718b1e349e41be.json"}}, {"family": "Seferbekova", "given": "Zaira", "initials": "Z", "orcid": "0000-0002-3131-3697", "researcher": {"href": "https://publications.scilifelab.se/researcher/b880e4cdf6594edab82e28ae3739a77d.json"}}, {"family": "Afasizhev", "given": "Robert", "initials": "R", "orcid": "0000-0002-3513-8873", "researcher": {"href": "https://publications.scilifelab.se/researcher/e21c2af9f4b8403795927dfa4287f2b4.json"}}, {"family": "Wami", "given": "Haleluya Tesfaye", "initials": "HT", "orcid": "0000-0002-9929-2570", "researcher": {"href": "https://publications.scilifelab.se/researcher/89117b1a4ee04e65b405bb13697b6b06.json"}}, {"family": "Katikaridis", "given": "Panagiotis", "initials": "P", "orcid": "0000-0001-5783-1487", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ba96692acd4b2b8412eca76ed1f1a9.json"}}, {"family": "Meins", "given": "Lena", "initials": "L", "orcid": "0000-0001-6214-477X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb7a68bdfc34a508235b978d4b59249.json"}}, {"family": "L\u00fcnsdorf", "given": "Heinrich", "initials": "H", "orcid": "0000-0003-2778-8611", "researcher": {"href": "https://publications.scilifelab.se/researcher/35509ad2567340b1b6fbc1355ba67db7.json"}}, {"family": "Dobrindt", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-9949-1898", "researcher": {"href": "https://publications.scilifelab.se/researcher/220a330bb66f48efaffd38d0efaa0f9e.json"}}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U", "orcid": "0000-0003-3812-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a59ac735d61485aa43ee7a2ae3a526d.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Mol. Microbiol.", "issn": "1365-2958", "volume": "115", "issue": "2", "pages": "255-271", "issn-l": "0950-382X"}, "abstract": "The ubiquitous human commensal Escherichia coli has been well investigated through its model representative E. coli K-12. In this work, we initially characterized E. coli Fec10, a recently isolated human commensal strain of phylogroup A/sequence type ST10. Compared to E. coli K-12, the 4.88 Mbp Fec10 genome is characterized by distinct single-nucleotide polymorphisms and acquisition of genomic islands. In addition, E. coli Fec10 possesses a 155.86 kbp IncY plasmid, a composite element based on phage P1. pFec10 harbours multiple cargo genes such as coding for a tetrathionate reductase and its corresponding regulatory two-component system. Among the cargo genes is also the Transmissible Locus of Protein Quality Control (TLPQC), which mediates tolerance to lethal temperatures in bacteria. The disaggregase ClpGGI of TLPQC constitutes a major determinant of the thermotolerance of E. coli Fec10. We confirmed stand-alone disaggregation activity, but observed distinct biochemical characteristics of ClpGGI-Fec10 compared to the nearly identical Pseudomonas aeruginosa ClpGGI-SG17M. Furthermore, we noted a unique contribution of ClpGGI-Fec10 to the exquisite thermotolerance of E. coli Fec10, suggesting functional differences between both disaggregases in vivo. Detection of thermotolerance in 10% of human commensal E. coli isolates hints to the successful establishment of food-borne heat-resistant strains in the human gut.", "doi": "10.1111/mmi.14614", "pmid": "32985020", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7984374"}], "notes": [], "created": "2020-12-07T16:29:51.854Z", "modified": "2024-01-16T13:48:40.873Z"}, {"entity": "publication", "iuid": "8d23fe4a3c0b49a69a66baaa4811acc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d23fe4a3c0b49a69a66baaa4811acc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d23fe4a3c0b49a69a66baaa4811acc2"}}, "title": "The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers.", "authors": [{"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Ibrahim", "given": "Ahmed", "initials": "A"}, {"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications.scilifelab.se/researcher/561d04f60c61426bb790ba83153ba651.json"}}, {"family": "Liu", "given": "Yanghong", "initials": "Y"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Williams", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0602-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/89989da8d4e64dd3a30b87fc62ceefae.json"}}], "type": "journal article", "published": "2021-01-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "3", "pages": "1354", "issn-l": null}, "abstract": "Colorectal cancer (CRC) is the third leading cause of cancer deaths. Advances within bioinformatics, such as machine learning, can improve biomarker discovery and ultimately improve CRC survival rates. There are clear sex differences in CRC characteristics, but the impact of sex has not been considered with regards to CRC biomarkers. Our aim here was to investigate sex differences in the transcriptome of a normal colon and CRC, and between paired normal and tumor tissue. Next, we attempted to identify CRC diagnostic and prognostic biomarkers and investigate if they are sex-specific. We collected paired normal and tumor tissue, performed RNA-seq, and applied feature selection in combination with machine learning to identify the top CRC diagnostic biomarkers. We used The Cancer Genome Atlas (TCGA) data to identify sex-specific CRC diagnostic biomarkers and performed an overall survival analysis to identify sex-specific prognostic biomarkers. We found transcriptomic sex differences in both the normal colon tissue and in CRC. Forty-four of the top-ranked biomarkers were sex-specific and 20 biomarkers showed a sex-specific prognostic value. Our data show the importance of sex in the discovery of CRC biomarkers. We propose 20 sex-specific CRC prognostic biomarkers, including ESM1, GUCA2A, and VWA2 for males and CLDN1 and FUT1 for females.", "doi": "10.3390/ijms22031354", "pmid": "33572952", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ijms22031354"}, {"db": "pmc", "key": "PMC7866425"}], "notes": [], "created": "2021-06-09T12:16:19.522Z", "modified": "2024-01-16T13:48:40.906Z"}, {"entity": "publication", "iuid": "c5cf7c75465a480c8ba26778bac156d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5cf7c75465a480c8ba26778bac156d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5cf7c75465a480c8ba26778bac156d6"}}, "title": "Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.", "authors": [{"family": "Norin", "given": "Ulrika", "initials": "U", "orcid": "0000-0003-1063-6339", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb0cc296604c46d0895f150b1905144c.json"}}, {"family": "Rintisch", "given": "Carola", "initials": "C"}, {"family": "Meng", "given": "Liesu", "initials": "L", "orcid": "0000-0003-1985-050X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9715869252ac4fdd913f94e044904c1a.json"}}, {"family": "Forster", "given": "Florian", "initials": "F"}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Tuncel", "given": "Jonatan", "initials": "J"}, {"family": "Klocke", "given": "Katrin", "initials": "K"}, {"family": "B\u00e4cklund", "given": "Johan", "initials": "J"}, {"family": "Yang", "given": "Min", "initials": "M"}, {"family": "Bonner", "given": "Michael Y", "initials": "MY"}, {"family": "Lahore", "given": "Gonzalo Fernandez", "initials": "GF"}, {"family": "James", "given": "Jaime", "initials": "J"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Bergquist", "given": "Maria", "initials": "M"}, {"family": "Gjertsson", "given": "Inger", "initials": "I"}, {"family": "Hubner", "given": "Norbert", "initials": "N", "orcid": "0000-0002-1218-6223", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84f34739c743838cea107286522e42.json"}}, {"family": "B\u00e4ckdahl", "given": "Liselotte", "initials": "L"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R", "orcid": "0000-0002-4969-2576", "researcher": {"href": "https://publications.scilifelab.se/researcher/49e60d22dd1a4dd1a4ca5a50d9fc4fc7.json"}}], "type": "journal article", "published": "2021-01-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "12", "issue": "1", "pages": "610"}, "abstract": "The introduction of the CTLA-4 recombinant fusion protein has demonstrated therapeutic effects by selectively modulating T-cell activation in rheumatoid arthritis. Here we show, using a forward genetic approach, that a mutation in the SH3gl1 gene encoding the endocytic protein Endophilin A2 is associated with the development of arthritis in rodents. Defective expression of SH3gl1 affects T cell effector functions and alters the activation threshold of autoreactive T cells, thereby leading to complete protection from chronic autoimmune inflammatory disease in both mice and rats. We further show that SH3GL1 regulates human T cell signaling and T cell receptor internalization, and its expression is upregulated in rheumatoid arthritis patients. Collectively our data identify SH3GL1 as a key regulator of T cell activation, and as a potential target for treatment of autoimmune diseases.", "doi": "10.1038/s41467-020-20586-2", "pmid": "33504785", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics (NBIS)": "Collaborative", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-20586-2"}, {"db": "pmc", "key": "PMC7840939"}], "notes": [], "created": "2021-01-28T14:33:53.228Z", "modified": "2025-10-17T13:04:28.145Z"}, {"entity": "publication", "iuid": "1f5e1b21a6a5486793d238251900e16e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f5e1b21a6a5486793d238251900e16e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f5e1b21a6a5486793d238251900e16e"}}, "title": "Ecological adaptation in European eels is based on phenotypic plasticity.", "authors": [{"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG"}, {"family": "Palm", "given": "Stefan", "initials": "S", "orcid": "0000-0002-9890-8265", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ebffe35bae646eb8a15163b0cb0820f.json"}}, {"family": "Wickstr\u00f6m", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6335-8833", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce9d80227974a21be858a2925338f93.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2021-01-26", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "4", "pages": "e2022620118", "issn-l": "0027-8424"}, "abstract": "The relative role of genetic adaptation and phenotypic plasticity is of fundamental importance in evolutionary ecology [M. J. West-Eberhard, Proc. Natl. Acad. Sci. U.S.A. 102 (suppl. 1), 6543-6549 (2005)]. European eels have a complex life cycle, including transitions between life stages across ecological conditions in the Sargasso Sea, where spawning occurs, and those in brackish and freshwater bodies from northern Europe to northern Africa. Whether continental eel populations consist of locally adapted and genetically distinct populations or comprise a single panmictic population has received conflicting support. Here we use whole-genome sequencing and show that European eels belong to one panmictic population. A complete lack of geographical genetic differentiation is demonstrated. We postulate that this is possible because the most critical life stages-spawning and embryonic development-take place under near-identical conditions in the Sargasso Sea. We further show that within-generation selection, which has recently been proposed as a mechanism for genetic adaptation in eels, can only marginally change allele frequencies between cohorts of eels from different geographic regions. Our results strongly indicate plasticity as the predominant mechanism for how eels respond to diverse environmental conditions during postlarval stages, ultimately solving a long-standing question for a classically enigmatic species.", "doi": "10.1073/pnas.2022620118", "pmid": "33479174", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2022620118"}, {"db": "pmc", "key": "PMC7848574"}], "notes": [], "created": "2021-06-09T12:16:45.953Z", "modified": "2024-01-16T13:48:40.922Z"}, {"entity": "publication", "iuid": "48f74c2afc0b4af8befb22016e4d7b0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48f74c2afc0b4af8befb22016e4d7b0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48f74c2afc0b4af8befb22016e4d7b0c"}}, "title": "Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.", "authors": [{"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Hottenga", "given": "Jouke- Jan", "initials": "JJ", "orcid": "0000-0002-5668-2368", "researcher": {"href": "https://publications.scilifelab.se/researcher/75553b594b1f4255833de730f7f7d170.json"}}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Perry", "given": "John R B", "initials": "JRB"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N", "orcid": "0000-0001-5424-2134", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f7af2cb2b7464abddf05692a292fc3.json"}}, {"family": "Marullo", "given": "Letizia", "initials": "L"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Jansen", "given": "Rick", "initials": "R", "orcid": "0000-0002-3333-6737", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcd392c9b9784ebe8c8730e05463377a.json"}}, {"family": "Min", "given": "Josine L", "initials": "JL", "orcid": "0000-0003-4456-9824", "researcher": {"href": "https://publications.scilifelab.se/researcher/5896cbc0cb8d427a954b194839adda52.json"}}, {"family": "Dimas", "given": "Antigone S", "initials": "AS"}, {"family": "Ulrich", "given": "Anna", "initials": "A"}, {"family": "Zudina", "given": "Liudmila", "initials": "L"}, {"family": "G\u00e5din", "given": "Jesper R", "initials": "JR"}, {"family": "Jiang", "given": "Longda", "initials": "L"}, {"family": "Faggian", "given": "Alessia", "initials": "A", "orcid": "0000-0002-3799-9722", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4f320f96474406c82fef88f1f78dd23.json"}}, {"family": "Bonnefond", "given": "Am\u00e9lie", "initials": "A", "orcid": "0000-0001-9976-3005", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea1984308c1544ba969d4df73971de69.json"}}, {"family": "Fadista", "given": "Joao", "initials": "J"}, {"family": "Stathopoulou", "given": "Maria G", "initials": "MG"}, {"family": "Isaacs", "given": "Aaron", "initials": "A", "orcid": "0000-0001-5037-4834", "researcher": {"href": "https://publications.scilifelab.se/researcher/38ebe49e62404f48bcb979d9671883e7.json"}}, {"family": "Willems", "given": "Sara M", "initials": "SM", "orcid": "0000-0002-6803-3007", "researcher": {"href": "https://publications.scilifelab.se/researcher/307c8a9b3ab54ab586c7b000c110e76b.json"}}, {"family": "Navarro", "given": "Pau", "initials": "P", "orcid": "0000-0001-5576-8584", "researcher": {"href": "https://publications.scilifelab.se/researcher/9420946aedec4a7b8925cc05c0a9abeb.json"}}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Jackson", "given": "Anne U", "initials": "AU", "orcid": "0000-0002-9672-2547", "researcher": {"href": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/19f5ce9936ca454c85f0af966acac5c0.json"}}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB", "orcid": "0000-0002-4176-2947", "researcher": {"href": "https://publications.scilifelab.se/researcher/657544a7f921459f926aae5cd0e2065c.json"}}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V", "orcid": "0000-0001-5696-0084", "researcher": {"href": "https://publications.scilifelab.se/researcher/d18327939c1541acba054b2340ac174f.json"}}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C", "orcid": "0000-0003-0075-6417", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6abf12d60c24032a1c2b315904b0721.json"}}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR", "orcid": "0000-0002-2149-0630", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7d00b649d284101b0501e2024fb651a.json"}}, {"family": "Stefansson", "given": "Kari", "initials": "K", "orcid": "0000-0003-1676-864X", "researcher": {"href": "https://publications.scilifelab.se/researcher/679465193fba4887a68e2aec34ccfd8e.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET", "orcid": "0000-0002-9302-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/3560d19929e94af1bb858a54e29a10cc.json"}}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM", "orcid": "0000-0002-4903-9374", "researcher": {"href": "https://publications.scilifelab.se/researcher/822d2f2a99814a7498f19976ed6381ef.json"}}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Froguel", "given": "Philippe", "initials": "P", "orcid": "0000-0003-2972-0784", "researcher": {"href": "https://publications.scilifelab.se/researcher/34edc6a0f1b343bb8a2abd439c2ee77f.json"}}, {"family": "Kaakinen", "given": "Marika A", "initials": "MA", "orcid": "0000-0002-9228-0462", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9f40717fdd4ce29b148bc569134451.json"}}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM", "orcid": "0000-0003-1015-0531", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4336f8845ac40dfb77ef0ea1a97bbd6.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J", "orcid": "0000-0003-2871-3603", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9edfafda7364890866115f5343a9583.json"}}, {"family": "Barroso", "given": "In\u00eas", "initials": "I", "orcid": "0000-0001-5800-4520", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2dc6be9aa194bdc9a161e551d5e6747.json"}}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)", "given": "", "initials": ""}], "type": "journal article", "published": "2021-01-05", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "24", "issn-l": "2041-1723"}, "abstract": "Differences between sexes contribute to variation in the levels of fasting glucose and insulin. Epidemiological studies established a higher prevalence of impaired fasting glucose in men and impaired glucose tolerance in women, however, the genetic component underlying this phenomenon is not established. We assess sex-dimorphic (73,089/50,404 women and 67,506/47,806 men) and sex-combined (151,188/105,056 individuals) fasting glucose/fasting insulin genetic effects via genome-wide association study meta-analyses in individuals of European descent without diabetes. Here we report sex dimorphism in allelic effects on fasting insulin at IRS1 and ZNF12 loci, the latter showing higher RNA expression in whole blood in women compared to men. We also observe sex-homogeneous effects on fasting glucose at seven novel loci. Fasting insulin in women shows stronger genetic correlations than in men with waist-to-hip ratio and anorexia nervosa. Furthermore, waist-to-hip ratio is causally related to insulin resistance in women, but not in men. These results position dissection of metabolic and glycemic health sex dimorphism as a steppingstone for understanding differences in genetic effects between women and men in related phenotypes.", "doi": "10.1038/s41467-020-19366-9", "pmid": "33402679", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19366-9"}, {"db": "pmc", "key": "PMC7785747"}], "notes": [], "created": "2021-01-08T16:30:26.062Z", "modified": "2021-11-10T12:27:48.827Z"}, {"entity": "publication", "iuid": "92dadee1d21d4a30a7666d6d1c9b5f54", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92dadee1d21d4a30a7666d6d1c9b5f54.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92dadee1d21d4a30a7666d6d1c9b5f54"}}, "title": "Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.", "authors": [{"family": "Khandagale", "given": "Avinash", "initials": "A"}, {"family": "Holmlund", "given": "Teresa", "initials": "T"}, {"family": "Entesarian", "given": "Miriam", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Kalwak", "given": "Krzysztof", "initials": "K"}, {"family": "Klaudel-Dreszler", "given": "Maja", "initials": "M"}, {"family": "Carlsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Henter", "given": "Jan-Inge", "initials": "JI"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Fadeel", "given": "Bengt", "initials": "B", "orcid": "0000-0001-5559-8482", "researcher": {"href": "https://publications.scilifelab.se/researcher/959b4accdbfe49158353b8cb12260d1b.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "volume": "192", "issue": "1", "pages": "200-211", "issn-l": "0007-1048"}, "abstract": "Severe congenital neutropenia (SCN) of autosomal recessive inheritance, also known as Kostmann disease, is characterised by a lack of neutrophils and a propensity for life-threatening infections. Using whole-exome sequencing, we identified homozygous JAGN1 mutations (p.Gly14Ser and p.Glu21Asp) in three patients with Kostmann-like SCN, thus confirming the recent attribution of JAGN1 mutations to SCN. Using the human promyelocytic cell line HL-60 as a model, we found that overexpression of patient-derived JAGN1 mutants, but not silencing of JAGN1, augmented cell death in response to the pro-apoptotic stimuli, etoposide, staurosporine, and thapsigargin. Furthermore, cells expressing mutant JAGN1 were remarkably susceptible to agonists that normally trigger degranulation and succumbed to a calcium-dependent cell death programme. This mode of cell death was completely prevented by pharmacological inhibition of calpain but unaffected by caspase inhibition. In conclusion, our results confirmed the association between JAGN1 mutations and SCN and showed that SCN-associated JAGN1 mutations unleash a calcium- and calpain-dependent cell death in myeloid cells.", "doi": "10.1111/bjh.17137", "pmid": "33206996", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7839451"}], "notes": [], "created": "2020-12-07T16:34:42.651Z", "modified": "2024-01-16T13:48:41.002Z"}, {"entity": "publication", "iuid": "9f8b33bd6320451d949e1d5d6500a865", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f8b33bd6320451d949e1d5d6500a865.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f8b33bd6320451d949e1d5d6500a865"}}, "title": "Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK", "orcid": "0000-0002-6304-9827", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ef542c596b64379941d3984dd73de63.json"}}, {"family": "Xu", "given": "Luohao", "initials": "L", "orcid": "0000-0002-3714-8047", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7a6a94d73cf4c50a22734e2a54099ba.json"}}, {"family": "Burri", "given": "Reto", "initials": "R"}, {"family": "Sullivan", "given": "Shawn", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Liachko", "given": "Ivan", "initials": "I"}, {"family": "Haryoko", "given": "Tri", "initials": "T"}, {"family": "J\u00f8nsson", "given": "Knud A", "initials": "KA"}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "volume": "21", "issue": "1", "pages": "263-286", "issn-l": "1755-098X"}, "abstract": "Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic \"dark matter\") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.", "doi": "10.1111/1755-0998.13252", "pmid": "32937018", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7757076"}], "notes": [], "created": "2020-10-13T18:30:03.195Z", "modified": "2024-01-16T13:48:41.036Z"}, {"entity": "publication", "iuid": "e78358779455418ba9c1128f301841ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e78358779455418ba9c1128f301841ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e78358779455418ba9c1128f301841ef"}}, "title": "Human population dynamics and Yersinia pestis in ancient northeast Asia.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef101ca28384bfabb088e7c87d0749e.json"}}, {"family": "D\u00f6nerta\u015f", "given": "Handan Melike", "initials": "HM", "orcid": "0000-0002-9788-6535", "researcher": {"href": "https://publications.scilifelab.se/researcher/99f355027fbd4691af8a17e78f1554f8.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Shergin", "given": "Dmitrij", "initials": "D"}, {"family": "Ivanov", "given": "Grigorij", "initials": "G", "orcid": "0000-0003-4316-7372", "researcher": {"href": "https://publications.scilifelab.se/researcher/f098ecc1f60d44e185f590c7f3b98a3d.json"}}, {"family": "Kichigin", "given": "Dmitrii", "initials": "D", "orcid": "0000-0003-3382-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fbe657eebfa460eb6eabd47c6f55384.json"}}, {"family": "Pestereva", "given": "Kjunnej", "initials": "K", "orcid": "0000-0001-6270-1230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c267495499114556b837c66845be6247.json"}}, {"family": "Volkov", "given": "Denis", "initials": "D", "orcid": "0000-0001-6064-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ce5ce75417640b4b778687b0dbd94a8.json"}}, {"family": "Mandryka", "given": "Pavel", "initials": "P", "orcid": "0000-0002-8647-3823", "researcher": {"href": "https://publications.scilifelab.se/researcher/5832247ccd844904b4421f7c89836815.json"}}, {"family": "Kharinskii", "given": "Artur", "initials": "A", "orcid": "0000-0002-4815-6069", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d0f94fca6d4c2388c64486891d28a4.json"}}, {"family": "Tishkin", "given": "Alexey", "initials": "A", "orcid": "0000-0002-7769-136X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff988500a4ec4fddb2b3f79b95127f77.json"}}, {"family": "Ineshin", "given": "Evgenij", "initials": "E"}, {"family": "Kovychev", "given": "Evgeniy", "initials": "E"}, {"family": "Stepanov", "given": "Aleksandr", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "2", "issn-l": "2375-2548"}, "abstract": "We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.", "doi": "10.1126/sciadv.abc4587", "pmid": "33523963", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/2/eabc4587"}, {"db": "pmc", "key": "PMC7787494"}], "notes": [], "created": "2021-06-09T12:15:48.048Z", "modified": "2024-01-16T13:48:41.043Z"}, {"entity": "publication", "iuid": "0dea1340046c4f0899f4a899263d1d0d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0dea1340046c4f0899f4a899263d1d0d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0dea1340046c4f0899f4a899263d1d0d"}}, "title": "Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.", "authors": [{"family": "N\u00e4svall", "given": "Karin", "initials": "K", "orcid": "0000-0002-2970-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/9173164aadbe47b0b4132d2c6e654cf3.json"}}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Mrazek", "given": "Veronika", "initials": "V"}, {"family": "K\u00fcnstner", "given": "Axel", "initials": "A"}, {"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Busch", "given": "Hauke", "initials": "H"}, {"family": "Vila", "given": "Roger", "initials": "R", "orcid": "0000-0002-2447-4388", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f9f7ce050d463bb9a67d6970b9428a.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "2", "pages": "499-516", "issn-l": "0962-1083"}, "abstract": "In a time with decreasing biodiversity, especially among insects, a detailed understanding about specific resource utilization strategies is crucial. The physiological and behavioural responses to host switches in phytophagous insects are poorly understood. Earlier studies indicate that a host plant switch might be associated with distinctive molecular and physiological responses in different lineages. Expanding the assessment of such associations across Lepidoptera will reveal if there are general patterns in adaptive responses, or if each switch event is more of a unique character. We investigated host plant preference, fitness consequences, effects on expression profiles and gut microbiome composition in two common wood white (Leptidea sinapis) populations with different host plant preferences from the extremes of the species distribution area (Sweden and Catalonia). Our results show that female Catalonian wood whites lack preference for either host plant (Lotus corniculatus or L. dorycnium), while Swedish females laid significantly more eggs on L. corniculatus. Individuals from both populations reared on L. dorycnium had longer developmental times and smaller body size as adults. This indicates that both environmental and genetic factors determine the choice to use a specific host plant. Gene expression analysis revealed a more pronounced response to host plant in the Catalonian compared to the Swedish population. In addition, host plant treatment resulted in a significant shift in microbiome community structure in the Catalonian population. Together, this suggests that population specific plasticity associated with local conditions underlies host plant utilisation in wood whites.", "doi": "10.1111/mec.15745", "pmid": "33219534", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7839524"}], "notes": [], "created": "2020-12-07T16:36:48.071Z", "modified": "2024-01-16T13:48:41.052Z"}, {"entity": "publication", "iuid": "a8c3d4fd270e400c9d3da9c6d8a6df9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8c3d4fd270e400c9d3da9c6d8a6df9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8c3d4fd270e400c9d3da9c6d8a6df9d"}}, "title": "Evaluating totipotency using criteria of increasing stringency.", "authors": [{"family": "Posfai", "given": "Eszter", "initials": "E", "orcid": "0000-0002-4871-6652", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e48e0d903c6461c80862a1ba7f93bc9.json"}}, {"family": "Schell", "given": "John Paul", "initials": "JP"}, {"family": "Janiszewski", "given": "Adrian", "initials": "A"}, {"family": "Rovic", "given": "Isidora", "initials": "I"}, {"family": "Murray", "given": "Alexander", "initials": "A"}, {"family": "Bradshaw", "given": "Brian", "initials": "B"}, {"family": "Yamakawa", "given": "Tatsuya", "initials": "T"}, {"family": "Pardon", "given": "Tine", "initials": "T"}, {"family": "El Bakkali", "given": "Mouna", "initials": "M"}, {"family": "Talon", "given": "Irene", "initials": "I"}, {"family": "De Geest", "given": "Natalie", "initials": "N"}, {"family": "Kumar", "given": "Pankaj", "initials": "P", "orcid": "0000-0002-8411-1634", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e9109710e2e45009c332e257c3c498a.json"}}, {"family": "To", "given": "San Kit", "initials": "SK", "orcid": "0000-0002-3057-2902", "researcher": {"href": "https://publications.scilifelab.se/researcher/844ba6692612452cb0d28ab1b3cbcfa4.json"}}, {"family": "Petropoulos", "given": "Sophie", "initials": "S"}, {"family": "Jurisicova", "given": "Andrea", "initials": "A"}, {"family": "Pasque", "given": "Vincent", "initials": "V", "orcid": "0000-0002-5129-0146", "researcher": {"href": "https://publications.scilifelab.se/researcher/78a401cc80624c45bd38f643dd36797b.json"}}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}, {"family": "Rossant", "given": "Janet", "initials": "J", "orcid": "0000-0002-3731-5466", "researcher": {"href": "https://publications.scilifelab.se/researcher/be15218445df4636ab47e1a1dcf8d69c.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Nat Cell Biol", "issn": "1476-4679", "volume": "23", "issue": "1", "pages": "49-60", "issn-l": null}, "abstract": "Totipotency is the ability of a single cell to give rise to all of the differentiated cell types that build the conceptus, yet how to capture this property in vitro remains incompletely understood. Defining totipotency relies on a variety of assays of variable stringency. Here, we describe criteria to define totipotency. We explain how distinct criteria of increasing stringency can be used to judge totipotency by evaluating candidate totipotent cell types in mice, including early blastomeres and expanded or extended pluripotent stem cells. Our data challenge the notion that expanded or extended pluripotent states harbour increased totipotent potential relative to conventional embryonic stem cells under in vitro and in vivo conditions.", "doi": "10.1038/s41556-020-00609-2", "pmid": "33420491", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41556-020-00609-2"}], "notes": [], "created": "2021-06-09T12:16:20.850Z", "modified": "2024-01-16T13:48:41.059Z"}, {"entity": "publication", "iuid": "1cffa41cd92b4f0aad44c320905ffe52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1cffa41cd92b4f0aad44c320905ffe52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1cffa41cd92b4f0aad44c320905ffe52"}}, "title": "Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing.", "authors": [{"family": "Morarach", "given": "Khomgrit", "initials": "K"}, {"family": "Mikhailova", "given": "Anastassia", "initials": "A"}, {"family": "Knoflach", "given": "Viktoria", "initials": "V"}, {"family": "Memic", "given": "Fatima", "initials": "F", "orcid": "0000-0002-8876-1212", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5dcdcbf16f4caab9cea24133389afb.json"}}, {"family": "Kumar", "given": "Rakesh", "initials": "R"}, {"family": "Li", "given": "Wei", "initials": "W"}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}, {"family": "Marklund", "given": "Ulrika", "initials": "U", "orcid": "0000-0003-1426-1271", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f82ee40ccd49adbbb72d2994df6cb9.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "issn-l": "1097-6256", "volume": "24", "issue": "1", "pages": "34-46"}, "abstract": "Autonomous regulation of the intestine requires the combined activity of functionally distinct neurons of the enteric nervous system (ENS). However, the variety of enteric neuron types and how they emerge during development remain largely unknown. Here, we define a molecular taxonomy of 12 enteric neuron classes within the myenteric plexus of the mouse small intestine using single-cell RNA sequencing. We present cell-cell communication features and histochemical markers for motor neurons, sensory neurons and interneurons, together with transgenic tools for class-specific targeting. Transcriptome analysis of the embryonic ENS uncovers a novel principle of neuronal diversification, where two neuron classes arise through a binary neurogenic branching and all other identities emerge through subsequent postmitotic differentiation. We identify generic and class-specific transcriptional regulators and functionally connect Pbx3 to a postmitotic fate transition. Our results offer a conceptual and molecular resource for dissecting ENS circuits and predicting key regulators for directed differentiation of distinct enteric neuron classes.", "doi": "10.1038/s41593-020-00736-x", "pmid": "33288908", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-020-00736-x"}, {"db": "pmc", "key": "PMC7610403"}, {"db": "mid", "key": "EMS118468"}], "notes": [], "created": "2020-12-10T11:10:40.536Z", "modified": "2024-01-16T13:48:41.067Z"}, {"entity": "publication", "iuid": "08437ea506ac46a5ac92c90dc3eb5eb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08437ea506ac46a5ac92c90dc3eb5eb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08437ea506ac46a5ac92c90dc3eb5eb7"}}, "title": "Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.", "authors": [{"family": "Barnett", "given": "Ross", "initials": "R"}, {"family": "Westbury", "given": "Michael V", "initials": "MV"}, {"family": "Sandoval-Velasco", "given": "Marcela", "initials": "M"}, {"family": "Vieira", "given": "Filipe Garrett", "initials": "FG"}, {"family": "Jeon", "given": "Sungwon", "initials": "S"}, {"family": "Zazula", "given": "Grant", "initials": "G"}, {"family": "Martin", "given": "Michael D", "initials": "MD"}, {"family": "Ho", "given": "Simon Y W", "initials": "SYW"}, {"family": "Mather", "given": "Niklas", "initials": "N"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Ramos-Madrigal", "given": "Jazm\u00edn", "initials": "J"}, {"family": "de Manuel", "given": "Marc", "initials": "M"}, {"family": "Zepeda-Mendoza", "given": "M Lisandra", "initials": "ML"}, {"family": "Antunes", "given": "Agostinho", "initials": "A"}, {"family": "Baez", "given": "Aldo Carmona", "initials": "AC"}, {"family": "De Cahsan", "given": "Binia", "initials": "B"}, {"family": "Larson", "given": "Greger", "initials": "G"}, {"family": "O'Brien", "given": "Stephen J", "initials": "SJ"}, {"family": "Eizirik", "given": "Eduardo", "initials": "E"}, {"family": "Johnson", "given": "Warren E", "initials": "WE"}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "KP", "orcid": "0000-0001-7281-0676", "researcher": {"href": "https://publications.scilifelab.se/researcher/178cb44eedd74528a956ad645fe3aa16.json"}}, {"family": "Wilting", "given": "Andreas", "initials": "A"}, {"family": "Fickel", "given": "J\u00f6rns", "initials": "J"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Hansen", "given": "Anders J", "initials": "AJ"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Bhak", "given": "Jong", "initials": "J"}, {"family": "Yamaguchi", "given": "Nobuyuki", "initials": "N"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2020-12-21", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "30", "issue": "24", "pages": "5018-5025.e5", "issn-l": "0960-9822"}, "abstract": "Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a \u223c7x nuclear genome and a \u223c38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (\u223c22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.", "doi": "10.1016/j.cub.2020.09.051", "pmid": "33065008", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(20)31421-4"}, {"db": "pmc", "key": "PMC7762822"}], "notes": [], "created": "2020-12-07T16:36:46.792Z", "modified": "2023-06-19T11:45:34.625Z"}, {"entity": "publication", "iuid": "7c65da05f8c44cc08507b044f77cc22e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c65da05f8c44cc08507b044f77cc22e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c65da05f8c44cc08507b044f77cc22e"}}, "title": "Moose genomes reveal past glacial demography and the origin of modern lineages.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "Heino", "given": "Matti T", "initials": "MT"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Ryman", "given": "Nils", "initials": "N"}, {"family": "Laikre", "given": "Linda", "initials": "L"}, {"family": "Ahlgren", "given": "Hans", "initials": "H"}, {"family": "Askeyev", "given": "Igor V", "initials": "IV"}, {"family": "Askeyev", "given": "Oleg V", "initials": "OV"}, {"family": "Shaymuratova", "given": "Dilyara N", "initials": "DN"}, {"family": "Askeyev", "given": "Arthur O", "initials": "AO"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Friedrich", "given": "Ronny", "initials": "R"}, {"family": "Lindauer", "given": "Susanne", "initials": "S"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Aspi", "given": "Jouni", "initials": "J"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}], "type": "journal article", "published": "2020-12-02", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "21", "issue": "1", "pages": "854"}, "abstract": "Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.\r\n\r\nWe found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.\r\n\r\nTaken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.", "doi": "10.1186/s12864-020-07208-3", "pmid": "33267779", "labels": {"NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07208-3"}, {"db": "pmc", "key": "PMC7709250"}], "notes": [], "created": "2020-12-07T16:36:41.615Z", "modified": "2023-09-07T14:58:17.282Z"}, {"entity": "publication", "iuid": "1ad131dd022d484f84ca9b9dcb288a09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ad131dd022d484f84ca9b9dcb288a09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ad131dd022d484f84ca9b9dcb288a09"}}, "title": "Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.", "authors": [{"family": "Nilsson", "given": "Hel\u00e9n", "initials": "H"}, {"family": "Lindgren", "given": "David", "initials": "D"}, {"family": "Axelson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Brueffer", "given": "Christian", "initials": "C", "orcid": "0000-0002-3826-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf6758bd7a54626bdf3b82888431296.json"}}, {"family": "Saal", "given": "Lao H", "initials": "LH"}, {"family": "Lundgren", "given": "Jaana", "initials": "J"}, {"family": "Johansson", "given": "Martin E", "initials": "ME", "orcid": "0000-0001-8510-3102", "researcher": {"href": "https://publications.scilifelab.se/researcher/b85588d272854ff2a9d6c4e364529971.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "J. Pathol.", "issn": "1096-9896", "issn-l": "0022-3417", "volume": "252", "issue": "4", "pages": "384-397"}, "abstract": "Clear cell renal cell carcinoma (ccRCC) is the most common form of renal cancer. Due to inactivation of the von Hippel-Lindau tumour suppressor, the hypoxia-inducible transcription factors (HIFs) are constitutively activated in these tumours, resulting in a pseudo-hypoxic phenotype. The HIFs induce the expression of genes involved in angiogenesis and cell survival, but they also reset the cellular metabolism to protect cells from oxygen and nutrient deprivation. ccRCC tumours are highly vascularized and the cytoplasm of the cancer cells is filled with lipid droplets and glycogen, resulting in the histologically distinctive pale (clear) cytoplasm. Intratumoural heterogeneity may occur, and in some tumours, areas with granular, eosinophilic cytoplasm are found. Little is known regarding these traits and how they relate to the coexistent clear cell component, yet eosinophilic ccRCC is associated with higher grade and clinically more aggressive tumours. In this study, we have for the first time performed RNA sequencing comparing histologically verified clear cell and eosinophilic areas from ccRCC tissue, aiming to analyse the characteristics of these cell types. Findings from RNA sequencing were confirmed by immunohistochemical staining of biphasic ccRCC. We found that the eosinophilic phenotype displayed a higher proliferative drive and lower differentiation, and we confirmed a correlation to tumours of higher stage. We further identified mutations of the tumour suppressor p53 (TP53) exclusively in the eosinophilic ccRCC component, where mTORC1 activity was also elevated. Also, eosinophilic areas were less vascularized, yet harboured more abundant infiltrating immune cells. The cytoplasm of clear cell ccRCC cells was filled with lipids but had very low mitochondrial content, while the reverse was found in eosinophilic tissue. We herein suggest possible transcriptional mechanisms behind these phenomena. \u00a9 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.", "doi": "10.1002/path.5532", "pmid": "32815150", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7756750"}], "notes": [], "created": "2020-12-07T16:32:32.781Z", "modified": "2024-01-16T13:48:41.254Z"}, {"entity": "publication", "iuid": "3c2e6b91baaf43ae9efca4b999d27a81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c2e6b91baaf43ae9efca4b999d27a81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c2e6b91baaf43ae9efca4b999d27a81"}}, "title": "Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Kalyandurg", "given": "Pruthvi B", "initials": "PB"}, {"family": "Saripella", "given": "Ganapathi Varma", "initials": "GV"}, {"family": "Sen", "given": "Diya", "initials": "D"}, {"family": "Gil", "given": "Jose Fernando", "initials": "JF"}, {"family": "Lukhovitskaya", "given": "Nina I", "initials": "NI"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Savenkov", "given": "Eugene I", "initials": "EI", "orcid": "0000-0002-5802-5089", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e4c252bb7ec444c935c0aae5387df53.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Arch Virol", "issn": "1432-8798", "volume": "165", "issue": "12", "pages": "2953-2959", "issn-l": null}, "abstract": "Chrysanthemum virus B encodes a multifunctional p12 protein that acts as a transcriptional activator in the nucleus and as a suppressor of RNA silencing in the cytoplasm. Here, we investigated the impact of p12 on accumulation of major classes of small RNAs (sRNAs). The results show dramatic changes in the sRNA profiles characterised by an overall reduction in sRNA accumulation, changes in the pattern of size distribution of canonical siRNAs and in the ratio between sense and antisense strands, lower abundance of siRNAs with a U residue at the 5'-terminus, and changes in the expression of certain miRNAs, most of which were downregulated.", "doi": "10.1007/s00705-020-04832-y", "pmid": "33040310", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00705-020-04832-y"}, {"db": "pmc", "key": "PMC7588395"}], "notes": [], "created": "2020-12-07T16:32:30.292Z", "modified": "2021-11-10T12:44:41.396Z"}, {"entity": "publication", "iuid": "673a6b733f014264bc7e01ea2db87556", "links": {"self": {"href": "https://publications.scilifelab.se/publication/673a6b733f014264bc7e01ea2db87556.json"}, "display": {"href": "https://publications.scilifelab.se/publication/673a6b733f014264bc7e01ea2db87556"}}, "title": "Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.", "authors": [{"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS", "orcid": "0000-0003-2498-5206", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0df178b81f149f48f3533bae976c511.json"}}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Lei", "given": "Jiayao", "initials": "J", "orcid": "0000-0002-4718-1414", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea2b0586a048449880a0843ef29a04c0.json"}}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Nordqvist Kleppe", "given": "Sara", "initials": "S"}, {"family": "Spar\u00e9n", "given": "P\u00e4r", "initials": "P", "orcid": "0000-0002-5184-8971", "researcher": {"href": "https://publications.scilifelab.se/researcher/48e73c79f3a24128b82c5a71616e3659.json"}}, {"family": "Sundstr\u00f6m", "given": "Karin", "initials": "K", "orcid": "0000-0002-6865-0224", "researcher": {"href": "https://publications.scilifelab.se/researcher/d037c005ee2c431fae353340f5589e20.json"}}, {"family": "Dillner", "given": "Joakim", "initials": "J", "orcid": "0000-0001-8588-6506", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b5c258635ad412f9e79994dcee4e323.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Br. J. Cancer", "issn": "1532-1827", "volume": "123", "issue": "12", "pages": "1790-1795", "issn-l": "0007-0920"}, "abstract": "Human papillomavirus (HPV) is a necessary cause of cervical cancer, although some invasive cervical cancers may test negative by HPV PCR. We previously requested all invasive cervical cancers in Sweden during 10 years and subjected them to PCR. We also optimised methods for deep sequencing of formalin-fixed paraffin-embedded samples.\n\nUsing Novaseq 6000, we simultaneously sequenced total DNA and cDNA from 392 HPV PCR-negative cervical cancers. Non-human reads were queried against all known HPVs. The complete database now contains PCR and/or deep sequencing data on 2850 invasive cervical cancers.\n\nHPV sequences were detected in 169/392 of HPV PCR-negative cervical cancers. Overall, 30 different HPV types were detected, but only 5 types were present in proportions above 3% of cancers. More than 92% of tumours were HPV-positive in PCR and/or sequencing (95% confidence interval: 91.1-93.1%). Exploring possible reasons for failure to previously detect HPV suggest that more sensitive type-specific PCRs for HPV 31, 33, 45 and 73 targeting retained regions of HPV would have detected most of these (117/392).\n\nUnbiased deep sequencing provides comprehensive data on HPV types in cervical cancers and appears to be an important tool for quality assurance of HPV screening.", "doi": "10.1038/s41416-020-01111-0", "pmid": "33020595", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41416-020-01111-0"}, {"db": "pmc", "key": "PMC7722749"}], "notes": [], "created": "2020-12-07T16:29:00.388Z", "modified": "2021-11-10T12:46:34.772Z"}, {"entity": "publication", "iuid": "3e21cc6163c14d55a5a03727b870e2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1"}}, "title": "Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.", "authors": [{"family": "Feuerborn", "given": "Tatiana R", "initials": "TR"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2020-11-30", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "844", "issn-l": "1471-2164"}, "abstract": "After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.\n\nHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.\n\nWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.", "doi": "10.1186/s12864-020-07229-y", "pmid": "33256612", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07229-y"}, {"db": "pmc", "key": "PMC7708127"}], "notes": [], "created": "2020-12-07T16:36:42.754Z", "modified": "2024-01-16T13:48:41.282Z"}, {"entity": "publication", "iuid": "0524f50dac7c4bf185787279724e5644", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0524f50dac7c4bf185787279724e5644.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0524f50dac7c4bf185787279724e5644"}}, "title": "Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions.", "authors": [{"family": "Sousa", "given": "Jo\u00e3o A B", "initials": "JAB"}, {"family": "Bolg\u00e1r", "given": "Andrea", "initials": "A"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}, {"family": "Bijmans", "given": "Martijn F M", "initials": "MFM"}, {"family": "Stams", "given": "Alfons J M", "initials": "AJM"}, {"family": "Plugge", "given": "Caroline M", "initials": "CM", "orcid": "0000-0002-3391-7742", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec1ba6106ef140598f83f1c73ec2b285.json"}}], "type": "journal article", "published": "2020-11-25", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "745", "issue": null, "pages": "141017", "issn-l": "0048-9697"}, "abstract": "Biological sulfate and thiosulfate reduction under haloalkaline conditions can be applied to treat waste streams from biodesulfurization systems. However, the lack of microbial aggregation under haloalkaline conditions limits the volumetric rates of sulfate and thiosulfate reducing bioreactors. As biomass retention in haloalkaline bioreactors has not been studied before, sand was chosen as a biomass carrier material to increase cell retention and consequently raise the volumetric rates. The results showed that ~10 fold higher biomass concentrations could be achieved with sand, compared to previous studies without carrier addition. The volumetric rates of sulfate/thiosulfate reduction increased approximately 4.5 times. Biomass attachment to the sand was restricted to cavities within the sand particles. Acetate produced by acetogenic bacteria from H2 and CO2 was used as carbon source for biomass growth, while formate that was also produced from H2 and CO2 enhanced sulfate reduction. The microbial community composition was analyzed by 16S rRNA gene amplicon sequencing, and Tindallia related bacteria were probably responsible for formate formation from hydrogen. The community attached to the sand particles was similar to the suspended fraction, but the relative abundance of sequences most closely related to Desulfohalobiaceae was much higher in the attached fraction compared to the suspended fraction (30% and 13%, respectively). The results indicated that even though the biomass attachment to sand was poor, it still increased the biomass concentration and consequently the sulfate and thiosulfate reduction volumetric rates.", "doi": "10.1016/j.scitotenv.2020.141017", "pmid": "32736107", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(20)34546-0"}], "notes": [], "created": "2020-12-07T16:29:56.594Z", "modified": "2021-11-10T12:45:01.994Z"}, {"entity": "publication", "iuid": "aac256774d0444cdbb512faa4cd1b346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aac256774d0444cdbb512faa4cd1b346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aac256774d0444cdbb512faa4cd1b346"}}, "title": "Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.", "authors": [{"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Hod\u00e9n", "given": "Kristian Persson", "initials": "KP"}, {"family": "Singh", "given": "Ravi Kumar", "initials": "RK"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2020-11-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "20577", "issn-l": "2045-2322"}, "abstract": "Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.", "doi": "10.1038/s41598-020-77593-y", "pmid": "33239724", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-77593-y"}, {"db": "pmc", "key": "PMC7689493"}], "notes": [], "created": "2020-12-07T16:36:39.190Z", "modified": "2021-11-10T12:45:03.177Z"}, {"entity": "publication", "iuid": "5c901b5af4f94bdf82bd969d255f0767", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c901b5af4f94bdf82bd969d255f0767.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c901b5af4f94bdf82bd969d255f0767"}}, "title": "Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury", "authors": [{"family": "Floriddia", "given": "Elisa M", "initials": "EM", "orcid": "0000-0003-2304-8114", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea55e5ce2b74a799fbcce59b53e62ac.json"}}, {"family": "Louren\u00e7o", "given": "T\u00e2nia", "initials": "T"}, {"family": "Zhang", "given": "Shupei", "initials": "S"}, {"family": "van Bruggen", "given": "David", "initials": "D", "orcid": "0000-0001-6794-7731", "researcher": {"href": "https://publications.scilifelab.se/researcher/d613135b6ba740c59062e3e7e4fd8174.json"}}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Kukanja", "given": "Petra", "initials": "P", "orcid": "0000-0003-1228-5923", "researcher": {"href": "https://publications.scilifelab.se/researcher/082ef6e681214c14b8ca36cd0188722b.json"}}, {"family": "Gon\u00e7alves dos Santos", "given": "Jo\u00e3o P", "initials": "JP"}, {"family": "Alt\u0131nk\u00f6k", "given": "M\u00fcge", "initials": "M"}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Llorens-Bobadilla", "given": "Enric", "initials": "E", "orcid": "0000-0002-7891-1272", "researcher": {"href": "https://publications.scilifelab.se/researcher/3144601c466246cfa70acbe8c7ee00ee.json"}}, {"family": "Mulinyawe", "given": "Sara B", "initials": "SB"}, {"family": "Gr\u00e3os", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-2707-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/86454440d6754732b4d8f813d399a9ed.json"}}, {"family": "Sun", "given": "Lu O", "initials": "LO", "orcid": "0000-0002-9293-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfd19d5fc054ae1a0e6c0c6f286daca.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}], "type": "journal-article", "published": "2020-11-17", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "11", "issue": "1", "pages": "5860"}, "abstract": "Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.", "doi": "10.1038/s41467-020-19453-x", "pmid": "33203872", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support for Computational Resources": "Service", "In Situ Sequencing": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7673029"}, {"db": "pii", "key": "10.1038/s41467-020-19453-x"}], "notes": [], "created": "2020-12-07T16:36:40.432Z", "modified": "2025-10-17T13:02:18.056Z"}, {"entity": "publication", "iuid": "4eaba3d139bf427eb332f2f93f77bf0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4eaba3d139bf427eb332f2f93f77bf0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4eaba3d139bf427eb332f2f93f77bf0a"}}, "title": "Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.", "authors": [{"family": "Calleja-Rodriguez", "given": "Ainhoa", "initials": "A"}, {"family": "Pan", "given": "Jin", "initials": "J"}, {"family": "Funda", "given": "Tomas", "initials": "T"}, {"family": "Chen", "given": "Zhiqiang", "initials": "Z"}, {"family": "Baison", "given": "John", "initials": "J"}, {"family": "Isik", "given": "Fikret", "initials": "F"}, {"family": "Abrahamsson", "given": "Sara", "initials": "S"}, {"family": "Wu", "given": "Harry X", "initials": "HX"}], "type": "journal article", "published": "2020-11-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "796", "issn-l": "1471-2164"}, "abstract": "Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers.\n\nGenomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection.\n\nAlthough prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.", "doi": "10.1186/s12864-020-07188-4", "pmid": "33198692", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07188-4"}, {"db": "pmc", "key": "PMC7667760"}], "notes": [], "created": "2020-12-08T23:32:05.662Z", "modified": "2024-01-16T13:48:41.324Z"}, {"entity": "publication", "iuid": "38f9cf370fca43aea73e0146f2e1a8e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/38f9cf370fca43aea73e0146f2e1a8e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/38f9cf370fca43aea73e0146f2e1a8e6"}}, "title": "Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.", "authors": [{"family": "Mahmud", "given": "A K M Firoj", "initials": "AKMF"}, {"family": "Nilsson", "given": "Kristina", "initials": "K"}, {"family": "Fahlgren", "given": "Anna", "initials": "A"}, {"family": "Navais", "given": "Roberto", "initials": "R"}, {"family": "Choudhury", "given": "Rajdeep", "initials": "R"}, {"family": "Avican", "given": "Kemal", "initials": "K"}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}], "type": "journal article", "published": "2020-11-10", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "5", "issue": "6", "pages": null, "issn-l": "2379-5077"}, "abstract": "RpoN, an alternative sigma factor commonly known as \u03c354, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN binding motif located at 103 inter- and intragenic sites on both sense and antisense strands. Deletion of rpoN had a large impact on gene expression, including downregulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. Matching differential gene expression with locations of the binding sites implicated around 130 genes or operons potentially activated or repressed by RpoN. Mutagenesis of selected intergenic binding sites confirmed both positive and negative regulatory effects of RpoN binding. Corresponding mutations of intragenic sense sites had less impact on associated gene expression. Surprisingly, mutating intragenic sites on the antisense strand commonly reduced expression of genes carried by the corresponding sense strand.IMPORTANCE The alternative sigma factor RpoN (\u03c354), which is widely distributed in eubacteria, has been implicated in controlling gene expression of importance for numerous functions including virulence. Proper responses to host environments are crucial for bacteria to establish infection, and regulatory mechanisms involved are therefore of high interest for development of future therapeutics. Little is known about the function of RpoN in the intestinal pathogen Y. pseudotuberculosis, and we therefore investigated its regulatory role in this pathogen. This regulator was indeed found to be critical for establishment of infection in mice, likely involving its requirement for motility and biofilm formation. The RpoN regulon involved both activating and suppressive effects on gene expression which could be confirmed with mutagenesis of identified binding sites. This is the first study of its kind of RpoN in Y. pseudotuberculosis, revealing complex regulation of gene expression involving both productive and silent effects of its binding to DNA, providing important information about RpoN regulation in enterobacteria.", "doi": "10.1128/mSystems.01006-20", "pmid": "33172972", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5/6/e01006-20"}, {"db": "pmc", "key": "PMC7657599"}], "notes": [], "created": "2020-11-21T09:21:23.391Z", "modified": "2024-01-16T13:48:41.377Z"}, {"entity": "publication", "iuid": "8278837d4b3745bab6470962fe1dc162", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8278837d4b3745bab6470962fe1dc162.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8278837d4b3745bab6470962fe1dc162"}}, "title": "Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.", "authors": [{"family": "Truv\u00e9", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2449-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c36d2ff5111435aa23416cdfc359b2d.json"}}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Vizlin-Hodzic", "given": "Dzeneta", "initials": "D", "orcid": "0000-0002-9696-7982", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a86a4c8b32a4af8a90240d44504b32b.json"}}, {"family": "Salmela", "given": "Susanne", "initials": "S"}, {"family": "Berger", "given": "Evelin", "initials": "E"}, {"family": "\u00c5gren", "given": "Hans", "initials": "H", "orcid": "0000-0003-0847-6700", "researcher": {"href": "https://publications.scilifelab.se/researcher/51b06f6b0b8d48fcabe31e6eaf1a08ce.json"}}, {"family": "Funa", "given": "Keiko", "initials": "K"}], "type": "journal article", "published": "2020-11-09", "journal": {"title": "Transl Psychiatry", "issn": "2158-3188", "issn-l": "2158-3188", "volume": "10", "issue": "1", "pages": "390"}, "abstract": "Identification of causative genetic variants leading to the development of bipolar disorder (BD) could result in genetic tests that would facilitate diagnosis. A better understanding of affected genes and pathways is also necessary for targeting of genes that may improve treatment strategies. To date several susceptibility genes have been reported from genome-wide association studies (GWAS), but little is known about specific variants that affect disease development. Here, we performed quantitative proteomics and whole-genome sequencing (WGS). Quantitative proteomics revealed NLRP2 as the most significantly up-regulated protein in neural stem cells and mature neural cells obtained from BD-patient cell samples. These results are in concordance with our previously published transcriptome analysis. Furthermore, the levels of FEZ2 and CADM2 proteins were also significantly differentially expressed in BD compared to control derived cells. The levels of FEZ2 were significantly downregulated in neural stem cells (NSC) while CADM2 was significantly up-regulated in mature neuronal cell culture. Promising novel candidate mutations were identified in the ANK3, NEK3, NEK7, TUBB, ANKRD1, and BRD2 genes. A literature search of candidate variants and deregulated proteins revealed that there are several connections to microtubule function for the molecules putatively involved. Microtubule function in neurons is critical for axon structure and axonal transport. A functional dynamic microtubule is also needed for an advocate response to cellular and environmental stress. If microtubule dynamics is compromised by mutations, it could be followed by deregulated expression forming a possible explanation for the inherited vulnerability to stressful life events that have been proposed to trigger mood episodes in BD patients.", "doi": "10.1038/s41398-020-01056-1", "pmid": "33168801", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41398-020-01056-1"}, {"db": "pmc", "key": "PMC7652854"}], "notes": [], "created": "2020-12-07T16:38:26.771Z", "modified": "2024-01-16T13:48:41.392Z"}, {"entity": "publication", "iuid": "5c4e7cd6c6ad47f5bd1054cafd7408a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c4e7cd6c6ad47f5bd1054cafd7408a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c4e7cd6c6ad47f5bd1054cafd7408a0"}}, "title": "Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the \"PI-POC\" Trial.", "authors": [{"family": "Gaudenzi", "given": "Giulia", "initials": "G", "orcid": "0000-0003-4923-6965", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba29165719cb46eba1a62c4c3e9cb232.json"}}, {"family": "Kumbakumba", "given": "Elias", "initials": "E", "orcid": "0000-0001-7206-0609", "researcher": {"href": "https://publications.scilifelab.se/researcher/8395ba3e303747e4ba9cb03c2ce8ef2c.json"}}, {"family": "Rasti", "given": "Reza", "initials": "R", "orcid": "0000-0001-7816-8338", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e28ed799ee044f89513d9bd672e64d9.json"}}, {"family": "Nanjebe", "given": "Deborah", "initials": "D", "orcid": "0000-0002-5440-7100", "researcher": {"href": "https://publications.scilifelab.se/researcher/e436dca4c9844756b2b13205a106296b.json"}}, {"family": "R\u00e9u", "given": "Pedro", "initials": "P", "orcid": "0000-0001-7454-7189", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6e427a91df4b13b68be281692efc68.json"}}, {"family": "Nyehangane", "given": "Dan", "initials": "D", "orcid": "0000-0002-1898-4162", "researcher": {"href": "https://publications.scilifelab.se/researcher/91b877a3dd1a42828a6133484ef66865.json"}}, {"family": "M\u00e5rtensson", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7504-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a064d85bb8d4da6a4e036fb887da577.json"}}, {"family": "Nassejje", "given": "Milly", "initials": "M", "orcid": "0000-0002-9964-1814", "researcher": {"href": "https://publications.scilifelab.se/researcher/c30c51e8624b45169c006d6617345a21.json"}}, {"family": "Karlsson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8005-9197", "researcher": {"href": "https://publications.scilifelab.se/researcher/a35fef42c1e04345a6a60557f3b770c6.json"}}, {"family": "Mzee", "given": "John", "initials": "J", "orcid": "0000-0002-9932-6953", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4bbfae70cab440da6a098fed5b6b388.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Businge", "given": "Stephen", "initials": "S", "orcid": "0000-0002-7094-1178", "researcher": {"href": "https://publications.scilifelab.se/researcher/949fae87c1124e9a8cfbf67f91397b05.json"}}, {"family": "Loh", "given": "Edmund", "initials": "E", "orcid": "0000-0001-7050-566X", "researcher": {"href": "https://publications.scilifelab.se/researcher/89e1fa0e881641c3999c556090a66a90.json"}}, {"family": "Boum Ii", "given": "Yap", "initials": "Y", "orcid": "0000-0002-6823-8539", "researcher": {"href": "https://publications.scilifelab.se/researcher/76ff1244bc9e4a7fb99b821c3598473e.json"}}, {"family": "Andersson-Svahn", "given": "Helene", "initials": "H", "orcid": "0000-0003-3409-276X", "researcher": {"href": "https://publications.scilifelab.se/researcher/608c083d9f924fdd9f3f4948d498f64e.json"}}, {"family": "Gantelius", "given": "Jesper", "initials": "J", "orcid": "0000-0002-2581-1542", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbb1b41e117142d18c0730183dc6eb28.json"}}, {"family": "Mwanga-Amumpaire", "given": "Juliet", "initials": "J", "orcid": "0000-0002-6738-477X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c024f8147ab94837b2344ce9aae0d92b.json"}}, {"family": "Alfv\u00e9n", "given": "Tobias", "initials": "T", "orcid": "0000-0002-2328-3512", "researcher": {"href": "https://publications.scilifelab.se/researcher/d808542ea67e466bbc93802c57574b8c.json"}}], "type": "journal article", "published": "2020-11-04", "journal": {"title": "JMIR Res Protoc", "issn": "1929-0748", "volume": "9", "issue": "11", "pages": "e21430", "issn-l": null}, "abstract": "A timely differential diagnostic is essential to identify the etiology of central nervous system (CNS) infections in children, in order to facilitate targeted treatment, manage patients, and improve clinical outcome.\n\nThe Pediatric Infection-Point-of-Care (PI-POC) trial is investigating novel methods to improve and strengthen the differential diagnostics of suspected childhood CNS infections in low-income health systems such as those in Southwestern Uganda. This will be achieved by evaluating (1) a novel DNA-based diagnostic assay for CNS infections, (2) a commercially available multiplex PCR-based meningitis/encephalitis (ME) panel for clinical use in a facility-limited laboratory setting, (3) proteomics profiling of blood from children with severe CNS infection as compared to outpatient controls with fever yet not severely ill, and (4) Myxovirus resistance protein A (MxA) as a biomarker in blood for viral CNS infection. Further changes in the etiology of childhood CNS infections after the introduction of the pneumococcal conjugate vaccine against Streptococcus pneumoniae will be investigated. In addition, the carriage and invasive rate of Neisseria meningitidis will be recorded and serotyped, and the expression of its major virulence factor (polysaccharide capsule) will be investigated.\n\nThe PI-POC trial is a prospective observational study of children including newborns up to 12 years of age with clinical features of CNS infection, and age-/sex-matched outpatient controls with fever yet not severely ill. Participants are recruited at 2 Pediatric clinics in Mbarara, Uganda. Cerebrospinal fluid (for cases only), blood, and nasopharyngeal (NP) swabs (for both cases and controls) sampled at both clinics are analyzed at the Epicentre Research Laboratory through gold-standard methods for CNS infection diagnosis (microscopy, biochemistry, and culture) and a commercially available ME panel for multiplex PCR analyses of the cerebrospinal fluid. An additional blood sample from cases is collected on day 3 after admission. After initial clinical analyses in Mbarara, samples will be transported to Stockholm, Sweden for (1) validation analyses of a novel nucleic acid-based POC test, (2) biomarker research, and (3) serotyping and molecular characterization of S. pneumoniae and N. meningitidis.\n\nA pilot study was performed from January to April 2019. The PI-POC trial enrollment of patients begun in April 2019 and will continue until September 2020, to include up to 300 cases and controls. Preliminary results from the PI-POC study are expected by the end of 2020.\n\nThe findings from the PI-POC study can potentially facilitate rapid etiological diagnosis of CNS infections in low-resource settings and allow for novel methods for determination of the severity of CNS infection in such environment.\n\nClinicalTrials.gov NCT03900091; https://clinicaltrials.gov/ct2/show/NCT03900091.\n\nDERR1-10.2196/21430.", "doi": "10.2196/21430", "pmid": "33146628", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "v9i11e21430"}, {"db": "pmc", "key": "PMC7690656"}, {"db": "ClinicalTrials.gov", "key": "NCT03900091"}], "notes": [], "created": "2020-12-07T16:38:28.050Z", "modified": "2021-11-10T12:45:31.567Z"}, {"entity": "publication", "iuid": "4f514cb335654c83b21a09ae787311a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f514cb335654c83b21a09ae787311a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f514cb335654c83b21a09ae787311a1"}}, "title": "MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.", "authors": [{"family": "Sumida", "given": "Noriyuki", "initials": "N", "orcid": "0000-0001-6121-4553", "researcher": {"href": "https://publications.scilifelab.se/researcher/82465febc13c4629b1ea5aa7e0b509c8.json"}}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8506000a14a4a5286aa557ab67ef690.json"}}, {"family": "Kiani", "given": "Narsis A", "initials": "NA"}, {"family": "Ronnegren", "given": "Anna Lewandowska", "initials": "AL"}, {"family": "Scholz", "given": "Barbara A", "initials": "BA"}, {"family": "Vestlund", "given": "Johanna", "initials": "J"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Tegner", "given": "Jesper", "initials": "J"}, {"family": "G\u00f6nd\u00f6r", "given": "Anita", "initials": "A"}, {"family": "Ohlsson", "given": "Rolf", "initials": "R", "orcid": "0000-0001-7308-3300", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5f1c0948c164764938b9c4bee768e35.json"}}], "type": "journal article", "published": "2020-11-04", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "48", "issue": "19", "pages": "10867-10876", "issn-l": "0305-1048"}, "abstract": "The relationship between stochastic transcriptional bursts and dynamic 3D chromatin states is not well understood. Using an innovated, ultra-sensitive technique, we address here enigmatic features underlying the communications between MYC and its enhancers in relation to the transcriptional process. MYC thus interacts with its flanking enhancers in a mutually exclusive manner documenting that enhancer hubs impinging on MYC detected in large cell populations likely do not exist in single cells. Dynamic encounters with pathologically activated enhancers responsive to a range of environmental cues, involved <10% of active MYC alleles at any given time in colon cancer cells. Being the most central node of the chromatin network, MYC itself likely drives its communications with flanking enhancers, rather than vice versa. We submit that these features underlie an acquired ability of MYC to become dynamically activated in response to a diverse range of environmental cues encountered by the cell during the neoplastic process.", "doi": "10.1093/nar/gkaa817", "pmid": "33051686", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5922798"}, {"db": "pmc", "key": "PMC7641766"}], "notes": [], "created": "2020-12-07T16:34:41.435Z", "modified": "2024-01-16T13:48:41.415Z"}, {"entity": "publication", "iuid": "50a7dfe154a54741bad9e00e32d6c6c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50a7dfe154a54741bad9e00e32d6c6c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50a7dfe154a54741bad9e00e32d6c6c5"}}, "title": "Evolution from adherent to suspension: systems biology of HEK293 cell line development.", "authors": [{"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Saghaleyni", "given": "Rasool", "initials": "R"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Giudici", "given": "Marco", "initials": "M"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}, {"family": "Field", "given": "Ray", "initials": "R"}, {"family": "Varley", "given": "Paul G", "initials": "PG"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Grassi", "given": "Luigi", "initials": "L"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "comparative study", "published": "2020-11-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "18996"}, "abstract": "The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production attributes and is currently used for manufacturing of several therapeutic proteins and viral vectors. Despite the increased popularity of this strain we still have limited knowledge on the genetic composition of its derivatives. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.", "doi": "10.1038/s41598-020-76137-8", "pmid": "33149219", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Systems Biology": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-76137-8"}, {"db": "pmc", "key": "PMC7642379"}], "notes": [], "created": "2020-12-07T16:34:45.132Z", "modified": "2022-02-14T12:16:01.662Z"}, {"entity": "publication", "iuid": "da5d0305f08e461393fa1eb8676813d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da5d0305f08e461393fa1eb8676813d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da5d0305f08e461393fa1eb8676813d0"}}, "title": "From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.", "authors": [{"family": "Gobbo", "given": "Erik", "initials": "E", "orcid": "0000-0001-9897-8610", "researcher": {"href": "https://publications.scilifelab.se/researcher/107736ba83dc4131b9b1f2033ce85d18.json"}}, {"family": "Lartillot", "given": "Nicolas", "initials": "N"}, {"family": "Hearn", "given": "Jack", "initials": "J", "orcid": "0000-0003-3358-4949", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fac223647864b76a5a7783ed7c19138.json"}}, {"family": "Stone", "given": "Graham N", "initials": "GN"}, {"family": "Abe", "given": "Yoshihisa", "initials": "Y"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Ide", "given": "Tatsuya", "initials": "T"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2020-11-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "11", "pages": "2060-2073", "issn-l": "1759-6653"}, "abstract": "Gall wasps (Hymenoptera: Cynipidae) induce complex galls on oaks, roses, and other plants, but the mechanism of gall induction is still unknown. Here, we take a comparative genomic approach to revealing the genetic basis of gall induction. We focus on Synergus itoensis, a species that induces galls inside oak acorns. Previous studies suggested that this species evolved the ability to initiate gall formation recently, as it is deeply nested within the genus Synergus, whose members are mostly inquilines that develop inside the galls of other species. We compared the genome of S. itoensis with that of three related Synergus inquilines to identify genomic changes associated with the origin of gall induction. We used a novel Bayesian selection analysis, which accounts for branch-specific and gene-specific selection effects, to search for signatures of selection in 7,600 single-copy orthologous genes shared by the four Synergus species. We found that the terminal branch leading to S. itoensis had more genes with a significantly elevated dN/dS ratio (positive signature genes) than the other terminal branches in the tree; the S. itoensis branch also had more genes with a significantly decreased dN/dS ratio. Gene set enrichment analysis showed that the positive signature gene set of S. itoensis, unlike those of the inquiline species, is enriched in several biological process Gene Ontology terms, the most prominent of which is \"Ovarian Follicle Cell Development.\" Our results indicate that the origin of gall induction is associated with distinct genomic changes, and provide a good starting point for further characterization of the genes involved.", "doi": "10.1093/gbe/evaa204", "pmid": "32986797", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5912529"}, {"db": "pmc", "key": "PMC7674688"}], "notes": [], "created": "2020-12-07T16:28:56.741Z", "modified": "2024-01-16T13:48:41.438Z"}, {"entity": "publication", "iuid": "0356d54a7a4c443ca3b5ba481e0ea20b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0356d54a7a4c443ca3b5ba481e0ea20b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0356d54a7a4c443ca3b5ba481e0ea20b"}}, "title": "Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Ibelli", "given": "Adriana Mercia Guaratini", "initials": "AMG"}, {"family": "Sharif", "given": "Maj El", "initials": "ME"}, {"family": "Poleti", "given": "Mirele Daiana", "initials": "MD"}, {"family": "Fr\u00f6hlich", "given": "Anna Sophie", "initials": "AS"}, {"family": "Rezaei", "given": "Shiva", "initials": "S"}, {"family": "Ledur", "given": "M\u00f4nica Corr\u00eaa", "initials": "MC"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Coutinho", "given": "Luiz Lehmann", "initials": "LL"}], "type": "journal article", "published": "2020-11-02", "journal": {"title": "Front Genet", "issn": "1664-8021", "issn-l": "1664-8021", "volume": "11", "issue": null, "pages": "508809"}, "abstract": "Production animals are constantly subjected to early adverse environmental conditions that influence the adult phenotype and produce epigenetic effects. CpG dinucleotide methylation in red blood cells (RBC) could be a useful epigenetic biomarker to identify animals subjected to chronic stress in the production environment. Here we compared a reduced fraction of the RBC methylome of chickens exposed to social isolation to non-exposed. These experiments were performed in two different locations: Brazil and Sweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposed in each facility and their different lineages. Birds were increasingly exposed to a social isolation treatment, combined with food and water deprivation, at random periods of the day from weeks 1-4 after hatching. We then collected the RBC DNA from individuals and compared a reduced fraction of their methylome between the experimental groups using two bioinformatic approaches to identify differentially methylated regions (DMRs): one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P \u2264 0.05, P \u2264 0.005, and P \u2264 0.0005) to identify DMRs between experimental groups, which were then used for different analyses. With both of the approaches more DMRs reached the defined significance thresholds in BR individuals compared to SW. However, more DMRs had higher fold change values in SW compared to BR individuals. Interestingly, ChrZ was enriched above expectancy for the presence of DMRs. Additionally, when analyzing the locations of these DMRs in relation to the transcription starting site (TSS), we found three peaks with high DMR presence: 10 kb upstream, the TSS itself, and 20-40 kb downstream. Interestingly, these peaks had DMRs with a high presence (>50%) of specific transcription factor binding sites. Three overlapping DMRs were found between the BR and SW population using the most relaxed p-value (P \u2264 0.05). With the most stringent p-value (P \u2264 0.0005), we found 7 and 4 DMRs between treatments in the BR and SW populations, respectively. This study is the first approximation to identify epigenetic biomarkers of long-term exposure to stress in different lineages of production animals.", "doi": "10.3389/fgene.2020.508809", "pmid": "33240310", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7667380"}], "notes": [], "created": "2020-12-07T16:38:30.735Z", "modified": "2021-11-10T12:45:39.955Z"}, {"entity": "publication", "iuid": "2aa9ff1359ee40c7a2ddf6c07a828ecf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2aa9ff1359ee40c7a2ddf6c07a828ecf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2aa9ff1359ee40c7a2ddf6c07a828ecf"}}, "title": "Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros.", "authors": [{"family": "Moodley", "given": "Yoshan", "initials": "Y", "orcid": "0000-0003-4216-2924", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de66994605d4a809f28b04c8dcf91c6.json"}}, {"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Russo", "given": "Isa-Rita M", "initials": "IM"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Rakotoarivelo", "given": "Andrinajoro", "initials": "A"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Tunstall", "given": "Tate", "initials": "T"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bruford", "given": "Michael W", "initials": "MW"}], "type": "journal article", "published": "2020-11-01", "journal": {"volume": "37", "issn": "1537-1719", "issue": "11", "pages": "3105-3117", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Africa's black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record \u223c5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa's Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.", "doi": "10.1093/molbev/msaa148", "pmid": "32585004", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5862640"}], "notes": [], "created": "2020-07-08T13:04:56.178Z", "modified": "2021-11-10T12:45:42.221Z"}, {"entity": "publication", "iuid": "2cb43ab5664d469db94c06796aaa296d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cb43ab5664d469db94c06796aaa296d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cb43ab5664d469db94c06796aaa296d"}}, "title": "Leaf shape in Populus tremula is a complex, omnigenic trait.", "authors": [{"family": "M\u00e4hler", "given": "Niklas", "initials": "N", "orcid": "0000-0003-2673-9113", "researcher": {"href": "https://publications.scilifelab.se/researcher/581734b34e9948438243f0c105e1094f.json"}}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B", "orcid": "0000-0002-9771-467X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12527c57f62e4a46b758e061ba3f80b1.json"}}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM", "orcid": "0000-0002-5249-604X", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d40626e73d49799c175a2ea14f5626.json"}}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Vu\u010dak", "given": "Matej", "initials": "M", "orcid": "0000-0002-3181-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e64ed41987741f392a5c352ec92480a.json"}}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Bailey", "given": "Mark E S", "initials": "MES", "orcid": "0000-0002-9788-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/3919edd84f254870a5644770152360b6.json"}}, {"family": "Jansson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-7906-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb9d3c17f4514903b3731d15c622a53d.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications.scilifelab.se/researcher/987fbb5763c74f6895bee64630528d8d.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "21", "pages": "11922-11940", "issn-l": "2045-7758"}, "abstract": "Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome-wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA-Seq data that we used to perform gene co-expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.", "doi": "10.1002/ece3.6691", "pmid": "33209260", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36691"}, {"db": "pmc", "key": "PMC7663049"}, {"db": "Dryad", "key": "10.5061/dryad.3n5tb2rdt"}], "notes": [], "created": "2020-12-07T16:34:40.237Z", "modified": "2024-01-16T13:48:41.464Z"}, {"entity": "publication", "iuid": "0cd1833de8764e41812f14260f5961b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd1833de8764e41812f14260f5961b5"}}, "title": "Dense sampling of bird diversity increases power of comparative genomics.", "authors": [{"family": "Feng", "given": "Shaohong", "initials": "S", "orcid": "0000-0002-2462-7348", "researcher": {"href": "https://publications.scilifelab.se/researcher/92ad360b09004877aee9cfde491c76a3.json"}}, {"family": "Stiller", "given": "Josefin", "initials": "J", "orcid": "0000-0001-6009-9581", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e54e7b719bb422aa18ccd99d6c2edf6.json"}}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Armstrong", "given": "Joel", "initials": "J", "orcid": "0000-0003-2077-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/63cfeea6ae9942b8a48e6e13ecf4bf0d.json"}}, {"family": "Fang", "given": "Qi", "initials": "Q", "orcid": "0000-0002-9181-8689", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9ff76a9a8bb42c8973d968c7e39a216.json"}}, {"family": "Reeve", "given": "Andrew Hart", "initials": "AH", "orcid": "0000-0001-5233-6030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9c0cc8c4ff44848960ec2d43dce41d7.json"}}, {"family": "Xie", "given": "Duo", "initials": "D", "orcid": "0000-0001-7010-3601", "researcher": {"href": "https://publications.scilifelab.se/researcher/9258a952a3c54596add7d930e1432ebe.json"}}, {"family": "Chen", "given": "Guangji", "initials": "G", "orcid": "0000-0002-9441-1155", "researcher": {"href": "https://publications.scilifelab.se/researcher/19514f67b1504dc6b4b7d393e97f8cc0.json"}}, {"family": "Guo", "given": "Chunxue", "initials": "C"}, {"family": "Faircloth", "given": "Brant C", "initials": "BC", "orcid": "0000-0002-1943-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df01b37d97a44ffb6f4d069085d7b64.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Wang", "given": "Zongji", "initials": 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Brandt", "initials": "TB", "orcid": "0000-0002-5517-6607", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4f74a843118404f8a54ee20f01263cf.json"}}, {"family": "Camenisch", "given": "Glauco", "initials": "G"}, {"family": "Keller", "given": "Lukas F", "initials": "LF", "orcid": "0000-0002-0149-0174", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e8b9b22d49e453f840f9cf565dd4a7f.json"}}, {"family": "DaCosta", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-8590-2083", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ba9fdc514fd40faa242fa3ca2d0bb6e.json"}}, {"family": "Hauber", "given": "Mark E", "initials": "ME", "orcid": "0000-0003-2014-4928", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0a93dad26a94057ac8e0348fe3c7bf8.json"}}, {"family": "Louder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4421-541X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b63646b95e0a496c987938e3d9637410.json"}}, {"family": "Witt", "given": "Christopher C", "initials": "CC", "orcid": "0000-0003-2781-1543", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a6a535b32f94e59acf1398df72a8cd1.json"}}, {"family": "McGuire", "given": "Jimmy A", "initials": "JA", "orcid": "0000-0002-9562-5585", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f9f692e01f24a98ad0ab40483a0fa9d.json"}}, {"family": "Mudge", "given": "Joann", "initials": "J", "orcid": "0000-0002-2972-1640", "researcher": {"href": "https://publications.scilifelab.se/researcher/796d05f22ef842428bddd4c9bdde9f0c.json"}}, {"family": "Megna", "given": "Libby C", "initials": "LC"}, {"family": "Carling", "given": "Matthew D", "initials": "MD", "orcid": "0000-0002-9401-7844", "researcher": {"href": "https://publications.scilifelab.se/researcher/49720bca1e624059b231875d1192f7df.json"}}, {"family": "Wang", "given": "Biao", "initials": "B"}, {"family": "Taylor", "given": "Scott A", "initials": "SA", "orcid": "0000-0001-9580-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/36c6baa1b23242e0bfd586d7e42c0cb9.json"}}, {"family": "Del-Rio", "given": "Glaucia", "initials": "G"}, {"family": "Aleixo", "given": "Alexandre", "initials": "A", "orcid": "0000-0002-7816-9725", "researcher": {"href": "https://publications.scilifelab.se/researcher/b397ed6da07246caa50a438c233820ab.json"}}, {"family": "Vasconcelos", "given": "Ana Tereza Ribeiro", "initials": "ATR", "orcid": "0000-0002-4632-2086", "researcher": {"href": "https://publications.scilifelab.se/researcher/69b1022e72a84534850b8d650ba2c1be.json"}}, {"family": "Mello", "given": "Claudio V", "initials": "CV", "orcid": "0000-0002-9826-8421", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9715cacaf7d45bda2337a32ea0ec526.json"}}, {"family": "Weir", "given": "Jason T", "initials": "JT", "orcid": "0000-0001-8372-9937", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c77b745d8b044d4aed9478d056be226.json"}}, {"family": "Haussler", "given": "David", "initials": "D", "orcid": "0000-0003-1533-4575", "researcher": {"href": "https://publications.scilifelab.se/researcher/de140026a4f24291be768e713e4881bb.json"}}, {"family": "Li", "given": "Qiye", "initials": "Q", "orcid": "0000-0002-5993-0312", "researcher": {"href": "https://publications.scilifelab.se/researcher/d807a3a13669425c9b00e4a2b7db672a.json"}}, {"family": "Yang", "given": "Huanming", "initials": "H"}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Rahbek", "given": "Carsten", "initials": "C"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Graves", "given": "Gary R", "initials": "GR", "orcid": "0000-0003-1406-5246", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc3b9edee185456d971f5b596c3086fe.json"}}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "587", "issue": "7833", "pages": "252-257", "issn-l": "0028-0836"}, "abstract": "Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.", "doi": "10.1038/s41586-020-2873-9", "pmid": "33177665", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-020-2873-9"}, {"db": "pmc", "key": "PMC7759463"}], "notes": [], "created": "2020-12-07T16:36:44.079Z", "modified": "2021-11-10T12:45:51.851Z"}, {"entity": "publication", "iuid": "9003c13437864efc9e4e530ff7595ac6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9003c13437864efc9e4e530ff7595ac6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9003c13437864efc9e4e530ff7595ac6"}}, "title": "Cytogenetically visible inversions are formed by multiple molecular mechanisms.", "authors": [{"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Breman", "given": "Amy M", "initials": "AM"}, {"family": "Cheung", "given": "Sau W", "initials": "SW"}, {"family": "Krepischi", "given": "Ana C V", "initials": "ACV"}, {"family": "Rosenberg", "given": "Carla", "initials": "C"}, {"family": "Lupski", "given": "James R", "initials": "JR", "orcid": "0000-0001-9907-9246", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dd1dee9767489aaf25865670feb7b7.json"}}, {"family": "Ottosson", "given": "Jesper", "initials": "J"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Gacic", "given": "Jelena", "initials": "J"}, {"family": "Lundberg", "given": "Elisabeth S", "initials": "ES"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Hum. Mutat.", "issn": "1098-1004", "volume": "41", "issue": "11", "pages": "1979-1998", "issn-l": "1059-7794"}, "abstract": "Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While nonallelic homologous recombination is thought to play a major role, recent data suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short-read whole-genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital polymerase chain reaction and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by a copy-number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the resolved inversions, the mutational signatures are consistent with nonhomologous end-joining (8/13, 62%) or microhomology-mediated break-induced replication (5/13, 38%). Our study indicates that short-read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication-based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy-number variation potentially contributing to the overall phenotypic presentation of those patients.", "doi": "10.1002/humu.24106", "pmid": "32906200", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7702065"}], "notes": [], "created": "2020-12-07T16:28:51.266Z", "modified": "2024-01-16T13:48:41.478Z"}, {"entity": "publication", "iuid": "ffa17d5833774c64ae24d57daf592ed5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffa17d5833774c64ae24d57daf592ed5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffa17d5833774c64ae24d57daf592ed5"}}, "title": "Origins and genetic legacy of prehistoric dogs.", "authors": [{"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0002-4096-9268", "researcher": {"href": "https://publications.scilifelab.se/researcher/77429e0da9574e9ab3d1a14ae5dbb803.json"}}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Schmidt", "given": "Ryan", "initials": "R"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Lebrasseur", "given": "Ophelie", "initials": "O", "orcid": "0000-0003-0687-8538", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f100bd635446739f54bcabbf1840bc.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}, {"family": "Lin", "given": "Audrey T", "initials": "AT", "orcid": "0000-0003-2505-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1f6e691ce04fd396757c4918535cc2.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG", "orcid": "0000-0003-1791-3175", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe55ca79f7a438dbbda3e97e3780223.json"}}, {"family": "Anthony", "given": "David", "initials": "D", "orcid": "0000-0001-9122-0313", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe0401df8e44a82a3c69a7a0478007d.json"}}, {"family": "Antipina", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-3003-942X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c0ad9634824dabbef732e81a68ec60.json"}}, {"family": "Amiri", "given": "Sarieh", "initials": "S", "orcid": "0000-0002-6835-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae40113ed34f4ed1a173637c864e1c38.json"}}, {"family": "Bar-Oz", "given": "Guy", "initials": "G"}, {"family": "Bazaliiskii", "given": "Vladimir I", "initials": "VI"}, {"family": "Bulatovi\u0107", "given": "Jelena", "initials": "J", "orcid": "0000-0002-0672-067X", "researcher": {"href": "https://publications.scilifelab.se/researcher/977f7acdf2e94256bc664d52f8b99922.json"}}, {"family": "Brown", "given": "Dorcas", "initials": "D"}, {"family": "Carmagnini", "given": "Alberto", "initials": "A"}, {"family": "Davy", "given": "Tom", "initials": "T", "orcid": "0000-0002-9466-5497", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9e9bebf8ad41d2a53d4c475f719b88.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", 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Lo\u017enjak", "initials": "DL", "orcid": "0000-0002-5769-2269", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb0100bc6c5d459aa8f9b05b2e236ba5.json"}}, {"family": "Mashkour", "given": "Marjan", "initials": "M", "orcid": "0000-0003-3630-9459", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d45bd37c43f4f7fba2c62c9a26e18c7.json"}}, {"family": "Novak", "given": "Mario", "initials": "M", "orcid": "0000-0002-4567-8742", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae952c508a1d444c9e3ee6cdb0c5a2ae.json"}}, {"family": "Onar", "given": "Vedat", "initials": "V", "orcid": "0000-0002-8359-243X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d129588489cb4684b204c29aba54b1fc.json"}}, {"family": "Orton", "given": "David", "initials": "D", "orcid": "0000-0003-4069-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b0e6ccfd34e49a1878181fa931114de.json"}}, {"family": "Pasari\u0107", "given": "Maja", "initials": "M"}, {"family": "Radivojevi\u0107", "given": "Miljana", "initials": "M", "orcid": "0000-0001-7329-305X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19d71e76741c4d7eacc555b9328291c7.json"}}, {"family": "Rajkovi\u0107", "given": "Dragana", "initials": "D"}, {"family": "Roberts", "given": "Benjamin", "initials": "B"}, {"family": "Ryan", "given": "Hannah", "initials": "H", "orcid": "0000-0002-4320-4594", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a07befb801c478692e3508b663d1a97.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Shidlovskiy", "given": "Fedor", "initials": "F"}, {"family": "Stojanovi\u0107", "given": "Ivana", "initials": "I", "orcid": "0000-0001-5271-680X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d603204ff3c04194a7246468a9f1754e.json"}}, {"family": "Tagliacozzo", "given": "Antonio", "initials": "A"}, {"family": "Trantalidou", "given": "Katerina", "initials": "K"}, {"family": "Ull\u00e9n", "given": "Inga", "initials": "I"}, {"family": "Villaluenga", "given": "Aritza", "initials": "A"}, {"family": "Wapnish", "given": "Paula", "initials": "P"}, {"family": "Dobney", "given": "Keith", "initials": "K", "orcid": "0000-0001-9036-4681", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ea25869ffa4984a013051452969efb.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Pinhasi", "given": "Ron", "initials": "R", "orcid": "0000-0003-1629-8131", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8eedf480ae494d9e6249ec58dd1867.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}], "type": "journal article", "published": "2020-10-30", "journal": {"title": "Science", "issn": "1095-9203", "volume": "370", "issue": "6516", "pages": "557-564", "issn-l": "0036-8075"}, "abstract": "Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.", "doi": "10.1126/science.aba9572", "pmid": "33122379", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "370/6516/557"}, {"db": "pmc", "key": "PMC7116352"}, {"db": "mid", "key": "EMS103415"}], "notes": [], "created": "2021-01-08T16:29:50.956Z", "modified": "2021-11-10T12:45:57.753Z"}, {"entity": "publication", "iuid": "41bc355c40704d2c82ce195de926f8b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41bc355c40704d2c82ce195de926f8b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41bc355c40704d2c82ce195de926f8b9"}}, "title": "Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.", "authors": [{"family": "Liang", "given": "Dong", "initials": "D"}, {"family": "Andersen", "given": "Christian Benjamin", "initials": "CB"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Dou", "given": "Daolong", "initials": "D"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2020-10-29", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "issue": null, "pages": "581698", "issn-l": "1664-302X"}, "abstract": "Crop protection strategies that are effective but that reduce our reliance on chemical pesticides are urgently needed to meet the UN sustainable development goals for global food security. Mycoparasitic oomycetes such as Pythium oligandrum and Pythium periplocum, have potential for the biological control of plant diseases that threaten crops and have attracted much attention due to their abilities to antagonize plant pathogens and modulate plant immunity. Studies of the molecular and genetic determinants of mycoparasitism in these species have been less well developed than those of their fungal counterparts. Carbohydrate-active enzymes (CAZymes) from P. oligandrum and P. periplocum are predicted to be important components of mycoparasitism, being involved in the degradation of the cell wall of their oomycete and fungal prey species. To explore the evolution of CAZymes of these species we performed an in silico identification and comparison of the full CAZyme complement (CAZyome) of the two mycoparasitic Pythium species (P. oligandrum and P. periplocum), with seven other Pythium species, and four Phytophthora species. Twenty CAZy gene families involved in the degradation of cellulose, hemicellulose, glucan, and chitin were expanded in, or unique to, mycoparasitic Pythium species and several of these genes were expressed during mycoparasitic interactions with either oomycete or fungal prey, as revealed by RNA sequencing and quantitative qRT-PCR. Genes from three of the cellulose and chitin degrading CAZy families (namely AA9, GH5_14, and GH19) were expanded via tandem duplication and predominantly located in gene sparse regions of the genome, suggesting these enzymes are putative pathogenicity factors able to undergo rapid evolution. In addition, five of the CAZy gene families were likely to have been obtained from other microbes by horizontal gene transfer events. The mycoparasitic species are able to utilize complex carbohydrates present in fungal cell walls, namely chitin and N-acetylglucosamine for growth, in contrast to their phytopathogenic counterparts. Nonetheless, a preference for the utilization of simple sugars for growth appears to be a common trait within the oomycete lineage.", "doi": "10.3389/fmicb.2020.581698", "pmid": "33329445", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7720654"}], "notes": [], "created": "2021-01-08T16:30:27.463Z", "modified": "2021-11-10T12:46:01.223Z"}, {"entity": "publication", "iuid": "61faf99df7d143678abba24c31bdb534", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61faf99df7d143678abba24c31bdb534.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61faf99df7d143678abba24c31bdb534"}}, "title": "Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.", "authors": [{"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Gyllenstrand", "given": "Niclas", "initials": "N"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Liljeb\u00e4ck", "given": "Niklas", "initials": "N"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}, {"family": "Sj\u00f6gren-Gulve", "given": "Per", "initials": "P"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2020-10-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "18347", "issn-l": "2045-2322"}, "abstract": "Interspecific introgression is considered a potential threat to endangered taxa. One example where this has had a major impact on conservation policy is the lesser white-fronted goose (LWfG). After a dramatic decline in Sweden, captive breeding birds were released between 1981-1999 with the aim to reinforce the population. However, the detection of greater white-fronted goose (GWfG) mitochondrial DNA in the LWfG breeding stock led to the release program being dismantled, even though the presence of GWfG introgression in the actual wild Swedish LWfG population was never documented. To examine this, we sequenced the complete genomes of 21 LWfG birds from the Swedish, Russian and Norwegian populations, and compared these with genomes from other goose species, including the GWfG. We found no evidence of interspecific introgression into the wild Swedish LWfG population in either nuclear genomic or mitochondrial data. Moreover, Swedish LWfG birds are genetically distinct from the Russian and Norwegian populations and display comparatively low genomic diversity and high levels of inbreeding. Our findings highlight the utility of genomic approaches in providing scientific evidence that can help improve conservation management as well as policies for breeding and reinforcement programmes.", "doi": "10.1038/s41598-020-75315-y", "pmid": "33110153", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-75315-y"}, {"db": "pmc", "key": "PMC7591532"}], "notes": [], "created": "2020-12-07T16:34:43.881Z", "modified": "2024-01-16T13:48:41.531Z"}, {"entity": "publication", "iuid": "25837b6d08ab4c55b52b7bcc80655783", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25837b6d08ab4c55b52b7bcc80655783.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25837b6d08ab4c55b52b7bcc80655783"}}, "title": "Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome.", "authors": [{"family": "Zhang", "given": "Chaofan", "initials": "C", "orcid": "0000-0003-0504-5999", "researcher": {"href": "https://publications.scilifelab.se/researcher/76aee864d3c0444d8c7eabe94b0df996.json"}}, {"family": "Mazzeu", "given": "Juliana F", "initials": "JF", "orcid": "0000-0002-6161-0510", "researcher": {"href": "https://publications.scilifelab.se/researcher/08c358e857ad458298fbd0cbb7621a2b.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Grochowski", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-3884-7720", "researcher": {"href": "https://publications.scilifelab.se/researcher/c94bd6d4a43e41f2990ae8b9426c0312.json"}}, {"family": "White", "given": "Janson", "initials": "J"}, {"family": "Akdemir", "given": "Zeynep C", "initials": "ZC"}, {"family": "Jhangiani", "given": "Shalini N", "initials": "SN"}, {"family": "Muzny", "given": "Donna M", "initials": "DM"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA", "orcid": "0000-0002-1356-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82176147e434163a72c946839708743.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Lupski", "given": "James R", "initials": "JR", "orcid": "0000-0001-9907-9246", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dd1dee9767489aaf25865670feb7b7.json"}}, {"family": "Sutton", "given": "V Reid", "initials": "VR"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}], "type": "journal article", "published": "2020-10-13", "journal": {"title": "Am. J. Med. Genet. A", "issn": "1552-4833", "volume": null, "issue": null, "issn-l": "1552-4825"}, "abstract": "Robinow syndrome (RS) is a genetically heterogeneous disorder characterized by skeletal dysplasia and a distinctive facial appearance. Previous studies have revealed locus heterogeneity with rare variants in DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A underlying the etiology of RS. The aforementioned \"Robinow-associated genes\" and their gene products all play a role in the WNT/planar cell polarity signaling pathway. We performed gene-targeted Sanger sequencing, exome sequencing, genome sequencing, and array comparative genomic hybridization on four subjects with a clinical diagnosis of RS who had not had prior DNA testing. Individuals in our cohort were found to carry pathogenic or likely pathogenic variants in three RS related genes: DVL1, ROR2, and NXN. One subject was found to have a nonsense variant (c.817C > T [p.Gln273*]) in NXN in trans with an ~1 Mb telomeric deletion on chromosome 17p containing NXN, which supports our contention that biallelic NXN variant alleles are responsible for a novel autosomal recessive RS locus. These findings provide increased understanding of the role of WNT signaling in skeletal development and maintenance. These data further support the hypothesis that dysregulation of the noncanonical WNT pathway in humans gives rise to RS.", "doi": "10.1002/ajmg.a.61908", "pmid": "33048444", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8445516"}, {"db": "mid", "key": "NIHMS1735294"}], "notes": [], "created": "2020-12-07T16:32:22.731Z", "modified": "2021-11-10T12:46:23.684Z"}, {"entity": "publication", "iuid": "d4fc956d9ba04d4e90ea6dae2139f961", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4fc956d9ba04d4e90ea6dae2139f961.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4fc956d9ba04d4e90ea6dae2139f961"}}, "title": "GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.", "authors": [{"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Planell-Picola", "given": "Nuria", "initials": "N"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}], "type": "journal article", "published": "2020-10-07", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "21", "issue": "1", "pages": "443", "issn-l": "1471-2105"}, "abstract": "Gene-set analysis tools, which make use of curated sets of molecules grouped based on their shared functions, aim to identify which gene-sets are over-represented in the set of features that have been associated with a given trait of interest. Such tools are frequently used in gene-centric approaches derived from RNA-sequencing or microarrays such as Ingenuity or GSEA, but they have also been adapted for interval-based analysis derived from DNA methylation or ChIP/ATAC-sequencing. Gene-set analysis tools return, as a result, a list of significant gene-sets. However, while these results are useful for the researcher in the identification of major biological insights, they may be complex to interpret because many gene-sets have largely overlapping gene contents. Additionally, in many cases the result of gene-set analysis consists of a large number of gene-sets making it complicated to identify the major biological insights.\n\nWe present GeneSetCluster, a novel approach which allows clustering of identified gene-sets, from one or multiple experiments and/or tools, based on shared genes. GeneSetCluster calculates a distance score based on overlapping gene content, which is then used to cluster them together and as a result, GeneSetCluster identifies groups of gene-sets with similar gene-set definitions (i.e. gene content). These groups of gene-sets can aid the researcher to focus on such groups for biological interpretations.\n\nGeneSetCluster is a novel approach for grouping together post gene-set analysis results based on overlapping gene content. GeneSetCluster is implemented as a package in R. The package and the vignette can be downloaded at https://github.com/TranslationalBioinformaticsUnit.", "doi": "10.1186/s12859-020-03784-z", "pmid": "33028195", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-020-03784-z"}, {"db": "pmc", "key": "PMC7542881"}], "notes": [], "created": "2020-12-07T16:28:58.011Z", "modified": "2024-01-16T13:48:41.580Z"}, {"entity": "publication", "iuid": "79b99a6601fc4ed1b69ef32e4b793129", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79b99a6601fc4ed1b69ef32e4b793129.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79b99a6601fc4ed1b69ef32e4b793129"}}, "title": "Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.", "authors": [{"family": "Sahraei", "given": "Shadi Eshghi", "initials": "SE"}, {"family": "Cleary", "given": "Michelle", "initials": "M"}, {"family": "Stenlid", "given": "Jan", "initials": "J"}, {"family": "Brandstr\u00f6m Durling", "given": "Mikael", "initials": "M"}, {"family": "Elfstrand", "given": "Malin", "initials": "M", "orcid": "0000-0002-0214-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/2957dac173f4495a9245f0d8a9750606.json"}}], "type": "journal article", "published": "2020-10-06", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "20", "issue": "1", "pages": "455", "issn-l": "1471-2229"}, "abstract": "With the expanding ash dieback epidemic that has spread across the European continent, an improved functional understanding of the disease development in afflicted hosts is needed. The study investigated whether differences in necrosis extension between common ash (Fraxinus excelsior) trees with different levels of susceptibility to the fungus Hymenoscyphus fraxineus are associated with, and can be explained by, the differences in gene expression patterns. We inoculated seemingly healthy branches of each of two resistant and susceptible ash genotypes with H. fraxineus grown in a common garden.\n\nTen months after the inoculation, the length of necrosis on the resistant genotypes were shorter than on the susceptible genotypes. RNA sequencing of bark samples collected at the border of necrotic lesions and from healthy tissues distal to the lesion revealed relatively limited differences in gene expression patterns between susceptible and resistant genotypes. At the necrosis front, only 138 transcripts were differentially expressed between the genotype categories while 1082 were differentially expressed in distal, non-symptomatic tissues. Among these differentially expressed genes, several genes in the mevalonate (MVA) and iridoid pathways were found to be co-regulated, possibly indicating increased fluxes through these pathways in response to H. fraxineus. Comparison of transcriptional responses of symptomatic and non-symptomatic ash in a controlled greenhouse experiment revealed a relatively small set of genes that were differentially and concordantly expressed in both studies. This gene-set included the rate-limiting enzyme in the MVA pathway and a number of transcription factors. Furthermore, several of the concordantly expressed candidate genes show significant similarity to genes encoding players in the abscisic acid- or Jasmonate-signalling pathways.\n\nA set of candidate genes, concordantly expressed between field and greenhouse experiments, was identified. The candidates are associated with hormone signalling and specialized metabolite biosynthesis pathways indicating the involvement of these pathways in the response of the host to infection by H. fraxineus.", "doi": "10.1186/s12870-020-02656-1", "pmid": "33023496", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12870-020-02656-1"}, {"db": "pmc", "key": "PMC7541206"}], "notes": [], "created": "2020-12-07T16:28:55.489Z", "modified": "2024-01-16T13:48:41.587Z"}, {"entity": "publication", "iuid": "d65d460e50e0405eaa0e81048974930c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d65d460e50e0405eaa0e81048974930c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d65d460e50e0405eaa0e81048974930c"}}, "title": "Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "S\u00e1nchez-Barreiro", "given": "F\u00e1tima", "initials": "F"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Willerslev", "given": "Eske", "initials": "E", "orcid": "0000-0002-7081-6748", "researcher": {"href": "https://publications.scilifelab.se/researcher/da0055841300427e85d9af38b1863ef1.json"}}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Shidlovskiy", "given": "Fedor", "initials": "F"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Bocherens", "given": "Herv\u00e9", "initials": "H"}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "van der Plicht", "given": "Johannes", "initials": "J", "orcid": "0000-0003-4298-7037", "researcher": {"href": "https://publications.scilifelab.se/researcher/c115c95efd014b748c698a802f25f2d5.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL", "orcid": "0000-0002-8073-4025", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fdb2d9af4bc439eb1572abe7000190d.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Potapova", "given": "Olga", "initials": "O", "orcid": "0000-0002-3589-2489", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a8a3f7d32434226be4d637673845820.json"}}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2020-10-05", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "30", "issue": "19", "pages": "3871-3879.e7", "issn-l": "0960-9822"}, "abstract": "Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a \u223c18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the B\u00f8lling-Aller\u00f8d interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.", "doi": "10.1016/j.cub.2020.07.046", "pmid": "32795436", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(20)31071-X"}], "notes": [], "created": "2020-08-24T09:00:42.045Z", "modified": "2024-01-16T13:48:41.594Z"}, {"entity": "publication", "iuid": "8c2a6093b4864656bdafe542e02de9f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8c2a6093b4864656bdafe542e02de9f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8c2a6093b4864656bdafe542e02de9f8"}}, "title": "Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.", "authors": [{"family": "Phoon", "given": "Yee Peng", "initials": "YP"}, {"family": "Chivukula", "given": "Indira V", "initials": "IV"}, {"family": "Tsoi", "given": "Yat Long", "initials": "YL"}, {"family": "Kanatani", "given": "Shigeaki", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P"}, {"family": "Kuiper", "given": "Raoul", "initials": "R"}, {"family": "Lendahl", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2020-10-01", "journal": {"title": "Exp. Cell Res.", "issn": "1090-2422", "volume": "395", "issue": "1", "pages": "112156", "issn-l": "0014-4827"}, "abstract": "Hyperactivated Notch signalling has been implicated in breast cancer, but how elevated levels of Notch signalling contribute to mammary dysplasia and tumorigenesis is not fully understood. In this study, we express an activated form of Notch1 in the mouse mammary luminal lineage and analyse the consequences for tumour formation and the transcriptomic landscape in the luminal lineage. Simultaneous conditional activation of a Notch1 intracellular domain (Notch1 ICD) and EGFP in the luminal lineage was achieved by removal of a stop cassette by CRE-recombinase expression from the whey acidic protein (WAP) promoter. Mice in which Notch1 ICD was activated in the luminal lineage (WAP-CRE;R26-N1ICD mice) exhibit ductal hyperplasia after lactation with an increase in branching frequency and in the number of side-branch ends in the ductal tree. A subset of the mice developed mammary tumours and the majority of the tumour cells expressed EGFP (as a proxy for Notch1 ICD), indicating that the tumours originate from the Notch1 ICD-expressing cells. Single-cell transcriptome analysis of the EGFP-positive mammary cells identified six subtypes of luminal cells. The same six subtypes were found in control mice (WAP-CRE;R26-tdTomato mice expressing the tdTomato reporter from WAP-CRE-mediated activation), but the proportion of cells in the various subtypes differed between the WAP-CRE;R26-N1ICD and control WAP-CRE;R26-tdTomato mice. In conclusion, we show that Notch1 ICD expression in the luminal lineage produces a ductal hyperplasia and branching phenotype accompanied by altered luminal cell subtype partitioning.", "doi": "10.1016/j.yexcr.2020.112156", "pmid": "32707133", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4827(20)30403-1"}], "notes": [], "created": "2020-12-07T16:34:36.716Z", "modified": "2024-01-16T13:48:41.602Z"}, {"entity": "publication", "iuid": "73ca2e71397248f8a37be2560bd5c0e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73ca2e71397248f8a37be2560bd5c0e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73ca2e71397248f8a37be2560bd5c0e7"}}, "title": "High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.", "authors": [{"family": "Hases", "given": "L", "initials": "L"}, {"family": "Archer", "given": "A", "initials": "A"}, {"family": "Indukuri", "given": "R", "initials": "R"}, {"family": "Birgersson", "given": "M", "initials": "M"}, {"family": "Savva", "given": "C", "initials": "C"}, {"family": "Korach-Andr\u00e9", "given": "M", "initials": "M"}, {"family": "Williams", "given": "C", "initials": "C"}], "type": "journal article", "published": "2020-09-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "16160", "issn-l": "2045-2322"}, "abstract": "There is a strong association between obesity and colorectal cancer (CRC), especially in men, whereas estrogen protects against both the metabolic syndrome and CRC. Colon is the first organ to respond to high-fat diet (HFD), and estrogen receptor beta (ER\u03b2) can attenuate CRC development. How estrogen impacts the colon under HFD and related sex differences has, however, not been investigated. To dissect this, mice were fed control diet or HFD for 13 weeks and administered receptor-selective estrogenic ligands for the last three weeks. We recorded impact on metabolism, colon crypt proliferation, macrophage infiltration, and the colon transcriptome. We found clear sex differences in the colon transcriptome and in the impact by HFD and estrogens, including on clock genes. ER\u03b1-selective activation reduced body weight and generated systemic effects, whereas ER\u03b2-selective activation had local effects in the colon, attenuating HFD-induced macrophage infiltration and epithelial cell proliferation. We here demonstrate how HFD and estrogens modulate the colon microenvironment in a sex- and ER-specific manner.", "doi": "10.1038/s41598-020-73166-1", "pmid": "32999402", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-73166-1"}, {"db": "pmc", "key": "PMC7527340"}], "notes": [], "created": "2020-12-07T16:32:31.546Z", "modified": "2024-01-16T13:48:41.674Z"}, {"entity": "publication", "iuid": "cde158ede680439a93d1a55b6b0aef96", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cde158ede680439a93d1a55b6b0aef96.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cde158ede680439a93d1a55b6b0aef96"}}, "title": "Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.", "authors": [{"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2020-09-25", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "issue": null, "pages": "588778", "issn-l": "1664-302X"}, "abstract": "Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced changes in bacterial growth, activity, and transcription related to DOM characteristics. Transcriptional responses differed between compound classes, with distinct gene sets (\"core genes\") distinguishing carbohydrates, proteins, and nucleic acids. Moreover, we found a strong divergence in functional transcription at the level of particular monomers and polymers (i.e., the condensation state), primarily in the carbohydrates and protein compound classes. These specific responses included a variety of cellular and metabolic processes that were mediated by distinct bacterial taxa, suggesting pronounced functional partitioning of organic matter. Collectively, our findings show that two important facets of DOM, compound class and condensation state, shape bacterial gene expression, and ultimately select for distinct bacterial (functional) groups. This emphasizes the interdependency of marine bacteria and labile carbon compounds for regulating the transformation of DOM in surface waters.", "doi": "10.3389/fmicb.2020.588778", "pmid": "33101262", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7546218"}], "notes": [], "created": "2020-12-07T16:36:37.841Z", "modified": "2024-01-16T13:48:41.701Z"}, {"entity": "publication", "iuid": "5efb2fa83f7f42c18ee609f625619eeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5efb2fa83f7f42c18ee609f625619eeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5efb2fa83f7f42c18ee609f625619eeb"}}, "title": "Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.", "authors": [{"family": "Ignatov", "given": "Dmitriy", "initials": "D"}, {"family": "Vaitkevicius", "given": "Karolis", "initials": "K"}, {"family": "Johansson", "given": "J\u00f6rgen", "initials": "J"}], "type": "journal article", "published": "2020-09-18", "journal": {"title": "STAR Protoc", "issn": "2666-1667", "volume": "1", "issue": "2", "pages": "100046", "issn-l": null}, "abstract": "The structure of 5' untranslated regions (5' UTRs) of bacterial mRNAs often determines the fate of the transcripts. Using a dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) approach, we developed a protocol to generate sequence libraries to determine the base-pairing status of adenines and cytosines in the 5' UTRs of bacterial mRNAs. Our method increases the sequencing depth of the 5' UTRs and allows detection of changes in their structures by sequencing libraries of moderate sizes. For complete details on the use and execution of this protocol, please refer to Ignatov et al. (2020).", "doi": "10.1016/j.xpro.2020.100046", "pmid": "33111092", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2666-1667(20)30033-2"}, {"db": "pmc", "key": "PMC7580233"}], "notes": [], "created": "2020-12-07T16:38:29.482Z", "modified": "2024-01-16T13:48:41.708Z"}, {"entity": "publication", "iuid": "0a4b469382934005bf79f0c29264def6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a4b469382934005bf79f0c29264def6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a4b469382934005bf79f0c29264def6"}}, "title": "Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.", "authors": [{"family": "Vaga", "given": "Stefania", "initials": "S"}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Ji", "given": "Boyang", "initials": "B"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Agr\u00e9us", "given": "Lars", "initials": "L"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Kovatcheva-Datchary", "given": "Petia", "initials": "P"}, {"family": "Park", "given": "Junseok", "initials": "J"}, {"family": "Lee", "given": "Doheon", "initials": "D"}, {"family": "Proctor", "given": "Gordon", "initials": "G"}, {"family": "Ehrlich", "given": "Stanislav Dusko", "initials": "SD"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}], "type": "clinical trial", "published": "2020-09-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "14977", "issn-l": "2045-2322"}, "abstract": "Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.", "doi": "10.1038/s41598-020-71939-2", "pmid": "32917913", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-71939-2"}, {"db": "pmc", "key": "PMC7486370"}], "notes": [], "created": "2020-12-07T16:28:54.238Z", "modified": "2024-01-16T13:48:41.733Z"}, {"entity": "publication", "iuid": "89662d49b5714d43b2d4ee811777dd15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89662d49b5714d43b2d4ee811777dd15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89662d49b5714d43b2d4ee811777dd15"}}, "title": "Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Nylander", "given": "Johan A A", "initials": "JAA"}, {"family": "Christidis", "given": "Les", "initials": "L"}, {"family": "Joseph", "given": "Leo", "initials": "L"}, {"family": "Qu", "given": "Yanhua", "initials": "Y"}], "type": "journal article", "published": "2020-09-01", "journal": {"title": "Syst. Biol.", "issn": "1076-836X", "volume": "69", "issue": "5", "pages": "820-829", "issn-l": "1063-5157"}, "abstract": "The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.].", "doi": "10.1093/sysbio/syaa040", "pmid": "32415976", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5838197"}, {"db": "pmc", "key": "PMC7440736"}], "notes": [], "created": "2020-07-08T13:05:12.870Z", "modified": "2024-01-16T13:48:41.780Z"}, {"entity": "publication", "iuid": "d1a66cc65c1c4d90bc501a532dbb1cc7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1a66cc65c1c4d90bc501a532dbb1cc7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1a66cc65c1c4d90bc501a532dbb1cc7"}}, "title": "The impact of damage-associated molecular patterns on the neurotransmitter release and gene expression in the ex vivo rat carotid body.", "authors": [{"family": "Mkrtchian", "given": "Souren", "initials": "S", "orcid": "0000-0001-9801-2736", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8d9ca2998c8420eaccaec545f606b64.json"}}, {"family": "K\u00e5hlin", "given": "Jessica", "initials": "J"}, {"family": "G\u00f3mez-Gal\u00e1n", "given": "Marta", "initials": "M"}, {"family": "Ebberyd", "given": "Anette", "initials": "A"}, {"family": "Yoshitake", "given": "Takashi", "initials": "T"}, {"family": "Schmidt", "given": "Staffan", "initials": "S"}, {"family": "Kehr", "given": "Jan", "initials": "J"}, {"family": "Hildenborg", "given": "Malin", "initials": "M"}, {"family": "Jonsson Fagerlund", "given": "Malin", "initials": "M"}, {"family": "Erlandsson Harris", "given": "Helena", "initials": "H"}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Exp. Physiol.", "issn": "1469-445X", "volume": "105", "issue": "9", "pages": "1634-1647", "issn-l": "0958-0670"}, "abstract": "What is the central question of this study? Are carotid bodies (CBs) modulated by the damage-associated molecular patterns (DAMPs) and humoral factors of aseptic tissue injury? What are the main findings and their importance? DAMPs (HMGB1, S100 A8/A9) and blood plasma from rats subjected to tibia surgery, a model of aseptic injury, stimulate the release of neurotransmitters (ATP, dopamine) and TNF-\u03b1 from ex vivo rat CBs. All-thiol HMGB1 mediates upregulation of immune-related biological pathways. These data suggest regulation of CB function by endogenous mediators of innate immunity.\n\nThe glomus cells of carotid bodies (CBs) are the primary sensors of arterial partial O2 and CO2 tensions and moreover serve as multimodal receptors responding also to other stimuli, such as pathogen-associated molecular patterns (PAMPs) produced by acute infection. Modulation of CB function by excessive amounts of these immunomodulators is suggested to be associated with a detrimental hyperinflammatory state. We have hypothesized that yet another class of immunomodulators, endogenous danger-associated molecular patterns (DAMPs), released upon aseptic tissue injury and recognized by the same pathogen recognition receptors as PAMPs, might modulate the CB activity in a fashion similar to PAMPs. We have tested this hypothesis by exposing rat CBs to various DAMPs, such as HMGB1 (all-thiol and disulfide forms) and S100 A8/A9 in a series of ex vivo experiments that demonstrated the release of dopamine and ATP, neurotransmitters known to mediate CB homeostatic responses. We observed a similar response after incubating CBs with conditioned blood plasma obtained from the rats subjected to tibia surgery, a model of aseptic injury. In addition, we have investigated global gene expression in the rat CB using an RNA sequencing approach. Differential gene expression analysis showed all-thiol HMGB1-driven upregulation of a number of prominent pro-inflammatory markers including Il1\u03b1 and Il1\u03b2. Interestingly, conditioned plasma had a more profound effect on the CB transcriptome resulting in inhibition rather than activation of the immune-related pathways. These data are the first to suggest potential modulation of CB function by endogenous mediators of innate immunity.", "doi": "10.1113/EP088705", "pmid": "32652583", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2021-01-08T16:29:48.218Z", "modified": "2021-11-10T12:47:37.875Z"}, {"entity": "publication", "iuid": "ac7ab01a344b4cbb87bc8b19e372caab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac7ab01a344b4cbb87bc8b19e372caab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac7ab01a344b4cbb87bc8b19e372caab"}}, "title": "Reconstructing marine plankton food web interactions using DNA metabarcoding.", "authors": [{"family": "Zamora-Terol", "given": "Sara", "initials": "S", "orcid": "0000-0002-7822-3197", "researcher": {"href": "https://publications.scilifelab.se/researcher/25e1b401fc9a49c5b6f89eaa18f89a57.json"}}, {"family": "Novotny", "given": "Andreas", "initials": "A"}, {"family": "Winder", "given": "Monika", "initials": "M"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "29", "issue": "17", "pages": "3380-3395", "issn-l": "0962-1083"}, "abstract": "Knowledge of zooplankton in situ diet is critical for accurate assessment of marine ecosystem function and structure, but due to methodological constraints, there is still a limited understanding of ecological networks in marine ecosystems. Here, we used DNA-metabarcoding to study trophic interactions, with the aim to unveil the natural diet of zooplankton species under temporal variation of food resources. Several target consumers, including copepods and cladocerans, were investigated by sequencing 16S rRNA and 18S rRNA genes to identify prokaryote and eukaryote potential prey present in their guts. During the spring phytoplankton bloom, we found a dominance of diatom and dinoflagellate trophic links to copepods. During the summer period, zooplankton including cladocerans showed a more diverse diet dominated by cyanobacteria and heterotrophic prey. Our study suggests that copepods present trophic plasticity, changing their natural diet over seasons, and adapting their feeding strategies to the available prey spectrum, with some species being more selective. We did not find a large overlap of prey consumed by copepods and cladocerans, based on prey diversity found in their guts, suggesting that they occupy different roles in the trophic web. This study represents the first molecular approach to investigate several zooplankton-prey associations under seasonal variation, and highlights how, unlike other techniques, the diversity coverage is high when using DNA, allowing the possibility to detect a wide range of trophic interactions in plankton communities.", "doi": "10.1111/mec.15555", "pmid": "32681684", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-07T16:34:37.952Z", "modified": "2024-01-16T13:48:41.803Z"}, {"entity": "publication", "iuid": "217d4684484246f2aec3ad0c479d36a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/217d4684484246f2aec3ad0c479d36a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/217d4684484246f2aec3ad0c479d36a0"}}, "title": "Linked-read sequencing enables haplotype-resolved resequencing at population scale.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Garc\u00eda", "given": "Jes\u00fas T", "initials": "JT", "orcid": "0000-0003-4126-9658", "researcher": {"href": "https://publications.scilifelab.se/researcher/699bf85902454a43aeef0a075ed38a39.json"}}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"volume": "20", "issn": "1755-0998", "issue": "5", "pages": "1311-1322", "title": "Mol Ecol Resour", "issn-l": "1755-098X"}, "abstract": "The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences - including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps - are still limited by the lack of high-quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25\u00d7, 20\u00d7, 15\u00d7, 10\u00d7, 7\u00d7, and 5\u00d7) with high-coverage data (46-68\u00d7) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15\u00d7 coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15\u00d7 coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25\u00d7 coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing at population scale.", "doi": "10.1111/1755-0998.13192", "pmid": "32419391", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-06-01T16:55:32.608Z", "modified": "2024-01-16T13:48:41.811Z"}, {"entity": "publication", "iuid": "b4d0b1c447554140a71deee30c1f4e81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4d0b1c447554140a71deee30c1f4e81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4d0b1c447554140a71deee30c1f4e81"}}, "title": "Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Ormestad", "given": "Mattias", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"volume": "20", "issn": "1755-0998", "issue": "5", "title": "Mol Ecol Resour", "pages": "1171-1181", "issn-l": "1755-098X"}, "abstract": "The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.", "doi": "10.1111/1755-0998.13009", "pmid": "30848092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-02T17:19:31.114Z", "modified": "2024-01-16T13:48:41.825Z"}, {"entity": "publication", "iuid": "28b02c11dee94c2dac39ef643d0f95e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28b02c11dee94c2dac39ef643d0f95e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28b02c11dee94c2dac39ef643d0f95e9"}}, "title": "Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.", "authors": [{"family": "Svedberg", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N"}, {"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}, {"family": "Apell\u00e1niz-Ruiz", "given": "Mar\u00eda", "initials": "M"}, {"family": "Rodr\u00edguez-Antona", "given": "Cristina", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Lung Cancer", "issn": "1872-8332", "volume": "147", "issue": null, "pages": "106-114", "issn-l": "0169-5002"}, "abstract": "Gemcitabine/carboplatin treatment is known to cause severe adverse drug reactions which can lead to the need for reduction or cessation of chemotherapy. It would be beneficial to identify patients at risk of severe hematological toxicity in advance before treatment start. This study aims to identify genetic markers for gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients.\n\nWhole-exome sequencing was performed on 215 patients. Association analysis was performed on single-nucleotide variants (SNVs) and genes, and the validation was based on an independent genome-wide association study (GWAS). Based on the association and validation analyses the genetic variants were then selected for and used in weighted genetic risk score (wGRS) prediction models for leukopenia and neutropenia.\n\nAssociation analysis identified 50 and 111 SNVs, and 12 and 20 genes, for leukopenia and neutropenia, respectively. Of these SNVS 20 and 19 were partially validated for leukopenia and neutropenia, respectively. The genes SVIL (p = 2.48E-06) and EFCAB2 (p = 4.63E-06) were significantly associated with leukopenia contain the partially validated SNVs rs3740003, rs10160013, rs1547169, rs10927386 and rs10927387. The wGRS prediction models showed significantly different risk scores for high and low toxicity patients.\n\nWe have identified and partially validated genetic biomarkers in SNVs and genes correlated to gemcitabine/carboplatin-induced leukopenia and neutropenia and created wGRS models for predicting the risk of chemotherapy-induced hematological toxicity. These results provide a strong foundation for further studies of chemotherapy-induced toxicity.", "doi": "10.1016/j.lungcan.2020.07.005", "pmid": "32683206", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0169-5002(20)30516-X"}], "notes": [], "created": "2020-12-07T16:27:05.896Z", "modified": "2021-11-10T12:47:43.408Z"}, {"entity": "publication", "iuid": "8005879a074c4abf932ec97a4b9e74b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8005879a074c4abf932ec97a4b9e74b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8005879a074c4abf932ec97a4b9e74b4"}}, "title": "DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.", "authors": [{"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Gomez", "given": "Yamenah", "initials": "Y"}, {"family": "Rezaei", "given": "Shiva", "initials": "S"}, {"family": "Gebhardt-Henrich", "given": "Sabine G", "initials": "SG"}, {"family": "V\u00f6geli", "given": "Sabine", "initials": "S"}, {"family": "Stratmann", "given": "Ariane", "initials": "A"}, {"family": "Voelkl", "given": "Bernhard", "initials": "B"}, {"family": "Toscano", "given": "Michael J", "initials": "MJ"}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Comp Biochem Physiol Part D Genomics Proteomics", "issn": "1878-0407", "volume": "35", "issue": null, "pages": "100700", "issn-l": null}, "abstract": "Domesticated animals are unique to investigate the contribution of genetic and non-genetic factors to specific phenotypes. Among non-genetic factors involved in phenotype formation are epigenetic mechanisms. Here we aimed to identify whether relative DNA methylation differences in the nidopallium between groups of individuals are among the non-genetic factors involved in the emergence of differential behavioral patterns in hens. The nidopallium was selected due to its important role in complex cognitive function (i.e., decision making) in birds. Behavioral patterns that spontaneously emerge in hens living in a highly controlled environment were identified with a unique tracking system that recorded their transitions between pen zones. Behavioral activity patterns were characterized through three classification schemes: (i) daily specific features of behavioral routines (Entropy), (ii) daily spatio-temporal activity patterns (Dynamic Time Warping), and (iii) social leading behavior (Leading Index). Unique differentially methylated regions (DMRs) were identified between behavioral patterns emerging within classification schemes, with entropy having the higher number. Functionally, DTW had double the proportion of affected promoters and half of the distal intergenic regions. Pathway enrichment analysis of DMR-associated genes revealed that Entropy relates mainly to cell cycle checkpoints, Leading Index to mitochondrial function, and DTW to gene expression regulation. Our study suggests that different biological functions within neurons (particularly in the nidopallium) could be responsible for the emergence of distinct behavior patterns and that epigenetic variation within brain tissues would be an important factor to explain behavioral variation.", "doi": "10.1016/j.cbd.2020.100700", "pmid": "32702621", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S1744-117X(20)30047-2"}], "notes": [], "created": "2020-12-07T16:34:39.070Z", "modified": "2021-11-10T12:47:44.502Z"}, {"entity": "publication", "iuid": "2a387a31c3c54f2f9d3abce4e7efdfe2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a387a31c3c54f2f9d3abce4e7efdfe2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a387a31c3c54f2f9d3abce4e7efdfe2"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/82499805c5c24c46b8c2ec6427345c89.json"}}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78aae6139714fa3ae8221f3fb380b5a.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications.scilifelab.se/researcher/083131be9eab46df9c789fb018316dff.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications.scilifelab.se/researcher/992734ee2f564e51b65c3d24770cc337.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J", "orcid": "0000-0001-8341-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/793924a7af814c28a4ad66ff2fabf136.json"}}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a4bfdfbcc54403b818b31b24934151.json"}}, {"family": "Wang", "given": "Hui", "initials": "H", "orcid": "0000-0002-5444-1579", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fc15d279b34209a72be7bd71a9338c.json"}}, {"family": "Matise", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-2998-9927", "researcher": {"href": "https://publications.scilifelab.se/researcher/f861ea74deb9478fa475c5036333dfd9.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications.scilifelab.se/researcher/26137676787f477fb374d629819d898b.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a093b1609b74f74a8a8546f02946782.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "6", "issue": "38", "pages": null}, "abstract": "How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modeling, we define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through down-regulation of Gli transcription. The circuitry conforms an incoherent feed-forward loop, whereby Gli proteins not only promote expression of Phox2b and thereby MN-fate but also account for a delayed activation of a self-promoting transforming growth factor-\u03b2 (Tgf\u03b2) node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf\u03b2 counteract noise and increase temporal accuracy at the population level, providing a functional rationale for the intrinsically programmed activation of extrinsic switch signals in temporal patterning. Our study defines how time is reliably encoded during the sequential specification of neurons.", "doi": "10.1126/sciadv.aba8196", "pmid": "32938678", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6/38/eaba8196"}, {"db": "pmc", "key": "PMC7494341"}], "notes": [], "created": "2020-12-07T16:28:52.509Z", "modified": "2024-01-16T13:48:41.848Z"}, {"entity": "publication", "iuid": "e86d241e17894bde94ff435f5c2ff8fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e86d241e17894bde94ff435f5c2ff8fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e86d241e17894bde94ff435f5c2ff8fa"}}, "title": "Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.", "authors": [{"family": "Soratto", "given": "Tatiany Aparecida Teixeira", "initials": "TAT", "orcid": "0000-0001-6263-6432", "researcher": {"href": "https://publications.scilifelab.se/researcher/2de2acb9e872401384dfb70eaadfb88c.json"}}, {"family": "Darban", "given": "Hamid", "initials": "H"}, {"family": "Bjerkner", "given": "Annelie", "initials": "A"}, {"family": "Coorens", "given": "Maarten", "initials": "M"}, {"family": "Albert", "given": "Jan", "initials": "J"}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2020-08-27", "journal": {"title": "Microbiol Resour Announc", "issn": "2576-098X", "volume": "9", "issue": "35", "issn-l": "2576-098X"}, "abstract": "Here, we report four coding-complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from Stockholm, Sweden, sampled in late April 2020. A rare variant at bp 23463 of the SARS-CoV-2 genome was found, which corresponds to the S1 subunit of the spike protein, changing an arginine (R) residue to histidine (H).", "doi": "10.1128/MRA.00934-20", "pmid": "32855259", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "9/35/e00934-20"}, {"db": "pmc", "key": "PMC7453295"}], "notes": [], "created": "2020-12-07T16:27:03.521Z", "modified": "2024-01-16T13:48:41.868Z"}, {"entity": "publication", "iuid": "be6dfc07d42b41648f42432ddcda8787", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be6dfc07d42b41648f42432ddcda8787.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be6dfc07d42b41648f42432ddcda8787"}}, "title": "Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.", "authors": [{"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "Badam", "given": "Tejaswi Venkata Satya", "initials": "TVS", "orcid": "0000-0002-6719-4861", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e4b28972942434fba0d715354352267.json"}}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H", "orcid": "0000-0001-5797-7873", "researcher": {"href": "https://publications.scilifelab.se/researcher/020d1b7e7693495484dc85c4ba6f2adc.json"}}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}, {"family": "Lubovac-Pilav", "given": "Zelmina", "initials": "Z", "orcid": "0000-0001-6427-0315", "researcher": {"href": "https://publications.scilifelab.se/researcher/af98c65fa2964875bd6d46f9c2488e6b.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gustafsson", "given": "Mika", "initials": "M", "orcid": "0000-0002-0048-4063", "researcher": {"href": "https://publications.scilifelab.se/researcher/466661ecb9274ecc8f1a832b95ef19b2.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-08-24", "journal": {"title": "npj Syst Biol Appl", "issn": "2056-7189", "volume": "6", "issue": "1", "pages": "25", "issn-l": "2056-7189"}, "abstract": "Gemcitabine/carboplatin chemotherapy commonly induces myelosuppression, including neutropenia, leukopenia, and thrombocytopenia. Predicting patients at risk of these adverse drug reactions (ADRs) and adjusting treatments accordingly is a long-term goal of personalized medicine. This study used whole-genome sequencing (WGS) of blood samples from 96 gemcitabine/carboplatin-treated non-small cell lung cancer (NSCLC) patients and gene network modules for predicting myelosuppression. Association of genetic variants in PLINK found 4594, 5019, and 5066 autosomal SNVs/INDELs with p \u2264 1 \u00d7 10-3 for neutropenia, leukopenia, and thrombocytopenia, respectively. Based on the SNVs/INDELs we identified the toxicity module, consisting of 215 unique overlapping genes inferred from MCODE-generated gene network modules of 350, 345, and 313 genes, respectively. These module genes showed enrichment for differentially expressed genes in rat bone marrow, human bone marrow, and human cell lines exposed to carboplatin and gemcitabine (p < 0.05). Then using 80% of the patients as training data, random LASSO reduced the number of SNVs/INDELs in the toxicity module into a feasible prediction model consisting of 62 SNVs/INDELs that accurately predict both the training and the test (remaining 20%) data with high (CTCAE 3-4) and low (CTCAE 0-1) maximal myelosuppressive toxicity completely, with the receiver-operating characteristic (ROC) area under the curve (AUC) of 100%. The present study shows how WGS, gene network modules, and random LASSO can be used to develop a feasible and tested model for predicting myelosuppressive toxicity. Although the proposed model predicts myelosuppression in this study, further evaluation in other studies is required to determine its reproducibility, usability, and clinical effect.", "doi": "10.1038/s41540-020-00146-6", "pmid": "32839457", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41540-020-00146-6"}, {"db": "pmc", "key": "PMC7445166"}], "notes": [], "created": "2020-12-07T16:27:04.771Z", "modified": "2024-01-16T13:48:41.889Z"}, {"entity": "publication", "iuid": "8b85fb5237c649c98d5e35c07b496e3c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b85fb5237c649c98d5e35c07b496e3c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b85fb5237c649c98d5e35c07b496e3c"}}, "title": "Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean \"island-shrews\".", "authors": [{"family": "Woods", "given": "Roseina", "initials": "R"}, {"family": "Turvey", "given": "Samuel T", "initials": "ST", "orcid": "0000-0002-3717-4800", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f9849b335e4e74b810b08cabe6759a.json"}}, {"family": "Brace", "given": "Selina", "initials": "S"}, {"family": "McCabe", "given": "Christopher V", "initials": "CV"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Rayfield", "given": "Emily J", "initials": "EJ"}, {"family": "Brown", "given": "Mark J F", "initials": "MJF"}, {"family": "Barnes", "given": "Ian", "initials": "I"}], "type": "journal article", "published": "2020-08-18", "journal": {"title": "BMC Evol. Biol.", "issn": "1471-2148", "volume": "20", "issue": "1", "pages": "106", "issn-l": "1471-2148"}, "abstract": "The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae (\"island-shrews\") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island.\n\nPrincipal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs.\n\nOur combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.", "doi": "10.1186/s12862-020-01668-7", "pmid": "32811443", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-020-01668-7"}, {"db": "pmc", "key": "PMC7437022"}], "notes": [], "created": "2020-12-07T16:29:53.095Z", "modified": "2021-11-10T12:48:12.533Z"}, {"entity": "publication", "iuid": "ec6422dbc5dc4b039f6c638f56ddcca9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec6422dbc5dc4b039f6c638f56ddcca9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec6422dbc5dc4b039f6c638f56ddcca9"}}, "title": "Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.", "authors": [{"family": "Carlstr\u00f6m", "given": "Karl E", "initials": "KE"}, {"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b85d1ae8136464788be19d62a8863d7.json"}}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Krabbendam", "given": "Inge E", "initials": "IE"}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b0733d3c25145139f42cad897d6726b.json"}}, {"family": "Falc\u00e3o", "given": "Ana Mendanha", "initials": "AM"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "Piehl", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8329-5219", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee04062fbee34836a4fa3f4d2e8076cd.json"}}], "type": "journal article", "published": "2020-08-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4071", "issn-l": "2041-1723"}, "abstract": "Arrest of oligodendrocyte (OL) differentiation and remyelination following myelin damage in multiple sclerosis (MS) is associated with neurodegeneration and clinical worsening. We show that Glutathione S-transferase 4\u03b1 (Gsta4) is highly expressed during adult OL differentiation and that Gsta4 loss impairs differentiation into myelinating OLs in vitro. In addition, we identify Gsta4 as a target of both dimethyl fumarate, an existing MS therapy, and clemastine fumarate, a candidate remyelinating agent in MS. Overexpression of Gsta4 reduces expression of Fas and activity of the mitochondria-associated Casp8-Bid-axis in adult oligodendrocyte precursor cells, leading to improved OL survival during differentiation. The Gsta4 effect on apoptosis during adult OL differentiation was corroborated in vivo in both lysolecithin-induced demyelination and experimental autoimmune encephalomyelitis models, where Casp8 activity was reduced in Gsta4-overexpressing OLs. Our results identify Gsta4 as an intrinsic regulator of OL differentiation, survival and remyelination, as well as a potential target for future reparative MS therapies.", "doi": "10.1038/s41467-020-17871-5", "pmid": "32792491", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-17871-5"}, {"db": "pmc", "key": "PMC7426940"}], "notes": [], "created": "2021-01-08T16:29:42.593Z", "modified": "2024-01-16T13:48:41.933Z"}, {"entity": "publication", "iuid": "be2d410b6d474dcdb78678c145767abe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be2d410b6d474dcdb78678c145767abe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be2d410b6d474dcdb78678c145767abe"}}, "title": "Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.", "authors": [{"family": "Liang", "given": "Shuo", "initials": "S"}, {"family": "Ezerskyte", "given": "Monika", "initials": "M"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Pelechano", "given": "Vicent", "initials": "V"}, {"family": "Dreij", "given": "Kristian", "initials": "K"}], "type": "journal article", "published": "2020-08-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "13513", "issn-l": "2045-2322"}, "abstract": "The transcriptional error rate can be significantly increased by the presence of DNA lesions that instruct mis-insertion during transcription; a process referred to as transcriptional mutagenesis (TM) that can result in altered protein function. Herein, we determined the effect of O6-methylguanine (O6-meG) on transcription and subsequent transactivation activity of p53 in human lung H1299 cells. Levels of TM and effects on transactivation were determined genome wide by RNA-seq. Results showed that 47% of all p53 transcripts contained an uridine misincorporation opposite the lesion at 6 h post transfection, which was decreased to 18% at 24 h. TM at these levels reduced DNA binding activity of p53 to 21% and 80% compared to wild type p53, respectively. Gene expression data were analysed to identify differentially expressed genes due to TM of p53. We show a temporal repression of transactivation of > 100 high confidence p53 target genes including regulators of the cell cycle, DNA damage response and apoptosis. In addition, TM repressed the transcriptional downregulation by p53 of several negative regulators of proliferation and differentiation. Our work demonstrates that TM, even when restricting its effect to an individual transcription factor, has the potential to alter gene expression programs and diversify cellular phenotypes.", "doi": "10.1038/s41598-020-70412-4", "pmid": "32782319", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-70412-4"}, {"db": "pmc", "key": "PMC7419513"}], "notes": [], "created": "2021-01-08T16:29:43.891Z", "modified": "2021-11-10T12:48:22.899Z"}, {"entity": "publication", "iuid": "1c72116bf22e498797792df3c564ce88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c72116bf22e498797792df3c564ce88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c72116bf22e498797792df3c564ce88"}}, "title": "Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.", "authors": [{"family": "Floudas", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-6119-2590", "researcher": {"href": "https://publications.scilifelab.se/researcher/d083c79383704b0f813c53f862e31ca2.json"}}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Johansson", "given": "Tomas", "initials": "T"}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0000-0001-9172-3068", "researcher": {"href": "https://publications.scilifelab.se/researcher/edffc6f9df60444a9480380c68e7d202.json"}}, {"family": "Tunlid", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2020-08-00", "journal": {"volume": "14", "issn": "1751-7370", "issue": "8", "title": "ISME J", "pages": "2046-2059", "issn-l": "1751-7362"}, "abstract": "Litter decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.", "doi": "10.1038/s41396-020-0667-6", "pmid": "32382073", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-020-0667-6"}, {"db": "pmc", "key": "PMC7368018"}, {"db": "Dryad", "key": "10.5061/dryad.pk0p2ngk1"}], "notes": [], "created": "2020-05-15T08:57:38.045Z", "modified": "2021-12-10T10:02:12.162Z"}, {"entity": "publication", "iuid": "ba8e61b15fdf4091b7ee12bca3608e26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba8e61b15fdf4091b7ee12bca3608e26"}}, "title": "The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.", "authors": [{"family": "Xu", "given": "Feifei", "initials": "F", "orcid": "0000-0003-1946-1520", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c51ec60768479f851e29ebc804f547.json"}}, {"family": "Jim\u00e9nez-Gonz\u00e1lez", "given": "Alejandro", "initials": "A", "orcid": "0000-0003-3493-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9c6b93b731741018637733969c308a6.json"}}, {"family": "Einarsson", "given": "Elin", "initials": "E", "orcid": "0000-0002-1242-5263", "researcher": {"href": "https://publications.scilifelab.se/researcher/be89fa4c7f9d484c858a0bf385f06c61.json"}}, {"family": "\u00c1stvaldsson", "given": "\u00c1sgeir", "initials": "\u00c1", "orcid": "0000-0002-0320-6974", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a3d973dc6d246b48426d2063eef8934.json"}}, {"family": "Peirasmaki", "given": "Dimitra", "initials": "D", "orcid": "0000-0001-5376-626X", "researcher": {"href": "https://publications.scilifelab.se/researcher/94231cbd0cab4644b42c3fab58cea9aa.json"}}, {"family": "Eckmann", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Jan O", "initials": "JO", "orcid": "0000-0002-3075-4896", "researcher": {"href": "https://publications.scilifelab.se/researcher/489ed7f61a7b49a3a7ebd9ee3c391f5b.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J", "orcid": "0000-0002-7992-7970", "researcher": {"href": "https://publications.scilifelab.se/researcher/622d380bca244d738f5551cbed742b3e.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Microb Genom", "issn": "2057-5858", "volume": "6", "issue": "8", "issn-l": null}, "abstract": "Diplomonad parasites of the genus Giardia have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic Giardia species, Giardia intestinalis, has been extensively studied at the genome and gene expression level, but no such information is available for other Giardia species. Comparative data would be particularly valuable for Giardia muris, which colonizes mice and is commonly used as a prototypic in vivo model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of G. muris. We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. G. muris and G. intestinalis share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to G. intestinalis, G. muris maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the G. muris genome suggest significant metabolic differences to G. intestinalis. Additionally, G. muris encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the Giardia genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the Giardia genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host-pathogen interaction in the G. muris-mouse pathosystem.", "doi": "10.1099/mgen.0.000402", "pmid": "32618561", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7641422"}], "notes": [], "created": "2021-01-08T16:29:45.383Z", "modified": "2021-11-10T12:48:32.906Z"}, {"entity": "publication", "iuid": "43ac5630ef6c48389d5164ecaf4a37f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43ac5630ef6c48389d5164ecaf4a37f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43ac5630ef6c48389d5164ecaf4a37f9"}}, "title": "Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.", "authors": [{"family": "Petrus-Reurer", "given": "Sandra", "initials": "S", "orcid": "0000-0002-7051-1741", "researcher": {"href": "https://publications.scilifelab.se/researcher/716f74c81a3240e5b612dab55e997267.json"}}, {"family": "Kumar", "given": "Pankaj", "initials": "P", "orcid": "0000-0002-8411-1634", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e9109710e2e45009c332e257c3c498a.json"}}, {"family": "Padrell S\u00e1nchez", "given": "Sara", "initials": "S"}, {"family": "Aronsson", "given": "Monica", "initials": "M"}, {"family": "Andr\u00e9", "given": "Helder", "initials": "H"}, {"family": "Bartuma", "given": "Hammurabi", "initials": "H"}, {"family": "Plaza Reyes", "given": "Alvaro", "initials": "A"}, {"family": "Nandrot", "given": "Emeline F", "initials": "EF"}, {"family": "Kvanta", "given": "Anders", "initials": "A"}, {"family": "Lanner", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-2771-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba53ce48a35d413eb86cd104488ce669.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Stem Cells Transl Med", "issn": "2157-6580", "issn-l": "2157-6564", "volume": "9", "issue": "8", "pages": "936-953"}, "abstract": "As pluripotent stem cell (PSC)-based reparative cell therapies are reaching the bedside, there is a growing need for the standardization of studies concerning safety of the derived products. Clinical trials using these promising strategies are in development, and treatment for age-related macular degeneration is one of the first that has reached patients. We have previously established a xeno-free and defined differentiation protocol to generate functional human embryonic stem cells (hESCs)-derived retinal pigment epithelial (RPE) cells. In this study, we perform preclinical safety studies including karyotype and whole-genome sequencing (WGS) to assess genome stability, single-cell RNA sequencing to ensure cell purity, and biodistribution and tumorigenicity analysis to rule out potential migratory or tumorigenic properties of these cells. WGS analysis illustrates that existing germline variants load is higher than the introduced variants acquired through in vitro culture or differentiation, and enforces the importance to examine the genome integrity at a deeper level than just karyotype. Altogether, we provide a strategy for preclinical evaluation of PSC-based therapies and the data support safety of the hESC-RPE cells generated through our in vitro differentiation methodology.", "doi": "10.1002/sctm.19-0396", "pmid": "32319201", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7381808"}], "notes": [], "created": "2020-10-06T11:06:47.295Z", "modified": "2024-01-16T13:48:42.005Z"}, {"entity": "publication", "iuid": "5446fda678b44232a03fb58e253bbb2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5446fda678b44232a03fb58e253bbb2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5446fda678b44232a03fb58e253bbb2f"}}, "title": "A 3D Cell Culture Model Identifies Wnt/\u03b2-Catenin Mediated Inhibition of p53 as a Critical Step during Human Hepatocyte Regeneration.", "authors": [{"family": "Oliva-Vilarnau", "given": "Nuria", "initials": "N", "orcid": "0000-0002-3083-6701", "researcher": {"href": "https://publications.scilifelab.se/researcher/29e93281648540e9ae407c2cefbc542e.json"}}, {"family": "Vorrink", "given": "Sabine U", "initials": "SU"}, {"family": "Ingelman-Sundberg", "given": "Magnus", "initials": "M"}, {"family": "Lauschke", "given": "Volker M", "initials": "VM", "orcid": "0000-0002-1140-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c123916fbf4948a911560c1a259496.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "7", "issue": "15", "pages": "2000248", "issn-l": null}, "abstract": "The liver is a highly regenerative organ. While mature hepatocytes under homeostatic conditions are largely quiescent, upon injury, they rapidly enter the cell cycle to recover the damaged tissue. In rodents, a variety of injury models have provided important insights into the molecular underpinnings that govern the proliferative activation of quiescent hepatocytes. However, little is known about the molecular mechanisms of human hepatocyte regeneration and experimental methods to expand primary human hepatocytes (PHH). Here, a 3D spheroid model of PHH is established to study hepatocyte regeneration and integrative time-lapse multi-omics analyses show that upon isolation from the native liver PHH acquire a regenerative phenotype, as seen in vivo upon partial hepatectomy. However, proliferation is limited. By analyzing global promoter motif activities, it is predicted that activation of Wnt/\u03b2-catenin and inhibition of p53 signaling are critical factors required for human hepatocyte proliferation. Functional validations reveal that activation of Wnt signaling through external cues alone is sufficient to inhibit p53 and its proliferative senescence-inducing target PAI1 (SERPINE1) and drive proliferation of >50% of all PHH. A scalable 3D culture model is established to study the molecular and cellular biology of human hepatocyte regeneration. By using this model, an essential role of Wnt/\u03b2-catenin signaling during human hepatocyte regeneration is identified.", "doi": "10.1002/advs.202000248", "pmid": "32775153", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "ADVS1906"}, {"db": "pmc", "key": "PMC7404138"}], "notes": [], "created": "2020-12-07T16:34:35.595Z", "modified": "2022-03-29T13:44:10.380Z"}, {"entity": "publication", "iuid": "8e7a9d42330c43e1965e9b1e2bc5fb5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e7a9d42330c43e1965e9b1e2bc5fb5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e7a9d42330c43e1965e9b1e2bc5fb5a"}}, "title": "Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.", "authors": [{"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Alberti", "given": "Federica", "initials": "F"}, {"family": "Plotnikov", "given": "Valery", "initials": "V"}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Grigoriev", "given": "Semyon", "initials": "S"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Barnes", "given": "Ian", "initials": "I"}, {"family": "Barnett", "given": "Ross", "initials": "R"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "D\u00f6ppes", "given": "Doris", "initials": "D"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2020-07-28", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "12621", "issn-l": "2045-2322"}, "abstract": "The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.", "doi": "10.1038/s41598-020-69474-1", "pmid": "32724178", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-69474-1"}, {"db": "pmc", "key": "PMC7387438"}], "notes": [], "created": "2020-12-07T16:29:55.459Z", "modified": "2021-11-10T12:48:58.284Z"}, {"entity": "publication", "iuid": "ecc643eb325e459ba96278ec8f94c919", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecc643eb325e459ba96278ec8f94c919.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecc643eb325e459ba96278ec8f94c919"}}, "title": "Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.", "authors": [{"family": "Ji", "given": "Andrew L", "initials": "AL"}, {"family": "Rubin", "given": "Adam J", "initials": "AJ"}, {"family": "Thrane", "given": "Kim", "initials": "K"}, {"family": "Jiang", "given": "Sizun", "initials": "S"}, {"family": "Reynolds", "given": "David L", "initials": "DL"}, {"family": "Meyers", "given": "Robin M", "initials": "RM"}, {"family": "Guo", "given": "Margaret G", "initials": "MG"}, {"family": "George", "given": "Benson M", "initials": "BM"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Bai", "given": "Yunhao", "initials": "Y"}, {"family": "Zhu", "given": "Bokai", "initials": "B"}, {"family": "Bhaduri", "given": "Aparna", "initials": "A"}, {"family": "Meyers", "given": "Jordan M", "initials": "JM"}, {"family": "Rovira-Clav\u00e9", "given": "Xavier", "initials": "X"}, {"family": "Hollmig", "given": "S Tyler", "initials": "ST"}, {"family": "Aasi", "given": "Sumaira Z", "initials": "SZ"}, {"family": "Nolan", "given": "Garry P", "initials": "GP"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Khavari", "given": "Paul A", "initials": "PA"}], "type": "journal article", "published": "2020-07-23", "journal": {"title": "Cell", "issn": "1097-4172", "volume": "182", "issue": "2", "pages": "497-514.e22", "issn-l": "0092-8674"}, "abstract": "To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.", "doi": "10.1016/j.cell.2020.05.039", "pmid": "32579974", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(20)30672-3"}, {"db": "pmc", "key": "PMC7391009"}], "notes": [], "created": "2020-07-08T13:03:43.753Z", "modified": "2021-11-10T12:49:04.897Z"}, {"entity": "publication", "iuid": "87e07ded7de44a53ae4395ae27dfc8d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87e07ded7de44a53ae4395ae27dfc8d4"}}, "title": "Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach", "authors": [{"family": "von der Heyde", "given": "Benedikt", "initials": "B", "orcid": "0000-0002-9889-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/803c0e0639174a50b59ae597802e824f.json"}}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Klingstr\u00f6m", "given": "Tiffany", "initials": "T"}, {"family": "Jumaa", "given": "Sitaf", "initials": "S"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Snieder", "given": "Harold", "initials": "H", "orcid": "0000-0003-1949-2298", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9276827839a4f3cb50dcaa2ad4708a5.json"}}, {"family": "de Geus", "given": "Eco", "initials": "E", "orcid": "0000-0001-6022-2666", "researcher": {"href": "https://publications.scilifelab.se/researcher/9abb01a905f347df8214d469d6c5ac45.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Ingelsson", "given": "Erik", "initials": "E", "orcid": "0000-0003-2256-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/689bc741ea6547d18de7080c84d0193e.json"}}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Brooke", "given": "Hannah L", "initials": "HL"}, {"family": "den Hoed", "given": "Marcel", "initials": "M", "orcid": "0000-0001-8081-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d712cc087d344b15ab9a7971640acebe.json"}}], "type": "journal-article", "published": "2020-07-16", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "10", "issue": "1", "pages": "11831"}, "abstract": "A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 \u00b5M ivabradine-an open channel blocker of HCNs-for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).", "doi": "10.1038/s41598-020-68567-1", "pmid": "32678143", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "BioImage Informatics": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Genome Engineering Zebrafish": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7367351"}, {"db": "pii", "key": "10.1038/s41598-020-68567-1"}], "notes": [], "created": "2020-08-19T09:27:04.550Z", "modified": "2024-01-16T13:48:42.137Z"}, {"entity": "publication", "iuid": "15981a63f8c94a17ab3bf14f021ef2bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15981a63f8c94a17ab3bf14f021ef2bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15981a63f8c94a17ab3bf14f021ef2bc"}}, "title": "Seamless integration of image and molecular analysis for spatial transcriptomics workflows.", "authors": [{"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2020-07-14", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "482", "issn-l": "1471-2164"}, "abstract": "Recent advancements in in situ gene expression technologies constitute a new and rapidly evolving field of transcriptomics. With the recent launch of the 10x Genomics Visium platform, such methods have started to become widely adopted. The experimental protocol is conducted on individual tissue sections collected from a larger tissue sample. The two-dimensional nature of this data requires multiple consecutive sections to be collected from the sample in order to construct a comprehensive three-dimensional map of the tissue. However, there is currently no software available that lets the user process the images, align stacked experiments, and finally visualize them together in 3D to create a holistic view of the tissue.\n\nWe have developed an R package named STUtility that takes 10x Genomics Visium data as input and provides features to perform standardized data transformations, alignment of multiple tissue sections, regional annotation, and visualizations of the combined data in a 3D model framework.\n\nSTUtility lets the user process, analyze and visualize multiple samples of spatially resolved RNA sequencing and image data from the 10x Genomics Visium platform. The package builds on the Seurat framework and uses familiar APIs and well-proven analysis methods. An introduction to the software package is available at https://ludvigla.github.io/STUtility_web_site/ .", "doi": "10.1186/s12864-020-06832-3", "pmid": "32664861", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-06832-3"}, {"db": "pmc", "key": "PMC7386244"}], "notes": [], "created": "2020-12-07T16:28:50.026Z", "modified": "2024-01-16T13:48:42.159Z"}, {"entity": "publication", "iuid": "92f8202f59a04becbbbcac6a1abbc60d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92f8202f59a04becbbbcac6a1abbc60d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92f8202f59a04becbbbcac6a1abbc60d"}}, "title": "Systems biology of acidophile biofilms for efficient metal extraction.", "authors": [{"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Herold", "given": "Malte", "initials": "M"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Hajjami", "given": "Mohamed El", "initials": "ME"}, {"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Ilie", "given": "Olga", "initials": "O"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Poetsch", "given": "Ansgar", "initials": "A"}, {"family": "Sand", "given": "Wolfgang", "initials": "W"}, {"family": "Vera", "given": "Mario", "initials": "M"}, {"family": "Pivkin", "given": "Igor V", "initials": "IV"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "dataset", "published": "2020-07-07", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "7", "issue": "1", "pages": "215", "issn-l": "2052-4463"}, "abstract": "Society's demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput \"omics\" performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.", "doi": "10.1038/s41597-020-0519-2", "pmid": "32636389", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-020-0519-2"}, {"db": "pmc", "key": "PMC7340779"}], "notes": [], "created": "2020-12-07T16:29:57.828Z", "modified": "2024-01-16T13:48:42.188Z"}, {"entity": "publication", "iuid": "110fc8367dec489db814cf5a89464741", "links": {"self": {"href": "https://publications.scilifelab.se/publication/110fc8367dec489db814cf5a89464741.json"}, "display": {"href": "https://publications.scilifelab.se/publication/110fc8367dec489db814cf5a89464741"}}, "title": "Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Sun", "given": "Xiaole", "initials": "X"}, {"family": "Stranne", "given": "Christian", "initials": "C"}, {"family": "Salgado", "given": "Marco G", "initials": "MG"}, {"family": "Bonaglia", "given": "Stefano", "initials": "S"}, {"family": "Geibel", "given": "Marc", "initials": "M"}, {"family": "Jakobsson", "given": "Martin", "initials": "M"}, {"family": "Norkko", "given": "Alf", "initials": "A"}, {"family": "Humborg", "given": "Christoph", "initials": "C"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2020-07-07", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "issue": null, "pages": "1536", "issn-l": "1664-302X"}, "abstract": "Coastal zones are transitional areas between land and sea where large amounts of organic and inorganic carbon compounds are recycled by microbes. Especially shallow zones near land have been shown to be the main source for oceanic methane (CH4) emissions. Water depth has been predicted as the best explanatory variable, which is related to CH4 ebullition, but exactly how sediment methanotrophs mediates these emissions along water depth is unknown. Here, we investigated the relative abundance and RNA transcripts attributed to methane oxidation proteins of aerobic methanotrophs in the sediment of shallow coastal zones with high CH4 concentrations within a depth gradient from 10-45 m. Field sampling consisted of collecting sediment (top 0-2 cm layer) from eight stations along this depth gradient in the coastal Baltic Sea. The relative abundance and RNA transcripts attributed to the CH4 oxidizing protein (pMMO; particulate methane monooxygenase) of the dominant methanotroph Methylococcales was significantly higher in deeper costal offshore areas (36-45 m water depth) compared to adjacent shallow zones (10-28 m). This was in accordance with the shallow zones having higher CH4 concentrations in the surface water, as well as more CH4 seeps from the sediment. Furthermore, our findings indicate that the low prevalence of Methylococcales and RNA transcripts attributed to pMMO was restrained to the euphotic zone (indicated by Photosynthetically active radiation (PAR) data, photosynthesis proteins, and 18S rRNA data of benthic diatoms). This was also indicated by a positive relationship between water depth and the relative abundance of Methylococcales and pMMO. How these processes are affected by light availability requires further studies. CH4 ebullition potentially bypasses aerobic methanotrophs in shallow coastal areas, reducing CH4 availability and limiting their growth. Such mechanism could help explain their reduced relative abundance and related RNA transcripts for pMMO. These findings can partly explain the difference in CH4 concentrations between shallow and deep coastal areas, and the relationship between CH4 concentrations and water depth.", "doi": "10.3389/fmicb.2020.01536", "pmid": "32733420", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7362727"}], "notes": [], "created": "2020-12-07T16:32:26.232Z", "modified": "2024-01-16T13:48:42.195Z"}, {"entity": "publication", "iuid": "5d3afacdca744fef83a8b327dedfaf5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d3afacdca744fef83a8b327dedfaf5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d3afacdca744fef83a8b327dedfaf5c"}}, "title": "Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.", "authors": [{"family": "Gonzalez", "given": "Francisco", "initials": "F"}, {"family": "Borrero-Echeverry", "given": "Felipe", "initials": "F"}, {"family": "J\u00f3svai", "given": "J\u00falia K", "initials": "JK"}, {"family": "Strandh", "given": "Maria", "initials": "M"}, {"family": "Unelius", "given": "C Rikard", "initials": "CR"}, {"family": "T\u00f3th", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Witzgall", "given": "Peter", "initials": "P", "orcid": "0000-0002-4697-3380", "researcher": {"href": "https://publications.scilifelab.se/researcher/548d4ff93a3f488e8133e5f7b1f79097.json"}}, {"family": "Bengtsson", "given": "Marie", "initials": "M"}, {"family": "Walker", "given": "William B", "initials": "WB"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "14", "pages": "7334-7348", "issn-l": "2045-7758"}, "abstract": "The search for mates and food is mediated by volatile chemicals. Insects sense food odorants and sex pheromones through odorant receptors (ORs) and pheromone receptors (PRs), which are expressed in olfactory sensory neurons. Molecular phylogenetics of ORs, informed by behavioral and functional data, generates sound hypotheses for the identification of semiochemicals driving olfactory behavior. Studying orthologous receptors and their ligands across taxa affords insights into the role of chemical communication in reproductive isolation and phylogenetic divergence. The female sex pheromone of green budworm moth Hedya nubiferana (Lepidoptera, Totricidae) is a blend of two unsaturated acetates, only a blend of both elicits male attraction. Females produce in addition codlemone, which is the sex pheromone of another tortricid, codling moth Cydia pomonella. Codlemone also attracts green budworm moth males. Concomitantly, green budworm and codling moth males are attracted to the host plant volatile pear ester. A congruent behavioral response to the same pheromone and plant volatile in two tortricid species suggests co-occurrence of dedicated olfactory channels. In codling moth, one PR is tuned to both compounds, the sex pheromone codlemone and the plant volatile pear ester. Our phylogenetic analysis finds that green budworm moth expresses an orthologous PR gene. Shared ancestry, and high levels of amino acid identity and sequence similarity, in codling and green budworm moth PRs offer an explanation for parallel attraction of both species to the same compounds. A conserved olfactory channel for a sex pheromone and a host plant volatile substantiates the alliance of social and habitat signals in insect chemical communication. Field attraction assays confirm that in silico investigations of ORs afford powerful predictions for an efficient identification of behavior-modifying semiochemicals, for an improved understanding of the mechanisms of host plant attraction in insect herbivores and for the further development of sustainable insect control.", "doi": "10.1002/ece3.6458", "pmid": "32760532", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36458"}, {"db": "pmc", "key": "PMC7391548"}], "notes": [], "created": "2020-12-07T16:29:50.620Z", "modified": "2024-01-16T13:48:42.276Z"}, {"entity": "publication", "iuid": "dfba8e4537274d90abb9a4c98eec18ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfba8e4537274d90abb9a4c98eec18ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfba8e4537274d90abb9a4c98eec18ae"}}, "title": "Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.", "authors": [{"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Hedberg", "given": "Johanna", "initials": "J"}, {"family": "Marzocchi", "given": "Ugo", "initials": "U", "orcid": "0000-0002-4746-9944", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d1ad4b2b3e48db9cc591f4574cb848.json"}}, {"family": "Iburg", "given": "Sven", "initials": "S"}, {"family": "Glud", "given": "Ronnie N", "initials": "RN", "orcid": "0000-0002-7069-893X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9598036867244f2a67d4041f179859c.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Mar Environ Res", "issn": "1879-0291", "volume": "159", "issue": null, "pages": "104968", "issn-l": null}, "abstract": "Oxygen depleted areas are widespread in the marine realm. Unlike macrofauna, meiofauna are abundant in hypoxic sediments. We studied to what extent meiofauna affect oxygen availability, sulfide removal and microbial communities. Meiofauna were extracted alive and added to intact sediments simulating abundance gradients previously reported in the area. A total of 324 porewater microprofiles were recorded over a 3-week incubation period and microbial community structure and cable bacteria densities were determined at the end of the experiment. At high abundances meiofauna activity deepened oxygen penetration by 85%, 59%, and 62% after 5, 14, and 22 days, respectively, compared to control sediment with scarce meiofauna. After 6 days, meiofauna increased the volume of oxidized, sulfide-free sediment by 68% and reduced sulfide fluxes from 8.8 to 0.4 mmol m-2 d-1. After 15 days, the difference with the control attenuated due to the presence of a cable bacteria population, which facilitated sulfides oxidation in all treatments. 16S rRNA gene analysis revealed that meiofauna affected microbial community structure (beta diversity). Thus, meiofauna bioturbation plays an important role in deepening oxygen penetration, counteracting euxinia and in structuring microbial diversity of hypoxic sediments. Co-existence with cable bacteria demonstrates neutralism interaction between these two ecosystem engineers.", "doi": "10.1016/j.marenvres.2020.104968", "pmid": "32662428", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0141-1136(19)30836-0"}, {"db": "pmc", "key": "PMC7369627"}], "notes": [], "created": "2020-12-07T16:32:28.789Z", "modified": "2024-01-16T13:48:42.283Z"}, {"entity": "publication", "iuid": "8526e68a3e854ed392784e2c39f600aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8526e68a3e854ed392784e2c39f600aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8526e68a3e854ed392784e2c39f600aa"}}, "title": "Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.", "authors": [{"family": "Ndegwa", "given": "Nelson", "initials": "N"}, {"family": "Ploner", "given": "Alexander", "initials": "A"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Zagai", "given": "Ulrika", "initials": "U"}, {"family": "Andreasson", "given": "Anna", "initials": "A"}, {"family": "Vieth", "given": "Michael", "initials": "M"}, {"family": "Talley", "given": "Nicholas J", "initials": "NJ"}, {"family": "Agreus", "given": "Lars", "initials": "L"}, {"family": "Ye", "given": "Weimin", "initials": "W"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Clin Transl Gastroenterol", "issn": "2155-384X", "volume": "11", "issue": "7", "pages": "e00191", "issn-l": "2155-384X"}, "abstract": "Non-Helicobacter pylori microbiota might account for some cases with unexplained chronic gastritis that may in a minority eventually progress to gastric cancer through the Correa cascade. We characterized gastric microbiota by describing the normal stomach, compared it with early precancerous lesions and other disease states, and assessed whether H. pylori status affects bacterial diversity.\n\nIn a population-based study of those with and without gastrointestinal symptoms, cytology brush samples were collected during endoscopy from 316 individuals. Mucosal status was classified as normal mucosa (171), nonatrophic H. pylori gastritis (33), atrophic gastritis (12), or antral chemical gastritis (61). The 16S rRNA gene sequencing and analysis were performed to characterize the microbiota.\n\nMicrobiota in atrophic gastritis and nonatrophic H. pylori gastritis stomachs were dysbiotic and differed from those in the normal stomach (P = 0.001). The normal stomach had the highest microbial diversity, followed by antral chemical gastritis. The atrophic gastritis and chronic H. pylori gastritis groups had the lowest diversity, a difference that was statistically significant (P = 0.01). Besides H. pylori, non-H. pylori bacteria accounted for group differences. Microbial network analysis showed that the normal group network was most highly connected, whereas the H. pylori gastritis group had the lowest connection. We found an increasing positive co-occurrence of oral bacteria in the stomach because samples deviated from the normal network, some of which were pathogens. The H. pylori-negative group had the highest microbial diversity (Shannon index) compared with the H. pylori-positive group (P = 0.001).\n\nIn this low-H. pylori prevalence general population, the gastric mucosal microbiota of the normal stomach differed significantly from those with nonatrophic or atrophic gastritis. There was an increasing abundance of pathogenic bacteria from the normal state to early precancerous states.", "doi": "10.14309/ctg.0000000000000191", "pmid": "32764211", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "01720094-202007000-00013"}, {"db": "pmc", "key": "PMC7431247"}], "notes": [], "created": "2020-09-17T15:25:36.522Z", "modified": "2024-01-16T13:48:42.307Z"}, {"entity": "publication", "iuid": "8cb53a7450cc4a7e80432a058a5d263d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cb53a7450cc4a7e80432a058a5d263d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cb53a7450cc4a7e80432a058a5d263d"}}, "title": "Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.", "authors": [{"family": "Zhong", "given": "Xiuqin", "initials": "X", "orcid": "0000-0002-4772-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1847f16fd2a4d1cac925c7b89b70684.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "10", "issue": "13", "pages": "6421-6434", "issn-l": "2045-7758"}, "abstract": "Different host species often differ considerably in susceptibility to a given pathogen, but the causes of such differences are rarely known. The natural hosts of the tick-transmitted bacterium Borrelia afzelii, which is one of causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Previous studies have shown that B. afzelii-infected bank voles (Myodes glareolus) have about ten times higher bacterial load than infected yellow-necked mice (Apodemus flavicollis), indicating that these two species differ in resistance. In this study, we compared the immune response to B. afzelii infection in these host species by using RNA sequencing to quantify gene expression in spleen. Gene set enrichment analysis (GSEA) showed that several immune pathways were down-regulated in infected animals in both bank voles and yellow-necked mice. Moreover, IFN\u03b1 response was up-regulated in B. afzelii-infected yellow-necked mice, while IL6 signaling and the complement pathway were down-regulated in infected bank voles; differences in regulation of these three pathways between bank voles and yellow-necked mice could thus contribute to the difference in resistance to B. afzelii between the species. This study provides knowledge of gene expression induced by a zoonotic pathogen in its natural host, and possible species-specific regulation of immune responses associated with resistance.", "doi": "10.1002/ece3.6377", "pmid": "32724523", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ECE36377"}, {"db": "pmc", "key": "PMC7381583"}, {"db": "Dryad", "key": "10.5061/dryad.t1g1jwt02"}], "notes": [], "created": "2020-12-07T16:29:59.033Z", "modified": "2024-01-16T13:48:42.326Z"}, {"entity": "publication", "iuid": "d44fd9d44752484f996cf097d055c88b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d44fd9d44752484f996cf097d055c88b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d44fd9d44752484f996cf097d055c88b"}}, "title": "CAM-Delam: an in vivo approach to visualize and quantify the delamination and invasion capacity of human cancer cells.", "authors": [{"family": "Palaniappan", "given": "Tamilarasan K", "initials": "TK"}, {"family": "\u0160lekien\u0117", "given": "Lina", "initials": "L"}, {"family": "Jonasson", "given": "Anna-Karin", "initials": "AK"}, {"family": "Gilthorpe", "given": "Jonathan", "initials": "J"}, {"family": "Gunhaga", "given": "Lena", "initials": "L"}], "type": "journal article", "published": "2020-06-26", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "10472", "issn-l": "2045-2322"}, "abstract": "The development of metastases is the major cause of cancer related death. To develop a standardized method that define the ability of human cancer cells to degrade the basement membrane, e.g. the delamination capacity, is of importance to assess metastatic aggressiveness. We now present the in vivo CAM-Delam assay to visualize and quantify the ability of human cancer cells to delaminate and invade. The method includes seeding cancer cells on the chick chorioallantoic membrane (CAM), followed by the evaluation of cancer-induced delamination and potential invasion within hours to a few days. By testing a range of human cancer cell lines in the CAM-Delam assay, our results show that the delamination capacity can be divided into four categories and used to quantify metastatic aggressiveness. Our results emphasize the usefulness of this assay for quantifying delamination capacity as a measurement of metastatic aggressiveness, and in unraveling the molecular mechanisms that regulate delamination, invasion, formation of micro-metastases and modulations of the tumor microenvironment. This method will be useful in both the preclinical and clinical characterization of tumor biopsies, and in the validation of compounds that may improve survival in metastatic cancer.", "doi": "10.1038/s41598-020-67492-7", "pmid": "32591581", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-67492-7"}, {"db": "pmc", "key": "PMC7320147"}], "notes": [], "created": "2021-12-06T13:45:24.619Z", "modified": "2021-12-06T13:45:24.635Z"}, {"entity": "publication", "iuid": "ad6c085540e747d5ac95fbe1622c8b7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad6c085540e747d5ac95fbe1622c8b7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad6c085540e747d5ac95fbe1622c8b7d"}}, "title": "RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.", "authors": [{"family": "Nilsson", "given": "Linn\u00e9a M", "initials": "LM"}, {"family": "Castresana-Aguirre", "given": "Miguel", "initials": "M", "orcid": "0000-0002-4665-6537", "researcher": {"href": "https://publications.scilifelab.se/researcher/df8394cb200743c4b13ee549bfe8492b.json"}}, {"family": "Scott", "given": "Lena", "initials": "L"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}], "type": "journal article", "published": "2020-06-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "10390", "issn-l": "2045-2322"}, "abstract": "Cell cultures are often used to study physiological processes in health and disease. It is well-known that cells change their gene expression in vitro compared to in vivo, but it is rarely experimentally addressed. High glucose is a known trigger of apoptosis in proximal tubular cells (PTC). Here we used RNA-seq to detect differentially expressed genes in cultures of primary rat PTC, 3 days old, compared to cells retrieved directly from rat outer renal cortex and between PTC exposed to 15 mM glucose and control for 8 h. The expression of 6,174 genes was significantly up- or downregulated in the cultures of PTC compared to the cells in the outer renal cortex. Most altered were mitochondrial and metabolism related genes. Gene expression of proapoptotic proteins were upregulated and gene expression of antiapoptotic proteins were downregulated in PTC. Expression of transporter related genes were generally downregulated. After 8 h, high glucose had not altered the gene expression in PTC. The current study provides evidence that cells alter their gene expression in vitro compared to in vivo and suggests that short-term high glucose exposure can trigger apoptosis in PTC without changing the gene expression levels of apoptotic proteins.", "doi": "10.1038/s41598-020-67361-3", "pmid": "32587318", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-67361-3"}, {"db": "pmc", "key": "PMC7316724"}], "notes": [], "created": "2020-12-07T16:27:02.399Z", "modified": "2021-11-10T12:50:06.705Z"}, {"entity": "publication", "iuid": "8b45074cc63c44b38845bd3e64899cdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b45074cc63c44b38845bd3e64899cdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b45074cc63c44b38845bd3e64899cdb"}}, "title": "Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.", "authors": [{"family": "Chapman", "given": "Mark A", "initials": "MA", "orcid": "0000-0001-9905-4022", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe649290e7b44079be880b52ea8fe98.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM"}, {"family": "Lindholm", "given": "Mal\u00e9ne E", "initials": "ME"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}], "type": "comparative study", "published": "2020-06-23", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "31", "issue": "12", "pages": "107808", "issn-l": null}, "abstract": "To better understand the health benefits of lifelong exercise in humans, we conduct global skeletal muscle transcriptomic analyses of long-term endurance- (9 men, 9 women) and strength-trained (7 men) humans compared with age-matched untrained controls (7 men, 8 women). Transcriptomic analysis, Gene Ontology, and genome-scale metabolic modeling demonstrate changes in pathways related to the prevention of metabolic diseases, particularly with endurance training. Our data also show prominent sex differences between controls and that these differences are reduced with endurance training. Additionally, we compare our data with studies examining muscle gene expression before and after a months-long training period in individuals with metabolic diseases. This analysis reveals that training shifts gene expression in individuals with impaired metabolism to become more similar to our endurance-trained group. Overall, our data provide an extensive examination of the accumulated transcriptional changes that occur with decades-long training and identify important \"exercise-responsive\" genes that could attenuate metabolic disease.", "doi": "10.1016/j.celrep.2020.107808", "pmid": "32579934", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(20)30789-0"}], "notes": [], "created": "2020-07-08T13:04:34.799Z", "modified": "2024-01-16T13:48:42.357Z"}, {"entity": "publication", "iuid": "d64c9f1bb86044c88061329283767e2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d64c9f1bb86044c88061329283767e2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d64c9f1bb86044c88061329283767e2e"}}, "title": "Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.", "authors": [{"family": "Remnest\u00e5l", "given": "Julia", "initials": "J", "orcid": "0000-0002-3908-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a88350afba45fb8200786904bf51ca.json"}}, {"family": "\u00d6ijerstedt", "given": "Linn", "initials": "L"}, {"family": "Ullgren", "given": "Abbe", "initials": "A"}, {"family": "Olofsson", "given": "Jennie", "initials": "J"}, {"family": "Bergstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Kultima", "given": "Kim", "initials": "K"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Graff", "given": "Caroline", "initials": "C"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2020-06-23", "journal": {"title": "Transl Neurodegener", "issn": "2047-9158", "volume": "9", "issue": "1", "pages": "27", "issn-l": null}, "abstract": "The clinical presentations of frontotemporal dementia (FTD) are diverse and overlap with other neurological disorders. There are, as of today, no biomarkers in clinical practice for diagnosing the disorders. Here, we aimed to find protein markers in cerebrospinal fluid (CSF) from patients with FTD, presymptomatic mutation carriers and non-carriers.\n\nAntibody suspension bead arrays were used to analyse 328 proteins in CSF from patients with behavioural variant FTD (bvFTD, n = 16) and progressive primary aphasia (PPA, n = 13), as well as presymptomatic mutation carriers (PMC, n = 16) and non-carriers (NC, n = 8). A total of 492 antibodies were used to measure protein levels by direct labelling of the CSF samples. The findings were further examined in an independent cohort including 13 FTD patients, 79 patients with Alzheimer's disease and 18 healthy controls.\n\nWe found significantly altered protein levels in CSF from FTD patients compared to unaffected individuals (PMC and NC) for 26 proteins. The analysis show patterns of separation between unaffected individuals and FTD patients, especially for those with a clinical diagnosis of bvFTD. The most statistically significant differences in protein levels were found for VGF, TN-R, NPTXR, TMEM132D, PDYN and NF-M. Patients with FTD were found to have higher levels of TN-R and NF-M, and lower levels of VGF, NPTXR, TMEM132D and PDYN, compared to unaffected individuals. The main findings were reproduced in the independent cohort.\n\nIn this pilot study, we show a separation of FTD patients from unaffected individuals based on protein levels in CSF. Further investigation is required to explore the CSF profiles in larger cohorts, but the results presented here has the potential to enable future clinical utilization of these potential biomarkers within FTD.", "doi": "10.1186/s40035-020-00198-y", "pmid": "32576262", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40035-020-00198-y"}, {"db": "pmc", "key": "PMC7310563"}], "notes": [], "created": "2021-01-08T16:29:12.262Z", "modified": "2024-01-16T13:48:42.365Z"}, {"entity": "publication", "iuid": "2b160d0829af493f9894f3148bb0ad8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b160d0829af493f9894f3148bb0ad8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b160d0829af493f9894f3148bb0ad8f"}}, "title": "CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.", "authors": [{"family": "Hagey", "given": "Daniel W", "initials": "DW", "orcid": "0000-0001-9246-6235", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9b5df8185a54da58f080ea7a7b956ef.json"}}, {"family": "Topcic", "given": "Danijal", "initials": "D"}, {"family": "Kee", "given": "Nigel", "initials": "N"}, {"family": "Reynaud", "given": "Florie", "initials": "F"}, {"family": "Bergsland", "given": "Maria", "initials": "M"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Muhr", "given": "Jonas", "initials": "J", "orcid": "0000-0003-0704-0788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6a665f02acc432e9d80feb5c61f4572.json"}}], "type": "journal article", "published": "2020-06-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "2898", "issn-l": "2041-1723"}, "abstract": "The sequential generation of layer-specific cortical neurons requires radial glia cells (RGCs) to precisely balance self-renewal and lineage commitment. While specific cell-cycle phases have been associated with these decisions, the mechanisms linking the cell-cycle machinery to cell-fate commitment remain obscure. Using single-cell RNA-sequencing, we find that the strongest transcriptional signature defining multipotent RGCs is that of G2/M-phase, and particularly CYCLIN-B1/2, while lineage-committed progenitors are enriched in G1/S-phase genes, including CYCLIN-D1. These data also reveal cell-surface markers that allow us to isolate RGCs and lineage-committed progenitors, and functionally confirm the relationship between cell-cycle phase enrichment and cell fate competence. Finally, we use cortical electroporation to demonstrate that CYCLIN-B1/2 cooperate with CDK1 to maintain uncommitted RGCs by activating the NOTCH pathway, and that CYCLIN-D1 promotes differentiation. Thus, this work establishes that cell-cycle phase-specific regulators act in opposition to coordinate the self-renewal and lineage commitment of RGCs via core stem cell regulatory pathways.", "doi": "10.1038/s41467-020-16597-8", "pmid": "32518258", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-16597-8"}, {"db": "pmc", "key": "PMC7283355"}], "notes": [], "created": "2020-12-07T16:26:58.923Z", "modified": "2024-01-16T13:48:42.396Z"}, {"entity": "publication", "iuid": "205793144c484b22a38e28d4a971f932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/205793144c484b22a38e28d4a971f932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/205793144c484b22a38e28d4a971f932"}}, "title": "Size-Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe-by-Design.", "authors": [{"family": "Rodrigues", "given": "Artur Filipe", "initials": "AF"}, {"family": "Newman", "given": "Leon", "initials": "L"}, {"family": "Jasim", "given": "Dhifaf", "initials": "D"}, {"family": "Mukherjee", "given": "Sourav P", "initials": "SP"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Vacchi", "given": "Isabella A", "initials": "IA"}, {"family": "M\u00e9nard-Moyon", "given": "C\u00e9cilia", "initials": "C"}, {"family": "Bianco", "given": "Alberto", "initials": "A"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}, {"family": "Kostarelos", "given": "Kostas", "initials": "K"}, {"family": "Bussy", "given": "Cyrill", "initials": "C", "orcid": "0000-0001-8870-443X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b7fc372c1ae437891bd4b8e3000e281.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Adv Sci (Weinh)", "issn": "2198-3844", "volume": "7", "issue": "12", "pages": "1903200", "issn-l": null}, "abstract": "Safety assessment of graphene-based materials (GBMs) including graphene oxide (GO) is essential for their safe use across many sectors of society. In particular, the link between specific material properties and biological effects needs to be further elucidated. Here, the effects of lateral dimensions of GO sheets in acute and chronic pulmonary responses after single intranasal instillation in mice are compared. Micrometer-sized GO induces stronger pulmonary inflammation than nanometer-sized GO, despite reduced translocation to the lungs. Genome-wide RNA sequencing also reveals distinct size-dependent effects of GO, in agreement with the histopathological results. Although large GO, but not the smallest GO, triggers the formation of granulomas that persists for up to 90 days, no pulmonary fibrosis is observed. These latter results can be partly explained by Raman imaging, which evidences the progressive biotransformation of GO into less graphitic structures. The findings demonstrate that lateral dimensions play a fundamental role in the pulmonary response to GO, and suggest that airborne exposure to micrometer-sized GO should be avoided in the production plant or applications, where aerosolized dispersions are likely to occur. These results are important toward the implementation of a safer-by-design approach for GBM products and applications, for the benefit of workers and end-users.", "doi": "10.1002/advs.201903200", "pmid": "32596109", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "ADVS1753"}, {"db": "pmc", "key": "PMC7312279"}], "notes": [], "created": "2020-12-07T16:28:59.251Z", "modified": "2021-11-10T12:50:32.651Z"}, {"entity": "publication", "iuid": "efddda9d626548608fed72f21c6fc1dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efddda9d626548608fed72f21c6fc1dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efddda9d626548608fed72f21c6fc1dc"}}, "title": "Single-cell RNA counting at allele and isoform resolution using Smart-seq3.", "authors": [{"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/3297f21f1a174cd388ac586eda2b5177.json"}}, {"family": "Chen", "given": "Ping", "initials": "P"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D", "orcid": "0000-0003-2892-673X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc367f2adb7c4379b7dc441be34e7ded.json"}}, {"family": "Hendriks", "given": "Gert-Jan", "initials": "GJ"}, {"family": "Larsson", "given": "Anton J M", "initials": "AJM"}, {"family": "Faridani", "given": "Omid R", "initials": "OR"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"volume": "38", "issn": "1546-1696", "issue": "6", "pages": "708-714", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": "Large-scale sequencing of RNA from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states1. However, current short-read single-cell RNA-sequencing methods have limited ability to count RNAs at allele and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells2,3. Here we introduce Smart-seq3, which combines full-length transcriptome coverage with a 5' unique molecular identifier RNA counting strategy that enables in silico reconstruction of thousands of RNA molecules per cell. Of the counted and reconstructed molecules, 60% could be directly assigned to allelic origin and 30-50% to specific isoforms, and we identified substantial differences in isoform usage in different mouse strains and human cell types. Smart-seq3 greatly increased sensitivity compared to Smart-seq2, typically detecting thousands more transcripts per cell. We expect that Smart-seq3 will enable large-scale characterization of cell types and states across tissues and organisms.", "doi": "10.1038/s41587-020-0497-0", "pmid": "32518404", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0497-0"}], "notes": [], "created": "2020-05-26T09:06:10.857Z", "modified": "2021-11-10T12:50:33.905Z"}, {"entity": "publication", "iuid": "b77ba73fb7c241d09a2734a4ef5e2832", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b77ba73fb7c241d09a2734a4ef5e2832.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b77ba73fb7c241d09a2734a4ef5e2832"}}, "title": "Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors.", "authors": [{"family": "Xu", "given": "Jiejia", "initials": "J", "orcid": "0000-0003-3885-3546", "researcher": {"href": "https://publications.scilifelab.se/researcher/144d8f8036b34c4f964c67255449c7a5.json"}}, {"family": "Zhou", "given": "Chikai", "initials": "C"}, {"family": "Foo", "given": "Kylie S", "initials": "KS"}, {"family": "Yang", "given": "Ran", "initials": "R"}, {"family": "Xiao", "given": "Yao", "initials": "Y"}, {"family": "Bylund", "given": "Kristine", "initials": "K"}, {"family": "Sahara", "given": "Makoto", "initials": "M"}, {"family": "Chien", "given": "Kenneth R", "initials": "KR"}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Stem Cells", "issn": "1549-4918", "volume": "38", "issue": "6", "pages": "741-755", "issn-l": "1066-5099"}, "abstract": "Cardiac progenitor formation is one of the earliest committed steps of human cardiogenesis and requires the cooperation of multiple gene sets governed by developmental signaling cascades. To determine the key regulators for cardiac progenitor formation, we have developed a two-stage genome-wide CRISPR-knockout screen. We mimicked the progenitor formation process by differentiating human pluripotent stem cells (hPSCs) into cardiomyocytes, monitored by two distinct stage markers of early cardiac mesodermal formation and commitment to a multipotent heart progenitor cell fate: MESP1 and ISL1, respectively. From the screen output, we compiled a list of 15 candidate genes. After validating seven of them, we identified ZIC2 as an essential gene for cardiac progenitor formation. ZIC2 is known as a master regulator of neurogenesis. hPSCs with ZIC2 mutated still express pluripotency markers. However, their ability to differentiate into cardiomyocytes was greatly attenuated. RNA-Seq profiling of the ZIC2-mutant cells revealed that the mutants switched their cell fate alternatively to the noncardiac cell lineage. Further, single cell RNA-seq analysis showed the ZIC2 mutants affected the apelin receptor-related signaling pathway during mesoderm formation. Our results provide a new link between ZIC2 and human cardiogenesis and document the potential power of a genome-wide unbiased CRISPR-knockout screen to identify the key steps in human mesoderm precursor cell- and heart progenitor cell-fate determination during in vitro hPSC cardiogenesis.", "doi": "10.1002/stem.3168", "pmid": "32129551", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7891398"}], "notes": [], "created": "2020-07-08T13:05:12.225Z", "modified": "2024-01-16T13:48:42.444Z"}, {"entity": "publication", "iuid": "ed70a147175843f5a31852a576f105bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed70a147175843f5a31852a576f105bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed70a147175843f5a31852a576f105bc"}}, "title": "Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.", "authors": [{"family": "Mereu", "given": "Elisabetta", "initials": "E"}, {"family": "Lafzi", "given": "Atefeh", "initials": "A"}, {"family": "Moutinho", "given": "Catia", "initials": "C"}, {"family": "Ziegenhain", "given": "Christoph", "initials": "C", "orcid": "0000-0003-2208-4877", "researcher": {"href": "https://publications.scilifelab.se/researcher/3297f21f1a174cd388ac586eda2b5177.json"}}, {"family": "McCarthy", "given": "Davis J", "initials": "DJ"}, {"family": "\u00c1lvarez-Varela", "given": "Adri\u00e1n", "initials": "A"}, {"family": "Batlle", "given": "Eduard", "initials": "E"}, {"family": "Gr\u00fcn", "given": "Dominic", "initials": "D", "orcid": "0000-0002-3364-5898", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ee67aea7fd94e56a66d33a92c32863b.json"}}, {"family": "Lau", "given": "Julia K", "initials": "JK"}, {"family": "Boutet", "given": "St\u00e9phane C", "initials": "SC"}, {"family": "Sanada", "given": "Chad", "initials": "C"}, {"family": "Ooi", "given": "Aik", "initials": "A"}, {"family": "Jones", "given": "Robert C", "initials": "RC", "orcid": "0000-0001-7235-9854", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fc0262d6f154970914dce5fa42fa83f.json"}}, {"family": "Kaihara", "given": "Kelly", "initials": "K"}, {"family": "Brampton", "given": "Chris", "initials": "C"}, {"family": "Talaga", "given": "Yasha", "initials": "Y"}, {"family": "Sasagawa", "given": "Yohei", "initials": "Y"}, {"family": "Tanaka", "given": "Kaori", "initials": "K"}, {"family": "Hayashi", "given": "Tetsutaro", "initials": "T"}, {"family": "Braeuning", "given": "Caroline", "initials": "C"}, {"family": "Fischer", "given": "Cornelius", "initials": "C", "orcid": "0000-0003-0329-2435", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dcb9bf2b11a45a9a95219a0e456388e.json"}}, {"family": "Sauer", "given": "Sascha", "initials": "S"}, {"family": "Trefzer", "given": "Timo", "initials": "T"}, {"family": "Conrad", "given": "Christian", "initials": "C"}, {"family": "Adiconis", "given": "Xian", "initials": "X"}, {"family": "Nguyen", "given": "Lan T", "initials": "LT"}, {"family": "Regev", "given": "Aviv", "initials": "A", "orcid": "0000-0003-3293-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/36ee05b2a25d42769587c29b909ba9db.json"}}, {"family": "Levin", "given": "Joshua Z", "initials": "JZ", "orcid": "0000-0002-0170-3598", "researcher": {"href": "https://publications.scilifelab.se/researcher/6aab17c0401f44df98fa2df56e8ddcae.json"}}, {"family": "Parekh", "given": "Swati", "initials": "S", "orcid": "0000-0002-4826-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/aeed2ef091514d25aa845563f9c41687.json"}}, {"family": "Janjic", "given": "Aleksandar", "initials": "A", "orcid": "0000-0001-7180-5381", "researcher": {"href": "https://publications.scilifelab.se/researcher/38aaef51d88e4c6795f38fb6e8cee5d5.json"}}, {"family": "Wange", "given": "Lucas E", "initials": "LE", "orcid": "0000-0002-3275-9156", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d25e9c8662444ecaad76339843df61e.json"}}, {"family": "Bagnoli", "given": "Johannes W", "initials": "JW"}, {"family": "Enard", "given": "Wolfgang", "initials": "W", "orcid": "0000-0002-4056-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bc85b7ab2ce48408c3d9e00895a7cbf.json"}}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Nikaido", "given": "Itoshi", "initials": "I", "orcid": "0000-0002-7261-2570", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5c5e9ef375146618fb7fbe1c95c2104.json"}}, {"family": "Gut", "given": "Ivo", "initials": "I", "orcid": "0000-0001-7219-632X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c14600c4e0d54a7aae393c728d9af088.json"}}, {"family": "Stegle", "given": "Oliver", "initials": "O"}, {"family": "Heyn", "given": "Holger", "initials": "H", "orcid": "0000-0002-3276-1889", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f8103bc9af4fb5a3bd1d544648e588.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "volume": "38", "issue": "6", "pages": "747-755", "issn-l": "1087-0156"}, "abstract": "Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile cell atlases of tissues, organs and organisms. However, the protocols differ substantially with respect to their RNA capture efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. In the present study, we generated benchmark datasets to systematically evaluate protocols in terms of their power to comprehensively describe cell types and states. We performed a multicenter study comparing 13 commonly used scRNA-seq and single-nucleus RNA-seq protocols applied to a heterogeneous reference sample resource. Comparative analysis revealed marked differences in protocol performance. The protocols differed in library complexity and their ability to detect cell-type markers, impacting their predictive value and suitability for integration into reference cell atlases. These results provide guidance both for individual researchers and for consortium projects such as the Human Cell Atlas.", "doi": "10.1038/s41587-020-0469-4", "pmid": "32518403", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0469-4"}], "notes": [], "created": "2020-07-08T13:04:12.225Z", "modified": "2021-11-10T12:50:42.946Z"}, {"entity": "publication", "iuid": "3de081fdf4d54781aae6830f27ddb7e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3de081fdf4d54781aae6830f27ddb7e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3de081fdf4d54781aae6830f27ddb7e7"}}, "title": "Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.", "authors": [{"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Zhong", "given": "Xiuqin", "initials": "X", "orcid": "0000-0002-4772-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1847f16fd2a4d1cac925c7b89b70684.json"}}, {"family": "Konrad", "given": "Anna", "initials": "A"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "R\u00e5berg", "given": "Lars", "initials": "L", "orcid": "0000-0001-5219-7448", "researcher": {"href": "https://publications.scilifelab.se/researcher/a732076e5acc4ede94cc864cd90c99f3.json"}}], "type": "journal article", "published": "2020-06-00", "journal": {"volume": "29", "issn": "1365-294X", "issue": "11", "pages": "1990-2003", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Pathogen-mediated balancing selection is commonly considered to play an important role in the maintenance of genetic diversity, in particular in immune genes. However, the factors that may influence which immune genes are the targets of such selection are largely unknown. To address this, here we focus on Pattern Recognition Receptor (PRR) signalling pathways, which play a key role in innate immunity. We used whole-genome resequencing data from a population of bank voles (Myodes glareolus) to test for associations between balancing selection, pleiotropy and gene function in a set of 123 PRR signalling pathway genes. To investigate the effect of gene function, we compared genes encoding (a) receptors for microbial ligands versus downstream signalling proteins, and (b) receptors recognizing components of microbial cell walls, flagella and capsids versus receptors recognizing features of microbial nucleic acids. Analyses based on the nucleotide diversity of full coding sequences showed that balancing selection primarily targeted receptor genes with a low degree of pleiotropy. Moreover, genes encoding receptors recognizing components of microbial cell walls etc. were more important targets of balancing selection than receptors recognizing nucleic acids. Tests for localized signatures of balancing selection in coding and noncoding sequences showed that such signatures were mostly located in introns, and more evenly distributed among different functional categories of PRR pathway genes. The finding that signatures of balancing selection in full coding sequences primarily occur in receptor genes, in particular those encoding receptors for components of microbial cell walls etc., is consistent with the idea that coevolution between hosts and pathogens is an important cause of balancing selection on immune genes.", "doi": "10.1111/mec.15459", "pmid": "32374503", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.2bvq83bms"}], "notes": [], "created": "2020-07-08T13:04:58.447Z", "modified": "2024-01-16T13:48:42.452Z"}, {"entity": "publication", "iuid": "e78f5c80e0f7468e9c635acda6db895d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e78f5c80e0f7468e9c635acda6db895d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e78f5c80e0f7468e9c635acda6db895d"}}, "title": "Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.", "authors": [{"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hedlund", "given": "Erika", "initials": "E"}, {"family": "Hjorth", "given": "Tomas", "initials": "T"}, {"family": "Rolff", "given": "Carl", "initials": "C"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Udekwu", "given": "Klas", "initials": "K"}, {"family": "Gunnarsson", "given": "Jonas S", "initials": "JS"}], "type": "journal article", "published": "2020-06-00", "journal": {"title": "Chemosphere", "issn": "1879-1298", "volume": "248", "issue": null, "pages": "126023", "issn-l": "0045-6535"}, "abstract": "Biodegradation by microorganisms is a useful tool that helps alleviating hydrocarbon pollution in nature. Microbes are more efficient in degradation under aerobic than anaerobic conditions, but the majority of sediment by volume is generally anoxic. Incubation experiments were conducted to study the biodegradation potential of naphthalene-a common polycyclic aromatic hydrocarbon (PAH)-and the diversity of microbial communities in presence/absence of activated carbon (AC) under aerobic/anaerobic conditions. Radio-respirometry experiments with endogenous microorganisms indicated that degradation of naphthalene was strongly stimulated (96%) by the AC addition under anaerobic conditions. In aerobic conditions, however, AC had no effects on naphthalene biodegradation. Bioaugmentation tests with cultured microbial populations grown on naphthalene showed that AC further stimulated (92%) naphthalene degradation in anoxia. Analysis of the 16S rRNA gene sequences implied that sediment amendment with AC increased microbial community diversity and changed community structure. Moreover, the relative abundance of Geobacter, Thiobacillus, Sulfuricurvum, and methanogenic archaea increased sharply after amendment with AC under anaerobic conditions. These results may be explained by the fact that AC particles promoted direct interspecies electron transfer (DIET) between microorganisms involved in PAH degradation pathways. We suggest that important ecosystem functions mediated by microbes-such as hydrocarbon degradation-can be induced and that AC enrichment strategies can be exploited for facilitating bioremediation of anoxic oil-contaminated sediments and soils.", "doi": "10.1016/j.chemosphere.2020.126023", "pmid": "32007777", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0045-6535(20)30216-2"}], "notes": [], "created": "2020-07-08T13:03:41.428Z", "modified": "2024-01-16T13:48:42.467Z"}, {"entity": "publication", "iuid": "00954388bf944b23a0de53ff10845a71", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00954388bf944b23a0de53ff10845a71.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00954388bf944b23a0de53ff10845a71"}}, "title": "Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.", "authors": [{"family": "Grankvist", "given": "Rikard", "initials": "R"}, {"family": "Chireh", "given": "Arvin", "initials": "A"}, {"family": "Sandell", "given": "Mikael", "initials": "M"}, {"family": "Mukarram", "given": "Abdul Kadir", "initials": "AK"}, {"family": "Jaff", "given": "Nasren", "initials": "N"}, {"family": "Berggren", "given": "Ingrid", "initials": "I"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Arnberg", "given": "Fabian", "initials": "F"}, {"family": "Lundberg", "given": "Johan", "initials": "J"}, {"family": "Ugander", "given": "Martin", "initials": "M"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Jonsson", "given": "Stefan", "initials": "S"}, {"family": "Daub", "given": "Carsten O", "initials": "CO", "orcid": "0000-0002-3295-8729", "researcher": {"href": "https://publications.scilifelab.se/researcher/eda6a90f9d9046ada163d9843d169393.json"}}, {"family": "Holmin", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2020-05-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "10", "issue": "1", "pages": "8029", "issn-l": "2045-2322"}, "abstract": "Endomyocardial biopsy is a valuable tool in cardiac diagnostics but is limited by low diagnostic yield and significant complication risks. Meanwhile, recent developments in transcriptomic and proteomic technologies promise a wealth of biological data from minimal tissue samples. To take advantage of the minimal tissue amount needed for molecular analyses, we have developed a sub-millimeter endovascular biopsy device, considerably smaller than current clinical equipment, and devised a low-input RNA-sequencing protocol for analyzing small tissue samples. In in vivo evaluation in swine, 81% of biopsy attempts (n = 157) were successful. High quality RNA-sequencing data was generated from 91% of the sequenced cardiac micro-biopsy samples (n = 32). Gene expression signatures of samples taken with the novel device were comparable with a conventional device. No major complications were detected either during procedures or during 7 days' follow-up, despite acquiring a relatively large number of biopsies (median 30) in each animal. In conclusion, the novel device coupled with RNA-sequencing provides a feasible method to obtain molecular data from the myocardium. The method is less traumatic and has a higher flexibility compared to conventional methods, enabling safer and more targeted sampling from different parts of the myocardium.", "doi": "10.1038/s41598-020-64900-w", "pmid": "32415191", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-020-64900-w"}, {"db": "pmc", "key": "PMC7229024"}], "notes": [], "created": "2020-07-08T13:04:40.159Z", "modified": "2024-01-16T13:48:42.501Z"}, {"entity": "publication", "iuid": "a8185c111fd34c76a142beed9b5d494a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8185c111fd34c76a142beed9b5d494a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8185c111fd34c76a142beed9b5d494a"}}, "title": "Srebf1 Controls Midbrain Dopaminergic Neurogenesis.", "authors": [{"family": "Toledo", "given": "Enrique M", "initials": "EM"}, {"family": "Yang", "given": "Shanzheng", "initials": "S"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "van Wijk", "given": "Kim E", "initials": "KE"}, {"family": "Sinha", "given": "Indranil", "initials": "I"}, {"family": "Varas-Godoy", "given": "Manuel", "initials": "M"}, {"family": "Grigsby", "given": "Christopher L", "initials": "CL"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Islam", "given": "Saiful", "initials": "S"}, {"family": "Steffensen", "given": "Knut R", "initials": "KR"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}], "type": "journal article", "published": "2020-05-05", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "31", "issue": "5", "pages": "107601", "issn-l": null}, "abstract": "Liver X receptors (LXRs) and their ligands are potent regulators of midbrain dopaminergic (mDA) neurogenesis and differentiation. However, the molecular mechanisms by which LXRs control these functions remain to be elucidated. Here, we perform a combined transcriptome and chromatin immunoprecipitation sequencing (ChIP-seq) analysis of midbrain cells after LXR activation, followed by bioinformatic analysis to elucidate the transcriptional networks controlling mDA neurogenesis. Our results identify the basic helix-loop-helix transcription factor sterol regulatory element binding protein 1 (SREBP1) as part of a cluster of proneural transcription factors in radial glia and as a regulator of transcription factors controlling mDA neurogenesis, such as Foxa2. Moreover, loss- and gain-of-function experiments in vitro and in vivo demonstrate that Srebf1 is both required and sufficient for mDA neurogenesis. Our data, thus, identify Srebf1 as a central player in mDA neurogenesis.", "doi": "10.1016/j.celrep.2020.107601", "pmid": "32375051", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(20)30550-7"}], "notes": [], "created": "2021-01-08T16:29:13.408Z", "modified": "2024-01-16T13:48:42.515Z"}, {"entity": "publication", "iuid": "7eec3c7141e540bfbf96f05692cc6378", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7eec3c7141e540bfbf96f05692cc6378.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7eec3c7141e540bfbf96f05692cc6378"}}, "title": "Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report.", "authors": [{"family": "Bieder", "given": "Andrea", "initials": "A"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Nilsson", "given": "Harriet E", "initials": "HE"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Dragomir", "given": "Anca", "initials": "A"}, {"family": "Paucar", "given": "Martin", "initials": "M"}, {"family": "Granberg", "given": "Tobias", "initials": "T"}, {"family": "Li", "given": "Tie-Qiang", "initials": "TQ"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Tapia-P\u00e1ez", "given": "Isabel", "initials": "I"}], "type": "case reports", "published": "2020-05-01", "journal": {"title": "BMC Med. Genet.", "issn": "1471-2350", "volume": "21", "issue": "1", "pages": "87", "issn-l": "1471-2350"}, "abstract": "Developmental dyslexia (DD) is a neurodevelopmental learning disorder with high heritability. A number of candidate susceptibility genes have been identified, some of which are linked to the function of the cilium, an organelle regulating left-right asymmetry development in the embryo. Furthermore, it has been suggested that disrupted left-right asymmetry of the brain may play a role in neurodevelopmental disorders such as DD. However, it is unknown whether there is a common genetic cause to DD and laterality defects or ciliopathies.\n\nHere, we studied two individuals with co-occurring situs inversus (SI) and DD using whole genome sequencing to identify genetic variants of importance for DD and SI. Individual 1 had primary ciliary dyskinesia (PCD), a rare, autosomal recessive disorder with oto-sino-pulmonary phenotype and SI. We identified two rare nonsynonymous variants in the dynein axonemal heavy chain 5 gene (DNAH5): a previously reported variant c.7502G > C; p.(R2501P), and a novel variant c.12043 T > G; p.(Y4015D). Both variants are predicted to be damaging. Ultrastructural analysis of the cilia revealed a lack of outer dynein arms and normal inner dynein arms. MRI of the brain revealed no significant abnormalities. Individual 2 had non-syndromic SI and DD. In individual 2, one rare variant (c.9110A > G;p.(H3037R)) in the dynein axonemal heavy chain 11 gene (DNAH11), coding for another component of the outer dynein arm, was identified.\n\nWe identified the likely genetic cause of SI and PCD in one individual, and a possibly significant heterozygosity in the other, both involving dynein genes. Given the present evidence, it is unclear if the identified variants also predispose to DD and further studies into the association between laterality, ciliopathies and DD are needed.", "doi": "10.1186/s12881-020-01020-2", "pmid": "32357925", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12881-020-01020-2"}, {"db": "pmc", "key": "PMC7193346"}], "notes": [], "created": "2020-07-08T13:04:09.826Z", "modified": "2021-11-10T12:51:23.871Z"}, {"entity": "publication", "iuid": "342bc12c089c4c7fa2ac81719202f980", "links": {"self": {"href": "https://publications.scilifelab.se/publication/342bc12c089c4c7fa2ac81719202f980.json"}, "display": {"href": "https://publications.scilifelab.se/publication/342bc12c089c4c7fa2ac81719202f980"}}, "title": "Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.", "authors": [{"family": "Yang", "given": "Xuyue", "initials": "X", "orcid": "0000-0003-2084-1651", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0959fee187345d497cec63bce88d136.json"}}, {"family": "Fors", "given": "Lisa", "initials": "L"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}, {"family": "Theopold", "given": "Ulrich", "initials": "U"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Hamb\u00e4ck", "given": "Peter A", "initials": "PA"}], "type": "journal article", "published": "2020-05-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "5", "pages": "522-534", "issn-l": "1759-6653"}, "abstract": "Endoparasitoid wasps are important natural enemies of many insect species and are major selective forces on the host immune system. Despite increased interest in insect antiparasitoid immunity, there is sparse information on the evolutionary dynamics of biological pathways and gene regulation involved in host immune defense outside Drosophila species. We de novo assembled transcriptomes from two beetle species and used time-course differential expression analysis to investigate gene expression differences in closely related species Galerucella pusilla and G. calmariensis that are, respectively, resistant and susceptible against parasitoid infection by Asecodes parviclava parasitoids. Approximately 271 million and 224 million paired-ended reads were assembled and filtered to form 52,563 and 59,781 transcripts for G. pusilla and G. calmariensis, respectively. In the whole-transcriptome level, an enrichment of functional categories related to energy production, biosynthetic process, and metabolic process was exhibited in both species. The main difference between species appears to be immune response and wound healing process mounted by G. pusilla larvae. Using reciprocal BLAST against the Drosophila melanogaster proteome, 120 and 121 immune-related genes were identified in G. pusilla and G. calmariensis, respectively. More immune genes were differentially expressed in G. pusilla than in G. calmariensis, in particular genes involved in signaling, hematopoiesis, and melanization. In contrast, only one gene was differentially expressed in G. calmariensis. Our study characterizes important genes and pathways involved in different immune functions after parasitoid infection and supports the role of signaling and hematopoiesis genes as key players in host immunity in Galerucella against parasitoid wasps.", "doi": "10.1093/gbe/evaa075", "pmid": "32282901", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5819554"}, {"db": "pmc", "key": "PMC7211424"}], "notes": [], "created": "2020-07-08T13:04:36.500Z", "modified": "2024-01-16T13:48:42.522Z"}, {"entity": "publication", "iuid": "342a9eea98eb46f1a43d7af5f008e709", "links": {"self": {"href": "https://publications.scilifelab.se/publication/342a9eea98eb46f1a43d7af5f008e709.json"}, "display": {"href": "https://publications.scilifelab.se/publication/342a9eea98eb46f1a43d7af5f008e709"}}, "title": "Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.", "authors": [{"family": "Plesser Duvdevani", "given": "Morasha", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Avraham", "given": "Ortal", "initials": "O"}, {"family": "Dagan", "given": "Judith", "initials": "J"}, {"family": "Frumkin", "given": "Ayala", "initials": "A", "orcid": "0000-0001-9103-9717", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dd5f9cab2744569bd4d1c1ebc62945f.json"}}, {"family": "Lupski", "given": "James R", "initials": "JR", "orcid": "0000-0001-9907-9246", "researcher": {"href": "https://publications.scilifelab.se/researcher/88dd1dee9767489aaf25865670feb7b7.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Harel", "given": "Tamar", "initials": "T", "orcid": "0000-0003-3595-7075", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f4e6a558c934ddd955531283e416a42.json"}}], "type": "case reports", "published": "2020-05-00", "journal": {"title": "Am. J. Med. Genet. A", "issn": "1552-4833", "volume": "182", "issue": "5", "pages": "1143-1151", "issn-l": "1552-4825"}, "abstract": "Clinical laboratory diagnostic evaluation of the genomes of children with suspected genetic disorders, including chromosomal microarray and exome sequencing, cannot detect copy number neutral genomic rearrangements such as inversions, balanced translocations, and complex chromosomal rearrangements (CCRs). We describe an infant with a clinical diagnosis of Cornelia de Lange syndrome (CdLS) in whom chromosome analysis revealed a de novo complex balanced translocation, 46,XY,t(5;7;6)(q11.2;q32;q13)dn. Subsequent molecular characterization by whole-genome sequencing (WGS) identified 23 breakpoints, delineating segments derived from four chromosomes (5;6;7;21) in ancestral or inverted orientation. One of the breakpoints disrupted a known CdLS gene, NIPBL. Further investigation revealed paternal origin of the CCR allele, clustering of the breakpoint junctions, and molecular repair signatures suggestive of a single catastrophic event. Notably, very short DNA segments (25 and 41 bp) were included in the reassembled chromosomes, lending additional support that the DNA repair machinery can detect and repair such segments. Interestingly, there was an independent paternally derived miniscule complex rearrangement, possibly predisposing to subsequent genomic instability. In conclusion, we report a CCR causing a monogenic Mendelian disorder, urging WGS analysis of similar unsolved cases with suspected Mendelian disorders. Breakpoint analysis allowed for identification of the underlying molecular diagnosis and implicated chromoanagenesis in CCR formation.", "doi": "10.1002/ajmg.a.61539", "pmid": "32125084", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7502196"}, {"db": "mid", "key": "NIHMS1625907"}], "notes": [], "created": "2020-07-08T13:05:13.646Z", "modified": "2024-01-16T13:48:42.530Z"}, {"entity": "publication", "iuid": "1db10b1c89f44f58a9844ca95744ecf0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1db10b1c89f44f58a9844ca95744ecf0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1db10b1c89f44f58a9844ca95744ecf0"}}, "title": "Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.", "authors": [{"family": "Chen", "given": "Yi", "initials": "Y", "orcid": "0000-0002-4891-8289", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ae866ca9a3244aba9678dc66a1e69e1.json"}}, {"family": "Hesla", "given": "Asle C", "initials": "AC"}, {"family": "Lin", "given": "Yingbo", "initials": "Y"}, {"family": "Ghaderi", "given": "Mehran", "initials": "M"}, {"family": "Liu", "given": "Mingzhi", "initials": "M"}, {"family": "Yang", "given": "Chen", "initials": "C"}, {"family": "Zhang", "given": "Yifan", "initials": "Y"}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P"}, {"family": "Larsson", "given": "Olle", "initials": "O"}, {"family": "Haglund", "given": "Felix", "initials": "F", "orcid": "0000-0002-7015-3841", "researcher": {"href": "https://publications.scilifelab.se/researcher/891cbee146fa4e27bc8d26111283b854.json"}}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "volume": "14", "issue": "5", "pages": "1101-1117", "issn-l": "1574-7891"}, "abstract": "Ewing sarcomas (ESs) are aggressive sarcomas driven by EWS fusion genes. We sought to investigate whether whole-transcriptome sequencing (RNA-seq) could be used to detect patterns associated with chemotherapy response or tumor progression after first-line treatment. Transcriptome sequencing (RNA-seq) of 13 ES cases was performed. Among the differentially expressed pathways, we identified IGF2 expression as a potential driver of chemotherapy response and progression. We investigated the effect of IGF2 on proliferation, radioresistance, apoptosis, and the transcriptome pattern in four ES cell lines and the effect of IGF2 expression in a validation series of 14 patients. Transcriptome analysis identified differentially expressed genes (adj. P < 0.005) and pathways associated with chemotherapy response (285 genes), short overall survival (662 genes), and progression after treatment (447 genes). Imprinting independent promoter P3-mediated IGF2 expression was identified in a subset of cases with aggressive clinical course. In ES cell lines, IGF2 induced proliferation, but promoted radioresistance only in CADO cells. High IGF2 expression was also significantly associated with shorter overall survival in patients with ES. Transcriptome analysis of the clinical samples and the cell lines revealed an IGF-dependent signature, potentially related to a stem cell-like phenotype. Transcriptome analysis is a potentially powerful complementary tool to predict the clinical behavior of ES and may be utilized for clinical trial stratification strategies and personalized oncology. Certain gene signatures, for example, IGF-related pathways, are coupled to biological functions that could be of clinical importance. Finally, our results indicate that IGF inhibition may be successful as a first-line therapy in conjunction with conventional radiochemotherapy for a subset of patients.", "doi": "10.1002/1878-0261.12655", "pmid": "32115849", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7191197"}], "notes": [], "created": "2020-07-08T13:04:54.124Z", "modified": "2024-01-16T13:48:42.546Z"}, {"entity": "publication", "iuid": "bb997306e41d4015a6818367c73c9090", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb997306e41d4015a6818367c73c9090.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb997306e41d4015a6818367c73c9090"}}, "title": "Next-Generation Sequencing Reveals Differential Responses to Acute versus Long-Term Exposures to Graphene Oxide in Human Lung Cells.", "authors": [{"family": "Mukherjee", "given": "Sourav P", "initials": "SP"}, {"family": "Gupta", "given": "Govind", "initials": "G"}, {"family": "Kl\u00f6ditz", "given": "Katharina", "initials": "K"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Rodrigues", "given": "Artur Filipe", "initials": "AF"}, {"family": "Kostarelos", "given": "Kostas", "initials": "K"}, {"family": "Fadeel", "given": "Bengt", "initials": "B", "orcid": "0000-0001-5559-8482", "researcher": {"href": "https://publications.scilifelab.se/researcher/959b4accdbfe49158353b8cb12260d1b.json"}}], "type": "journal article", "published": "2020-05-00", "journal": {"title": "Small", "issn": "1613-6829", "volume": "16", "issue": "21", "pages": "e1907686", "issn-l": "1613-6810"}, "abstract": "Numerous studies have addressed the biological impact of graphene-based materials including graphene oxide (GO), yet few have focused on long-term effects. Here, RNA sequencing is utilized to unearth responses of human lung cells to GO. To this end, the BEAS-2B cell line derived from normal human bronchial epithelium is subjected to repeated, low-dose exposures of GO (1 or 5 \u00b5g mL-1 ) for 28 days or to the equivalent, cumulative amount of GO for 48 h. Then, samples are analyzed by using the NovaSeq 6000 sequencing system followed by pathway analysis and gene ontology enrichment analysis of the differentially expressed genes. Significant differences are seen between the low-dose, long-term exposures and the high-dose, short-term exposures. Hence, exposure to GO for 48 h results in mitochondrial dysfunction. In contrast, exposure to GO for 28 days is characterized by engagement of apoptosis pathways with downregulation of genes belonging to the inhibitor of apoptosis protein (IAP) family. Validation experiments confirm that long-term exposure to GO affects the apoptosis threshold in lung cells, accompanied by a loss of IAPs. These studies reveal the sensitivity of RNA-sequencing approaches and show that acute exposure to GO is not a good predictor of the long-term effects of GO.", "doi": "10.1002/smll.201907686", "pmid": "32227449", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2020-07-08T13:04:38.790Z", "modified": "2021-11-10T12:51:36.115Z"}, {"entity": "publication", "iuid": "f724f6c819fe4b4fb8005fa9c3dc68f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f724f6c819fe4b4fb8005fa9c3dc68f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f724f6c819fe4b4fb8005fa9c3dc68f7"}}, "title": "Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.", "authors": [{"family": "Atherton", "given": "Sarah", "initials": "S", "orcid": "0000-0003-2847-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/6582e2e560474080a7d89240a3d43edd.json"}}, {"family": "Jondelius", "given": "Ulf", "initials": "U", "orcid": "0000-0003-2847-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/6582e2e560474080a7d89240a3d43edd.json"}}], "type": "journal article", "published": "2020-04-27", "journal": {"title": "Biodivers Data J", "issn": "1314-2828", "volume": "8", "issue": null, "pages": "e51813", "issn-l": null}, "abstract": "The meiofauna is an important part of the marine ecosystem, but its composition and distribution patterns are relatively unexplored. Here we assessed the biodiversity and community structure of meiofauna from five locations on the Swedish western and southern coasts using a high-throughput DNA sequencing (metabarcoding) approach. The mitochondrial cytochrome oxidase 1 (COI) mini-barcode and nuclear 18S small ribosomal subunit (18S) V1-V2 region were amplified and sequenced using Illumina MiSeq technology. Our analyses revealed a higher number of species than previously found in other areas: thirteen samples comprising 6.5 dm3 sediment revealed 708 COI and 1,639 18S metazoan OTUs. Across all sites, the majority of the metazoan biodiversity was assigned to Arthropoda, Nematoda and Platyhelminthes. Alpha and beta diversity measurements showed that community composition differed significantly amongst sites. OTUs initially assigned to Acoela, Gastrotricha and the two Platyhelminthes sub-groups Macrostomorpha and Rhabdocoela were further investigated and assigned to species using a phylogeny-based taxonomy approach. Our results demonstrate that there is great potential for discovery of new meiofauna species even in some of the most extensively studied locations.", "doi": "10.3897/BDJ.8.e51813", "pmid": "32390756", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "51813"}, {"db": "pmc", "key": "PMC7198628"}], "notes": [], "created": "2020-07-08T13:04:39.455Z", "modified": "2024-01-16T13:48:42.575Z"}, {"entity": "publication", "iuid": "4317205fc07d449db7735d0732d85a4c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4317205fc07d449db7735d0732d85a4c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4317205fc07d449db7735d0732d85a4c"}}, "title": "Molecular profiling of driver events in metastatic uveal melanoma.", "authors": [{"family": "Karlsson", "given": "Joakim", "initials": "J", "orcid": "0000-0001-6332-4043", "researcher": {"href": "https://publications.scilifelab.se/researcher/6190c1a8a7d54cd6807f120e8748cfcd.json"}}, {"family": "Nilsson", "given": "Lisa M", "initials": "LM"}, {"family": "Mitra", "given": "Suman", "initials": "S"}, {"family": "Als\u00e9n", "given": "Samuel", "initials": "S"}, {"family": "Shelke", "given": "Ganesh Vilas", "initials": "GV", "orcid": "0000-0001-5883-8082", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaee610fe341d79fa92f2f4f9a9683.json"}}, {"family": "Sah", "given": "Vasu R", "initials": "VR"}, {"family": "Forsberg", "given": "Elin M V", "initials": "EMV", "orcid": "0000-0002-4196-3060", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e6342bc14ba426bbf61704b4873377a.json"}}, {"family": "Stierner", "given": "Ulrika", "initials": "U"}, {"family": "All-Eriksson", "given": "Charlotta", "initials": "C"}, {"family": "Einarsdottir", "given": "Berglind", "initials": "B"}, {"family": "Jespersen", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6543-5369", "researcher": {"href": "https://publications.scilifelab.se/researcher/d220a3bcbfea44228722a123b25ec1b2.json"}}, {"family": "Ny", "given": "Lars", "initials": "L"}, {"family": "Lindn\u00e9r", "given": "Per", "initials": "P"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Olofsson Bagge", "given": "Roger", "initials": "R", "orcid": "0000-0001-5795-0355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1f8016d5e64418ca71f230e64e415ba.json"}}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA", "orcid": "0000-0003-0346-6837", "researcher": {"href": "https://publications.scilifelab.se/researcher/27f0581f25124e98b0bd0eef8c3f3331.json"}}], "type": "journal article", "published": "2020-04-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "1894", "issn-l": "2041-1723"}, "abstract": "Metastatic uveal melanoma is less well understood than its primary counterpart, has a distinct biology compared to skin melanoma, and lacks effective treatments. Here we genomically profile metastatic tumors and infiltrating lymphocytes. BAP1 alterations are overrepresented and found in 29/32 of cases. Reintroducing a functional BAP1 allele into a deficient patient-derived cell line, reveals a broad shift towards a transcriptomic subtype previously associated with better prognosis of the primary disease. One outlier tumor has a high mutational burden associated with UV-damage. CDKN2A deletions also occur, which are rarely present in primaries. A focused knockdown screen is used to investigate overexpressed genes associated withcopy number gains. Tumor-infiltrating lymphocytes are in several cases found tumor-reactive, but expression of the immune checkpoint receptors TIM-3, TIGIT and LAG3 is also abundant. This study represents the largest whole-genome analysis of uveal melanoma to date, and presents an updated view of the metastatic disease.", "doi": "10.1038/s41467-020-15606-0", "pmid": "32313009", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-15606-0"}, {"db": "pmc", "key": "PMC7171146"}], "notes": [], "created": "2020-07-08T13:04:38.039Z", "modified": "2024-01-16T13:48:42.590Z"}, {"entity": "publication", "iuid": "b44914598864495388f1d615d5e95c2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b44914598864495388f1d615d5e95c2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b44914598864495388f1d615d5e95c2b"}}, "title": "Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.", "authors": [{"family": "Larsson", "given": "Ida", "initials": "I"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2020-04-17", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "11", "issue": null, "pages": "381", "issn-l": "1664-8021"}, "abstract": "Glioblastoma (GBM) is an aggressive type of brain cancer with a poor prognosis for affected patients. The current line of treatment only gives the patients a survival time of on average 15 months. In this work, we use genome-scale metabolic models (GEMs) together with other systems biology tools to examine the global transcriptomics-data of GBM-patients obtained from The Cancer Genome Atlas (TCGA). We reveal the molecular mechanisms underlying GBM and identify potential therapeutic targets for effective treatment of patients. The work presented consists of two main parts. The first part stratifies the patients into two groups, high and low survival, and compares their gene expression. The second part uses GBM and healthy brain tissue GEMs to simulate gene knockout in a GBM cell model to find potential therapeutic targets and predict their side effect in healthy brain tissue. We (1) find that genes upregulated in the patients with low survival are linked to various stages of the glioma invasion process, and (2) identify five essential genes for GBM, whose inhibition is non-toxic to healthy brain tissue, therefore promising to investigate further as therapeutic targets.", "doi": "10.3389/fgene.2020.00381", "pmid": "32362913", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7181968"}], "notes": [], "created": "2020-07-08T13:04:35.735Z", "modified": "2024-01-16T13:48:42.598Z"}, {"entity": "publication", "iuid": "cd9171508710494ba8bad2c1d95b8651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd9171508710494ba8bad2c1d95b8651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd9171508710494ba8bad2c1d95b8651"}}, "title": "Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.", "authors": [{"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Sundberg", "given": "Katarina", "initials": "K"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Hedhammar", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}], "type": "journal article", "published": "2020-04-16", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "307", "issn-l": "1471-2164"}, "abstract": "Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the disease development. In this study, we sought to identify the genetic risk factors potentially involved in the susceptibility to the disease in the high-risk Giant Schnauzer dog breed.\n\nBy employing genome-wide association followed by fine-mapping (top variant p-value = 5.7 \u00d7 10- 6), integrated with whole-genome resequencing and copy number variation analysis, we detected a ~ 8.9 kbp deletion strongly associated (p-value = 0.0001) with protection against development of hypothyroidism. The deletion is located between two predicted Interferon alpha (IFNA) genes and it may eliminate functional elements potentially involved in the transcriptional regulation of these genes. Remarkably, type I IFNs have been extensively associated to human autoimmune hypothyroidism and general autoimmunity. Nonetheless, the extreme genomic complexity of the associated region on CFA11 warrants further long-read sequencing and annotation efforts in order to ascribe functions to the identified deletion and to characterize the canine IFNA gene cluster in more detail.\n\nOur results expand the current knowledge on genetic determinants of canine hypothyroidism by revealing a significant link with the human counterpart disease, potentially translating into better diagnostic tools across species, and may contribute to improved canine breeding strategies.", "doi": "10.1186/s12864-020-6700-3", "pmid": "32299354", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-6700-3"}, {"db": "pmc", "key": "PMC7160888"}], "notes": [], "created": "2020-07-08T13:04:54.893Z", "modified": "2024-01-16T13:48:42.606Z"}, {"entity": "publication", "iuid": "4914e822a6ff4ce4ad8cafdded9ef574", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4914e822a6ff4ce4ad8cafdded9ef574.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4914e822a6ff4ce4ad8cafdded9ef574"}}, "title": "Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.", "authors": [{"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}], "type": "journal article", "published": "2020-04-15", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "298", "issn-l": "1471-2164"}, "abstract": "Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and co-expression of cells in tissues. Unfortunately, manual preparation of high-quality sequencing libraries is time-consuming and subject to technical variability due to human error during manual pipetting, which results in sample swapping and the accidental introduction of batch effects. All these factors complicate the production and interpretation of biological datasets.\n\nWe have integrated an Agilent Bravo Automated Liquid Handling Platform into the Spatial Transcriptomics workflow. Compared to the previously reported Magnatrix 8000+ automated protocol, this approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples. The new approach is also shown to be highly accurate and almost completely free from technical variability between prepared samples.\n\nThe new automated Spatial Transcriptomics protocol using the Agilent Bravo Automated Liquid Handling Platform rapidly generates high-quality Spatial Transcriptomics libraries. Given the wide use of the Agilent Bravo Automated Liquid Handling Platform in research laboratories and facilities, this will allow many researchers to quickly create robust Spatial Transcriptomics libraries.", "doi": "10.1186/s12864-020-6631-z", "pmid": "32293264", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-6631-z"}, {"db": "pmc", "key": "PMC7158132"}], "notes": [], "created": "2020-07-08T13:03:44.517Z", "modified": "2024-01-16T13:48:42.620Z"}, {"entity": "publication", "iuid": "6733f592fb4a45bf9135c7dcc59e9c3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6733f592fb4a45bf9135c7dcc59e9c3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6733f592fb4a45bf9135c7dcc59e9c3d"}}, "title": "Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.", "authors": [{"family": "Petrus-Reurer", "given": "Sandra", "initials": "S"}, {"family": "Winblad", "given": "Nerges", "initials": "N"}, {"family": "Kumar", "given": "Pankaj", "initials": "P"}, {"family": "Gorchs", "given": "Laia", "initials": "L"}, {"family": "Chrobok", "given": "Michael", "initials": "M"}, {"family": "Wagner", "given": "Arnika Kathleen", "initials": "AK"}, {"family": "Bartuma", "given": "Hammurabi", "initials": "H"}, {"family": "Lardner", "given": "Emma", "initials": "E"}, {"family": "Aronsson", "given": "Monica", "initials": "M"}, {"family": "Plaza Reyes", "given": "\u00c1lvaro", "initials": "\u00c1"}, {"family": "Andr\u00e9", "given": "Helder", "initials": "H"}, {"family": "Alici", "given": "Evren", "initials": "E"}, {"family": "Kaipe", "given": "Helen", "initials": "H"}, {"family": "Kvanta", "given": "Anders", "initials": "A"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2020-04-14", "journal": {"title": "Stem Cell Reports", "issn": "2213-6711", "volume": "14", "issue": "4", "pages": "648-662", "issn-l": "2213-6711"}, "abstract": "Human embryonic stem cell-derived retinal pigment epithelial (hESC-RPE) cells could serve as a replacement therapy in advanced stages of age-related macular degeneration. However, allogenic hESC-RPE transplants trigger immune rejection, supporting a strategy to evade their immune recognition. We established single-knockout beta-2 microglobulin (SKO-B2M), class II major histocompatibility complex transactivator (SKO-CIITA) and double-knockout (DKO) hESC lines that were further differentiated into corresponding hESC-RPE lines lacking either surface human leukocyte antigen class I (HLA-I) or HLA-II, or both. Activation of CD4+ and CD8+ T-cells was markedly lower by hESC-RPE DKO cells, while natural killer cell cytotoxic response was not increased. After transplantation of SKO-B2M, SKO-CIITA, or DKO hESC-RPEs in a preclinical rabbit model, donor cell rejection was reduced and delayed. In conclusion, we have developed cell lines that lack both HLA-I and -II antigens, which evoke reduced T-cell responses in vitro together with reduced rejection in a large-eyed animal model.", "doi": "10.1016/j.stemcr.2020.02.006", "pmid": "32197113", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2213-6711(20)30062-X"}, {"db": "pmc", "key": "PMC7160308"}], "notes": [], "created": "2020-07-08T13:05:34.265Z", "modified": "2024-01-16T13:48:42.627Z"}, {"entity": "publication", "iuid": "db1ed54638e64638ab235cfb62758387", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db1ed54638e64638ab235cfb62758387.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db1ed54638e64638ab235cfb62758387"}}, "title": "Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.", "authors": [{"family": "Shafeeq", "given": "Sulman", "initials": "S"}, {"family": "Wang", "given": "Xiaoda", "initials": "X", "orcid": "0000-0003-0175-435X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a7de54a021a47f09821f26fb4ee2f4e.json"}}, {"family": "L\u00fcnsdorf", "given": "Heinrich", "initials": "H"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U", "orcid": "0000-0003-3812-6621", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a59ac735d61485aa43ee7a2ae3a526d.json"}}], "type": "journal article", "published": "2020-04-05", "journal": {"volume": "8", "issn": "2076-2607", "issue": "4", "title": "Microorganisms", "pages": "522", "issn-l": "2076-2607"}, "abstract": ": Enterobacter ludwigii is a fermentative Gram-negative environmental species and accidental human pathogen that belongs to the Enterobacter cloacae complex with the general characteristics of the genus Enterobacter. The clinical isolate E. ludwigii CEB04 was derived from a urinary tract catheter of an individual not suffering from catheter-associated urinary tract infection. The draft genome sequence of the high biofilm forming E. ludwigii CEB04 was determined by PacBio sequencing. The chromosome of E. ludwigii CEB04 is comprised of one contig of 4,892,375 bps containing 4596 predicted protein-coding genes and 120 noncoding RNAs. E. ludwigii CEB04 harbors several antimicrobial resistance markers and has an extended cyclic-di-GMP signaling network compared to Escherichia coli K-12.", "doi": "10.3390/microorganisms8040522", "pmid": "32260576", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7232144"}, {"db": "pii", "key": "microorganisms8040522"}], "notes": [], "created": "2020-05-04T14:34:04.659Z", "modified": "2024-01-16T13:48:42.641Z"}, {"entity": "publication", "iuid": "c415e1ad145e4e3980e7a96e3c492895", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c415e1ad145e4e3980e7a96e3c492895.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c415e1ad145e4e3980e7a96e3c492895"}}, "title": "Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.", "authors": [{"family": "Andersson", "given": "Natalie", "initials": "N"}, {"family": "Bakker", "given": "Bjorn", "initials": "B", "orcid": "0000-0003-3095-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2f6637d70ea487bbd752150140416dc.json"}}, {"family": "Karlsson", "given": "Jenny", "initials": "J"}, {"family": "Valind", "given": "Anders", "initials": "A"}, {"family": "Holmquist Mengelbier", "given": "Linda", "initials": "L", "orcid": "0000-0002-3632-2760", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6729b3f10e84432839564c382473607.json"}}, {"family": "Spierings", "given": "Diana C J", "initials": "DCJ", "orcid": "0000-0001-8403-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/62825465dc084c7ebd10b71e274d5eb2.json"}}, {"family": "Foijer", "given": "Floris", "initials": "F"}, {"family": "Gisselsson", "given": "David", "initials": "D"}], "type": "journal article", "published": "2020-04-01", "journal": {"title": "Cancer Res.", "issn": "1538-7445", "volume": "80", "issue": "7", "pages": "1512-1523", "issn-l": "0008-5472"}, "abstract": "Darwinian evolution of tumor cells remains underexplored in childhood cancer. We here reconstruct the evolutionary histories of 56 pediatric primary tumors, including 24 neuroblastomas, 24 Wilms tumors, and 8 rhabdomyosarcomas. Whole-genome copy-number and whole-exome mutational profiling of multiple regions per tumor were performed, followed by clonal deconvolution to reconstruct a phylogenetic tree for each tumor. Overall, 88% of the tumors exhibited genetic variation among primary tumor regions. This variability typically emerged through collateral phylogenetic branching, leading to spatial variability in the distribution of more than 50% (96/173) of detected diagnostically informative genetic aberrations. Single-cell sequencing of 547 individual cancer cells from eight solid pediatric tumors confirmed branching evolution to be a fundamental underlying principle of genetic variation in all cases. Strikingly, cell-to-cell genetic diversity was almost twice as high in aggressive compared with clinically favorable tumors (median Simpson index of diversity 0.45 vs. 0.88; P = 0.029). Similarly, a comparison of multiregional sampling data from a total of 274 tumor regions showed that new phylogenetic branches emerge at a higher frequency per sample and carry a higher mutational load in high-risk than in low-risk tumors. Timelines based on spatial genetic variation showed that the mutations most influencing relapse risk occur at initiation of clonal expansion in neuroblastoma and rhabdomyosarcoma, whereas in Wilms tumor, they are late events. Thus, from an evolutionary standpoint, some high-risk childhood cancers are born bad, whereas others grow worse over time. SIGNIFICANCE: Different pediatric cancers with a high risk of relapse share a common generic pattern of extensively branching evolution of somatic mutations. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/7/1512/F1.large.jpg.", "doi": "10.1158/0008-5472.CAN-19-3468", "pmid": "32041836", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-19-3468"}], "notes": [], "created": "2020-07-08T13:05:37.152Z", "modified": "2021-11-10T12:52:26.783Z"}, {"entity": "publication", "iuid": "4e3cb3704b79480991034259edc854ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e3cb3704b79480991034259edc854ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e3cb3704b79480991034259edc854ea"}}, "title": "Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.", "authors": [{"family": "Eriksen", "given": "Anne K", "initials": "AK", "orcid": "0000-0002-4535-3788", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc9f2263b20b42cf96dc666317b5818e.json"}}, {"family": "Brunius", "given": "Carl", "initials": "C"}, {"family": "Mazidi", "given": "Mohsen", "initials": "M"}, {"family": "Hellstr\u00f6m", "given": "Per M", "initials": "PM"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Iversen", "given": "Kia N", "initials": "KN"}, {"family": "Fristedt", "given": "Rikard", "initials": "R"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Huang", "given": "Yi", "initials": "Y"}, {"family": "N\u00f8rskov", "given": "Natalja P", "initials": "NP"}, {"family": "Knudsen", "given": "Knud Erik B", "initials": "KEB"}, {"family": "Kyr\u00f8", "given": "Cecilie", "initials": "C"}, {"family": "Olsen", "given": "Anja", "initials": "A", "orcid": "0000-0003-4788-503X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1236514511b54a5b9e633248151957a4.json"}}, {"family": "Tj\u00f8nneland", "given": "Anne", "initials": "A", "orcid": "0000-0003-4385-2097", "researcher": {"href": "https://publications.scilifelab.se/researcher/de22a0e2f07d43e19f370599a051f239.json"}}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Landberg", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2020-04-01", "journal": {"title": "Am. J. Clin. Nutr.", "issn": "1938-3207", "volume": "111", "issue": "4", "pages": "864-876", "issn-l": "0002-9165"}, "abstract": "A whole-grain (WG)-rich diet has shown to have potential for both prevention and treatment of the metabolic syndrome (MetS), which is a cluster of risk factors that increase the risk of type 2 diabetes and cardiovascular disease. Different WGs may have different health effects. WG rye, in particular, may improve glucose homeostasis and blood lipids, possibly mediated through fermentable dietary fiber and lignans. Recent studies have also suggested a crucial role of the gut microbiota in response to WG.\n\nThe aim was to investigate WG rye, alone and with lignan supplements [secoisolariciresinol diglucoside (SDG)], and WG wheat diets on glucose tolerance [oral-glucose-tolerance test (OGTT)], other cardiometabolic outcomes, enterolignans, and microbiota composition. Moreover, we exploratively evaluated the role of gut microbiota enterotypes in response to intervention diets.\n\nForty men with MetS risk profile were randomly assigned to WG diets in an 8-wk crossover study. The rye diet was supplemented with 280 mg SDG at weeks 4-8. Effects of treatment were evaluated by mixed-effects modeling, and effects on microbiota composition and the role of gut microbiota as a predictor of response to treatment were analyzed by random forest plots.\n\nThe WG rye diet (\u00b1 SDG supplements) did not affect the OGTT compared with WG wheat. Total and LDL cholesterol were lowered (-0.06 and -0.09 mmol/L, respectively; P < 0.05) after WG rye compared with WG wheat after 4 wk but not after 8 wk. WG rye resulted in higher abundance of Bifidobacterium [fold-change (FC) = 2.58, P < 0.001] compared with baseline and lower abundance of Clostridium genus compared with WG wheat (FC = 0.54, P = 0.02). The explorative analyses suggest that baseline enterotype is associated with total and LDL-cholesterol response to diet.\n\nWG rye, alone or with SDG supplementation, compared with WG wheat did not affect glucose metabolism but caused transient LDL-cholesterol reduction. The effect of WG diets appeared to differ according to enterotype. This trial was registered at www.clinicaltrials.gov as NCT02987595.", "doi": "10.1093/ajcn/nqaa026", "pmid": "32097450", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5758012"}, {"db": "ClinicalTrials.gov", "key": "NCT02987595"}], "notes": [], "created": "2021-01-08T16:29:15.845Z", "modified": "2024-01-16T13:48:42.669Z"}, {"entity": "publication", "iuid": "5706e39b31514be89be947515ceebdee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5706e39b31514be89be947515ceebdee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5706e39b31514be89be947515ceebdee"}}, "title": "Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome.", "authors": [{"family": "Rutgersson", "given": "Carolin", "initials": "C"}, {"family": "Ebmeyer", "given": "Stefan", "initials": "S"}, {"family": "Lassen", "given": "Simon Bo", "initials": "SB"}, {"family": "Karkman", "given": "Antti", "initials": "A"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Brandt", "given": "Kristian K", "initials": "KK"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2020-04-00", "journal": {"title": "Environ Int", "issn": "1873-6750", "volume": "137", "issue": null, "pages": "105339", "issn-l": "0160-4120"}, "abstract": "The widespread practice of applying sewage sludge to arable land makes use of nutrients indispensable for crops and reduces the need for inorganic fertilizer, however this application also provides a potential route for human exposure to chemical contaminants and microbial pathogens in the sludge. A recent concern is that such practice could promote environmental selection and dissemination of antibiotic resistant bacteria or resistance genes. Understanding the risks of sludge amendment in relation to antibiotic resistance development is important for sustainable agriculture, waste treatment and infectious disease management. To assess such risks, we took advantage of an agricultural field trial in southern Sweden, where land used for growing different crops has been amended with sludge every four years since 1981. We sampled raw, semi-digested and digested and stored sludge together with soils from the experimental plots before and two weeks after the most recent amendment in 2017. Levels of selected antimicrobials and bioavailable metals were determined and microbial effects were evaluated using both culture-independent metagenome sequencing and conventional culturing. Antimicrobials or bioavailable metals (Cu and Zn) did not accumulate to levels of concern for environmental selection of antibiotic resistance, and no coherent signs, neither on short or long time scales, of enrichment of antibiotic-resistant bacteria or resistance genes were found in soils amended with digested and stored sewage sludge in doses up to 12 metric tons per hectare. Likewise, only very few and slight differences in microbial community composition were observed after sludge amendment. Taken together, the current study does not indicate risks of sludge amendment related to antibiotic resistance development under the given conditions. Extrapolations should however be done with care as sludge quality and application practices vary between regions. Hence, the antibiotic concentrations and resistance load of the sludge are likely to be higher in regions with larger antibiotic consumption and resistance burden than Sweden.", "doi": "10.1016/j.envint.2019.105339", "pmid": "32036119", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0160-4120(19)31788-X"}], "notes": [], "created": "2021-01-08T16:29:11.107Z", "modified": "2021-11-10T12:52:35.828Z"}, {"entity": "publication", "iuid": "c83707e3be244e97b835f054f03476c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c83707e3be244e97b835f054f03476c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c83707e3be244e97b835f054f03476c1"}}, "title": "Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.", "authors": [{"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Svedberg", "given": "Anna", "initials": "A"}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S", "orcid": "0000-0002-0834-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1917cb059924a779ac38e3023778461.json"}}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H", "orcid": "0000-0001-5797-7873", "researcher": {"href": "https://publications.scilifelab.se/researcher/020d1b7e7693495484dc85c4ba6f2adc.json"}}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "de Petris", "given": "Luigi", "initials": "L"}, {"family": "Apell\u00e1niz-Ruiz", "given": "Maria", "initials": "M"}, {"family": "Rodr\u00edguez-Antona", "given": "Cristina", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2020-04-00", "journal": {"volume": "20", "issn": "1473-1150", "issue": "2", "title": "Pharmacogenomics J.", "pages": "179-191", "issn-l": "1470-269X"}, "abstract": "Chemotherapy-induced myelosuppression, including thrombocytopenia, is a recurrent problem during cancer treatments that may require dose alterations or cessations that could affect the antitumor effect of the treatment. To identify genetic markers associated with treatment-induced thrombocytopenia, we whole-exome sequenced 215 non-small cell lung cancer patients homogeneously treated with gemcitabine/carboplatin. The decrease in platelets (defined as nadir/baseline) was used to assess treatment-induced thrombocytopenia. Association between germline genetic variants and thrombocytopenia was analyzed at single-nucleotide variant (SNV) (based on the optimal false discovery rate, the severity of predicted consequence, and effect), gene, and pathway levels. These analyses identified 130 SNVs/INDELs and 25 genes associated with thrombocytopenia (P-value < 0.002). Twenty-three SNVs were validated in an independent genome-wide association study (GWAS). The top associations include rs34491125 in JMJD1C (P-value = 9.07 \u00d7 10-5), the validated variants rs10491684 in DOCK8 (P-value = 1.95 \u00d7 10-4), rs6118 in SERPINA5 (P-value = 5.83 \u00d7 10-4), and rs5877 in SERPINC1 (P-value = 1.07 \u00d7 10-3), and the genes CAPZA2 (P-value = 4.03 \u00d7 10-4) and SERPINC1 (P-value = 1.55 \u00d7 10-3). The SNVs in the top-scoring pathway \"Factors involved in megakaryocyte development and platelet production\" (P-value = 3.34 \u00d7 10-4) were used to construct weighted genetic risk score (wGRS) and logistic regression models that predict thrombocytopenia. The wGRS predict which patients are at high or low toxicity risk levels, for CTCAE (odds ratio (OR) = 22.35, P-value = 1.55 \u00d7 10-8), and decrease (OR = 66.82, P-value = 5.92 \u00d7 10-9). The logistic regression models predict CTCAE grades 3-4 (receiver operator characteristics (ROC) area under the curve (AUC) = 0.79), and large decrease (ROC AUC = 0.86). We identified and validated genetic variations within hematopoiesis-related pathways that provide a solid foundation for future studies using genetic markers for predicting chemotherapy-induced thrombocytopenia and personalizing treatments.", "doi": "10.1038/s41397-019-0099-8", "pmid": "31616045", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41397-019-0099-8"}], "notes": [], "created": "2019-12-02T16:50:30.268Z", "modified": "2021-11-10T12:52:36.985Z"}, {"entity": "publication", "iuid": "a34d9cdcb8744d77a97282ebb665da1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a34d9cdcb8744d77a97282ebb665da1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a34d9cdcb8744d77a97282ebb665da1a"}}, "title": "Transcriptome Profiling and Toxicity Following Long-Term, Low Dose Exposure of Human Lung Cells to Ni and NiO Nanoparticles-Comparison with NiCl2.", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Di Bucchianico", "given": "Sebastiano", "initials": "S", "orcid": "0000-0002-6396-892X", "researcher": {"href": "https://publications.scilifelab.se/researcher/22ab671e103c40038515391da27d859c.json"}}, {"family": "\u00c5kerlund", "given": "Emma", "initials": "E"}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}], "type": "journal article", "published": "2020-03-31", "journal": {"title": "Nanomaterials (Basel)", "issn": "2079-4991", "volume": "10", "issue": "4", "pages": "649", "issn-l": "2079-4991"}, "abstract": "Production of nickel (Ni) and nickel oxide (NiO) nanoparticles (NPs) leads to a risk of exposure and subsequent health effects. Understanding the toxicological effects and underlying mechanisms using relevant in vitro methods is, therefore, needed. The aim of this study is to explore changes in gene expression using RNA sequencing following long term (six weeks) low dose (0.5 \u00b5g Ni/mL) exposure of human lung cells (BEAS-2B) to Ni and NiO NPs as well as soluble NiCl2. Genotoxicity and cell transformation as well as cellular dose of Ni are also analyzed. Exposure to NiCl2 resulted in the largest number of differentially expressed genes (197), despite limited uptake, suggesting a major role of extracellular receptors and downstream signaling. Gene expression changes for all Ni exposures included genes coding for calcium-binding proteins (S100A14 and S100A2) as well as TIMP3, CCND2, EPCAM, IL4R and DDIT4. Several top enriched pathways for NiCl2 were defined by upregulation of, e.g., interleukin-1A and -1B, as well as Vascular Endothelial Growth Factor A (VEGFA). All Ni exposures caused DNA strand breaks (comet assay), whereas no induction of micronuclei was observed. Taken together, this study provides an insight into Ni-induced toxicity and mechanisms occurring at lower and more realistic exposure levels.", "doi": "10.3390/nano10040649", "pmid": "32244462", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "nano10040649"}, {"db": "pmc", "key": "PMC7221965"}], "notes": [], "created": "2020-07-08T13:04:59.092Z", "modified": "2021-11-10T12:52:42.707Z"}, {"entity": "publication", "iuid": "ed38171ac9fb4267b06326f783d43541", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed38171ac9fb4267b06326f783d43541.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed38171ac9fb4267b06326f783d43541"}}, "title": "Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.", "authors": [{"family": "Andersson", "given": "Kristofer", "initials": "K"}, {"family": "Malmgren", "given": "Barbro", "initials": "B"}, {"family": "\u00c5str\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Dahll\u00f6f", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2020-03-31", "journal": {"title": "Orphanet J Rare Dis", "issn": "1750-1172", "volume": "15", "issue": "1", "pages": "80", "issn-l": "1750-1172"}, "abstract": "Osteogenesis imperfecta (OI) is a heterogeneous connective tissue disorder characterized by an increased tendency for fractures throughout life. Autosomal dominant (AD) mutations in COL1A1 and COL1A2 are causative in approximately 85% of cases. In recent years, recessive variants in genes involved in collagen processing have been found. Hypodontia (< 6 missing permanent teeth) and oligodontia (\u2265 6 missing permanent teeth) have previously been reported in individuals with OI. The aim of the present cross-sectional study was to investigate whether children and adolescents with OI and oligodontia and hypodontia also present with variants in other genes with potential effects on tooth development. The cohort comprised 10 individuals (7.7-19.9 years of age) with known COL1A1/A2 variants who we clinically and radiographically examined and further genetically evaluated by whole-genome sequencing. All study participants were treated at the Astrid Lindgren Children's Hospital at Karolinska University Hospital, Stockholm (Sweden's national multidisciplinary pediatric OI team). We evaluated a panel of genes that were associated with nonsyndromic and syndromic hypodontia or oligodontia as well as that had been found to be involved in tooth development in animal models.\n\nWe detected a homozygous nonsense variant in CREB3L1, p.Tyr428*, c.1284C > A in one boy previously diagnosed with OI type III. COL1A1 and COL1A2 were the only two genes among 9 individuals which carried a pathogenic mutation. We found rare variants with unknown significance in several other genes related to tooth development.\n\nOur findings suggest that mutations in COL1A1, COL1A2, and CREB3L1 may cause hypodontia and oligodontia in OI. The findings cannot exclude additive effects from other modifying or interacting genes that may contribute to the severity of the expressed phenotype. Larger cohorts and further functional studies are needed.", "doi": "10.1186/s13023-020-01361-4", "pmid": "32234057", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13023-020-01361-4"}, {"db": "pmc", "key": "PMC7110904"}], "notes": [], "created": "2020-07-08T13:04:37.345Z", "modified": "2021-11-10T12:52:44.175Z"}, {"entity": "publication", "iuid": "fa45dc8f027c484fab11c81fa878996a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa45dc8f027c484fab11c81fa878996a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa45dc8f027c484fab11c81fa878996a"}}, "title": "An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.", "authors": [{"family": "Ignatov", "given": "Dmitriy", "initials": "D"}, {"family": "Vaitkevicius", "given": "Karolis", "initials": "K"}, {"family": "Durand", "given": "Sylvain", "initials": "S"}, {"family": "Cahoon", "given": "Laty", "initials": "L"}, {"family": "Sandberg", "given": "Stefanie S", "initials": "SS"}, {"family": "Liu", "given": "Xijia", "initials": "X"}, {"family": "Kallipolitis", "given": "Birgitte H", "initials": "BH"}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P"}, {"family": "Freitag", "given": "Nancy", "initials": "N"}, {"family": "Condon", "given": "Ciar\u00e1n", "initials": "C"}, {"family": "Johansson", "given": "J\u00f6rgen", "initials": "J"}], "type": "journal article", "published": "2020-03-24", "journal": {"title": "Cell Rep", "issn": "2211-1247", "volume": "30", "issue": "12", "pages": "4027-4040.e7", "issn-l": null}, "abstract": "Bacterial pathogens often employ RNA regulatory elements located in the 5' untranslated regions (UTRs) to control gene expression. Using a comparative structural analysis, we examine the structure of 5' UTRs at a global scale in the pathogenic bacterium Listeria monocytogenes under different conditions. In addition to discovering an RNA thermoswitch and detecting simultaneous interaction of ribosomes and small RNAs with mRNA, we identify structural changes in the 5' UTR of an mRNA encoding the post-translocation chaperone PrsA2 during infection conditions. We demonstrate that the 5' UTR of the prsA2 mRNA base pairs with the 3' UTR of the full-length hly mRNA encoding listeriolysin O, thus preventing RNase J1-mediated degradation of the prsA2 transcript. Mutants lacking the hly-prsA2 interaction exhibit reduced virulence properties. This work highlights an additional level of RNA regulation, where the mRNA encoding a chaperone is stabilized by the mRNA encoding its substrate.", "doi": "10.1016/j.celrep.2020.03.006", "pmid": "32209466", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(20)30304-1"}], "notes": [], "created": "2020-12-07T16:27:00.041Z", "modified": "2024-01-16T13:48:42.745Z"}, {"entity": "publication", "iuid": "bbd542002470460c855f69cf5746f481", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbd542002470460c855f69cf5746f481.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbd542002470460c855f69cf5746f481"}}, "title": "Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.", "authors": [{"family": "Rantapero", "given": "Tommi", "initials": "T"}, {"family": "Wahlfors", "given": "Tiina", "initials": "T"}, {"family": "K\u00e4hler", "given": "Anna", "initials": "A"}, {"family": "Hultman", "given": "Christina", "initials": "C"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Tammela", "given": "Teuvo Lj", "initials": "TL"}, {"family": "Nykter", "given": "Matti", "initials": "M"}, {"family": "Schleutker", "given": "Johanna", "initials": "J"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-4623-0544", "researcher": {"href": "https://publications.scilifelab.se/researcher/0650e45c937b4cf3bb36b60ae369c67e.json"}}], "type": "journal article", "published": "2020-03-14", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "11", "issue": "3", "pages": "314", "issn-l": "2073-4425"}, "abstract": "Germline variants in DNA repair genes are associated with aggressive prostate cancer (PrCa). The aim of this study was to characterize germline variants in DNA repair genes associated with lethal PrCa in Finnish and Swedish populations. Whole-exome sequencing was performed for 122 lethal and 60 unselected PrCa cases. Among the lethal cases, a total of 16 potentially damaging protein-truncating variants in DNA repair genes were identified in 15 men (12.3%). Mutations were found in six genes with CHEK2 (4.1%) and ATM (3.3%) being most frequently mutated. Overall, the carrier rate of truncating variants in DNA repair genes among men with lethal PrCa significantly exceeded the carrier rate of 0% in 60 unselected PrCa cases (p = 0.030), and the prevalence of 1.6% (p < 0.001) and 5.4% (p = 0.040) in Swedish and Finnish population controls from the Exome Aggregation Consortium. No significant difference in carrier rate of potentially damaging nonsynonymous single nucleotide variants between lethal and unselected PrCa cases was observed (p = 0.123). We confirm that DNA repair genes are strongly associated with lethal PrCa in Sweden and Finland and highlight the importance of population-specific assessment of variants contributing to PrCa aggressiveness.", "doi": "10.3390/genes11030314", "pmid": "32183364", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes11030314"}, {"db": "pmc", "key": "PMC7140841"}], "notes": [], "created": "2020-07-08T13:04:09.131Z", "modified": "2024-01-16T13:48:42.766Z"}, {"entity": "publication", "iuid": "b666d402dd5343929e0fbb695aca0efe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe"}}, "title": "Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d517d4f20046c08405f8aeecf4ad2a.json"}}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S", "orcid": "0000-0003-3707-4487", "researcher": {"href": "https://publications.scilifelab.se/researcher/5358a1e162474073a69b08c32e7c5420.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Quince", "given": "Christopher", "initials": "C"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-03-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "119", "issn-l": "2399-3642"}, "abstract": "The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.", "doi": "10.1038/s42003-020-0856-x", "pmid": "32170201", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0856-x"}, {"db": "pmc", "key": "PMC7070063"}], "notes": [], "created": "2020-07-08T13:04:08.349Z", "modified": "2024-01-16T13:48:42.773Z"}, {"entity": "publication", "iuid": "8afecd15e6b94e65880a25e3aa12d789", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8afecd15e6b94e65880a25e3aa12d789.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8afecd15e6b94e65880a25e3aa12d789"}}, "title": "Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies.", "authors": [{"family": "Sunde", "given": "Johanna", "initials": "J"}, {"family": "Y\u0131ld\u0131r\u0131m", "given": "Ye\u015ferin", "initials": "Y"}, {"family": "Tibblin", "given": "Petter", "initials": "P"}, {"family": "Forsman", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2020-03-13", "journal": {"title": "Front Genet", "issn": "1664-8021", "volume": "11", "issue": null, "pages": "218", "issn-l": "1664-8021"}, "abstract": "Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies. Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (Esox lucius) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (N = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (N = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset pointed to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.", "doi": "10.3389/fgene.2020.00218", "pmid": "32231687", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7082332"}], "notes": [], "created": "2020-07-08T13:05:36.511Z", "modified": "2024-01-16T13:48:42.781Z"}, {"entity": "publication", "iuid": "6ef6a5481f8043e3a6bd28a7ef84d080", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ef6a5481f8043e3a6bd28a7ef84d080.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ef6a5481f8043e3a6bd28a7ef84d080"}}, "title": "Uncovering diversity and metabolic spectrum of animals in dead zone sediments.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Bonaglia", "given": "Stefano", "initials": "S", "orcid": "0000-0003-4366-0677", "researcher": {"href": "https://publications.scilifelab.se/researcher/c02dd99f9fd14dd89d5c231260806720.json"}}, {"family": "Holovachov", "given": "Oleksandr", "initials": "O", "orcid": "0000-0002-4285-0754", "researcher": {"href": "https://publications.scilifelab.se/researcher/7887fd76b35c47aaa67ac8ab7a1d07d5.json"}}, {"family": "Marzocchi", "given": "Ugo", "initials": "U", "orcid": "0000-0002-4746-9944", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d1ad4b2b3e48db9cc591f4574cb848.json"}}, {"family": "Hall", "given": "Per O J", "initials": "POJ"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2020-03-06", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "106", "issn-l": "2399-3642"}, "abstract": "Ocean deoxygenation driven by global warming and eutrophication is a primary concern for marine life. Resistant animals may be present in dead zone sediments, however there is lack of information on their diversity and metabolism. Here we combined geochemistry, microscopy, and RNA-seq for estimating taxonomy and functionality of micrometazoans along an oxygen gradient in the largest dead zone in the world. Nematodes are metabolically active at oxygen concentrations below 1.8 \u00b5mol L-1, and their diversity and community structure are different between low oxygen areas. This is likely due to toxic hydrogen sulfide and its potential to be oxidized by oxygen or nitrate. Zooplankton resting stages dominate the metazoan community, and these populations possibly use cytochrome c oxidase as an oxygen sensor to exit dormancy. Our study sheds light on mechanisms of animal adaptation to extreme environments. These biological resources can be essential for recolonization of dead zones when oxygen conditions improve.", "doi": "10.1038/s42003-020-0822-7", "pmid": "32144383", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0822-7"}, {"db": "pmc", "key": "PMC7060179"}], "notes": [], "created": "2020-07-08T13:05:16.537Z", "modified": "2024-01-16T13:48:42.803Z"}, {"entity": "publication", "iuid": "bb89d24bf5de4738810b72a84a0ad0b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb89d24bf5de4738810b72a84a0ad0b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb89d24bf5de4738810b72a84a0ad0b6"}}, "title": "An atlas of the protein-coding genes in the human, pig, and mouse brain.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Mitsios", "given": "Nicholas", "initials": "N", "orcid": "0000-0001-6243-4953", "researcher": {"href": "https://publications.scilifelab.se/researcher/38efa44f5ed64192b432d6384584f00d.json"}}, {"family": "Adori", "given": "Csaba", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Limiszewska", "given": "Agnieszka", "initials": "A", "orcid": "0000-0003-1601-8195", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e7b9e0e376422491d8bd1d76d6f774.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F", "orcid": "0000-0002-3750-9308", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e8c8f511fef466dafd7d704e17d2e30.json"}}, {"family": "Huang", "given": "Jinrong", "initials": "J", "orcid": "0000-0001-8085-9939", "researcher": {"href": "https://publications.scilifelab.se/researcher/00a7eea9544b457b8b058c98e0f4ee94.json"}}, {"family": "Du", "given": "Yutao", "initials": "Y"}, {"family": "Lin", "given": "Lin", "initials": "L", "orcid": "0000-0002-7546-4948", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6436e2b14cd4a629aeebed48b3ae0a9.json"}}, {"family": "Dong", "given": "Zhanying", "initials": "Z"}, {"family": "Yang", "given": "Ling", "initials": "L", "orcid": "0000-0002-5425-8256", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e150be60a3740b89511174e0fd8fa6e.json"}}, {"family": "Liu", "given": "Xin", "initials": "X", "orcid": "0000-0003-3256-2940", "researcher": {"href": "https://publications.scilifelab.se/researcher/b130e21a82a94eb7acd0333f3e62b6ba.json"}}, {"family": "Jiang", "given": "Hui", "initials": "H"}, {"family": "Xu", "given": "Xun", "initials": "X", "orcid": "0000-0002-5338-5173", "researcher": {"href": "https://publications.scilifelab.se/researcher/c96e82115f8d493ea665e5dfe2a374e9.json"}}, {"family": "Wang", "given": "Jian", "initials": "J"}, {"family": "Yang", "given": "Huanming", "initials": "H", "orcid": "0000-0003-1703-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/6575b8191e414162b52d26df8d9af26a.json"}}, {"family": "Bolund", "given": "Lars", "initials": "L"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aad9ec706674ed6ab358a445ba1989d.json"}}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}], "type": "comparative study", "published": "2020-03-06", "journal": {"title": "Science", "issn": "1095-9203", "volume": "367", "issue": "6482", "pages": "eaay5947", "issn-l": "0036-8075"}, "abstract": "The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.", "doi": "10.1126/science.aay5947", "pmid": "32139519", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "367/6482/eaay5947"}], "notes": [], "created": "2020-12-07T16:26:57.513Z", "modified": "2024-01-16T13:48:42.811Z"}, {"entity": "publication", "iuid": "e7b62282c0ab4fa298b3a15c0daefd80", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7b62282c0ab4fa298b3a15c0daefd80.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7b62282c0ab4fa298b3a15c0daefd80"}}, "title": "The Molecular Anatomy of Mouse Skin during Hair Growth and Rest.", "authors": [{"family": "Joost", "given": "Simon", "initials": "S"}, {"family": "Annusver", "given": "Karl", "initials": "K"}, {"family": "Jacob", "given": "Tina", "initials": "T"}, {"family": "Sun", "given": "Xiaoyan", "initials": "X"}, {"family": "Dalessandri", "given": "Tim", "initials": "T"}, {"family": "Sivan", "given": "Unnikrishnan", "initials": "U"}, {"family": "Sequeira", "given": "In\u00eas", "initials": "I"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Kasper", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2020-03-05", "journal": {"volume": "26", "issn": "1875-9777", "issue": "3", "pages": "441-457.e7", "title": "Cell Stem Cell", "issn-l": null}, "abstract": "Skin homeostasis is orchestrated by dozens of cell types that together direct stem cell renewal, lineage commitment, and differentiation. Here, we use single-cell RNA sequencing and single-molecule RNA FISH to provide a systematic molecular atlas of full-thickness skin, determining gene expression profiles and spatial locations that define 56 cell types and states during hair growth and rest. These findings reveal how the outer root sheath (ORS) and inner hair follicle layers coordinate hair production. We found that the ORS is composed of two intermingling but transcriptionally distinct cell types with differing capacities for interactions with stromal cell types. Inner layer cells branch from transcriptionally uncommitted progenitors, and each lineage differentiation passes through an intermediate state. We also provide an online tool to explore this comprehensive skin cell atlas, including epithelial and stromal cells such as fibroblasts, vascular, and immune cells, to spur further discoveries in skin biology.", "doi": "10.1016/j.stem.2020.01.012", "pmid": "32109378", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1934-5909(20)30012-6"}], "notes": [], "created": "2020-03-02T10:57:50.903Z", "modified": "2024-01-16T13:48:42.819Z"}, {"entity": "publication", "iuid": "202e5326e1f74688bebee61065aa45e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/202e5326e1f74688bebee61065aa45e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/202e5326e1f74688bebee61065aa45e6"}}, "title": "The nf-core framework for community-curated bioinformatics pipelines.", "authors": [{"family": "Ewels", "given": "Philip A", "initials": "PA", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Peltzer", "given": "Alexander", "initials": "A", "orcid": "0000-0002-6503-2180", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bc79fd3ce6b40d989966e0dbe88487c.json"}}, {"family": "Fillinger", "given": "Sven", "initials": "S", "orcid": "0000-0001-8835-2219", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e2007321e9641c2bcc17ead2e037a5b.json"}}, {"family": "Patel", "given": "Harshil", "initials": "H", "orcid": "0000-0003-2707-7940", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcb1a5f414814b5096deac0f1a61cbaa.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Wilm", "given": "Andreas", "initials": "A"}, {"family": "Garcia", "given": "Maxime Ulysse", "initials": "MU", "orcid": "0000-0003-2827-9261", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf9b1b223f04296adcb6bd091c548de.json"}}, {"family": "Di Tommaso", "given": "Paolo", "initials": "P"}, {"family": "Nahnsen", "given": "Sven", "initials": "S", "orcid": "0000-0002-4375-0691", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b0b5e235dcc49bcb07248a1053cb610.json"}}], "type": "letter", "published": "2020-03-00", "journal": {"volume": "38", "issn": "1546-1696", "issue": "3", "pages": "276-278", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": "The standardization, portability and reproducibility of analysis pipelines are key issues within the bioinformatics community. Most bioinformatics pipelines are designed for use on-premises; as a result, the associated software dependencies and execution logic are likely to be tightly coupled with proprietary computing environments. This can make it difficult or even impossible for others to reproduce the ensuing results, which is a fundamental requirement for the validation of scientific findings. Here, we introduce the nf-core framework as a means for the development of collaborative, peer-reviewed, best-practice analysis pipelines (Fig. 1). All nf-core pipelines are written in Nextflow and so inherit the ability to be executed on most computational infrastructures, as well as having native support for container technologies such as Docker and Singularity. The nf-core community (Supplementary Fig. 1) has developed a suite of tools that automate pipeline creation, testing, deployment and synchronization. Our goal is to provide a framework for high-quality bioinformatics pipelines that can be used across all institutions and research facilities.", "doi": "10.1038/s41587-020-0439-x", "pmid": "32055031", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Stockholm (Genomics Applications)": "Technology development", "NGI Stockholm (Genomics Production)": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1038/s41587-020-0439-x"}], "notes": [], "created": "2020-06-01T16:52:53.192Z", "modified": "2021-11-10T12:53:28.620Z"}, {"entity": "publication", "iuid": "4c85c4f3e9624ded9b910cee95bfc2b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c85c4f3e9624ded9b910cee95bfc2b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c85c4f3e9624ded9b910cee95bfc2b8"}}, "title": "Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.", "authors": [{"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Hartmann", "given": "Stefanie", "initials": "S"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Preick", "given": "Michaela", "initials": "M"}, {"family": "Ridush", "given": "Bogdan", "initials": "B", "orcid": "0000-0002-5896-6073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4615423b4a504bdcbfc76429f38b48ea.json"}}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Rathgeber", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6549-6543", "researcher": {"href": "https://publications.scilifelab.se/researcher/39c4006697bf419ba19fa020e80de5c4.json"}}, {"family": "Ziegler", "given": "Reinhard", "initials": "R"}, {"family": "Baryshnikov", "given": "Gennady", "initials": "G"}, {"family": "Sheng", "given": "Guilian", "initials": "G", "orcid": "0000-0003-2314-1650", "researcher": {"href": "https://publications.scilifelab.se/researcher/e96cf70da0364db0926d5312a9076a97.json"}}, {"family": "Ludwig", "given": "Arne", "initials": "A", "orcid": "0000-0001-7249-9953", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5bba6af461445c7bd4a2b6ee97bbd2e.json"}}, {"family": "Wiesel", "given": "Ingrid", "initials": "I"}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bibi", "given": "Faysal", "initials": "F", "orcid": "0000-0002-9414-5547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac6a6d03a0c440328ca1a58fd70cf0f3.json"}}, {"family": "Werdelin", "given": "Lars", "initials": "L"}, {"family": "Heller", "given": "Rasmus", "initials": "R", "orcid": "0000-0001-6583-6923", "researcher": {"href": "https://publications.scilifelab.se/researcher/0289add03723441ab92592b4e3702a2c.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "11", "pages": "eaay0456", "issn-l": "2375-2548"}, "abstract": "The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.", "doi": "10.1126/sciadv.aay0456", "pmid": "32201717", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "aay0456"}, {"db": "pmc", "key": "PMC7069707"}], "notes": [], "created": "2020-07-08T13:04:56.878Z", "modified": "2021-11-10T12:53:35.972Z"}, {"entity": "publication", "iuid": "30a54de97a514ce29242a464f143a6f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30a54de97a514ce29242a464f143a6f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30a54de97a514ce29242a464f143a6f9"}}, "title": "Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.", "authors": [{"family": "Marisca", "given": "Roberta", "initials": "R"}, {"family": "Hoche", "given": "Tobias", "initials": "T"}, {"family": "Agirre", "given": "Eneritz", "initials": "E", "orcid": "0000-0002-5012-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/a507b19745c64c3bb8ef5dce800c8687.json"}}, {"family": "Hoodless", "given": "Laura Jane", "initials": "LJ"}, {"family": "Barkey", "given": "Wenke", "initials": "W"}, {"family": "Auer", "given": "Franziska", "initials": "F"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2247-9393", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1a8fb48114340b8e390ca1f9e3321.json"}}, {"family": "Czopka", "given": "Tim", "initials": "T", "orcid": "0000-0002-6824-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a9b1bd37a6a4ec2ac6b236795531d81.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Nat. Neurosci.", "issn": "1546-1726", "volume": "23", "issue": "3", "pages": "363-374", "issn-l": "1097-6256"}, "abstract": "Recent reports have revealed that oligodendrocyte precursor cells (OPCs) are heterogeneous. It remains unclear whether such heterogeneity reflects different subtypes of cells with distinct functions or instead reflects transiently acquired states of cells with the same function. By integrating lineage formation of individual OPC clones, single-cell transcriptomics, calcium imaging and neural activity manipulation, we show that OPCs in the zebrafish spinal cord can be divided into two functionally distinct groups. One subgroup forms elaborate networks of processes and exhibits a high degree of calcium signaling, but infrequently differentiates despite contact with permissive axons. Instead, these OPCs divide in an activity- and calcium-dependent manner to produce another subgroup, with higher process motility and less calcium signaling and that readily differentiates. Our data show that OPC subgroups are functionally diverse in their response to neurons and that activity regulates the proliferation of a subset of OPCs that is distinct from the cells that generate differentiated oligodendrocytes.", "doi": "10.1038/s41593-019-0581-2", "pmid": "32066987", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-019-0581-2"}, {"db": "pmc", "key": "PMC7292734"}, {"db": "mid", "key": "EMS85307"}], "notes": [], "created": "2020-07-08T13:05:15.850Z", "modified": "2024-01-16T13:48:42.870Z"}, {"entity": "publication", "iuid": "c9b0fa4d11e0486c8d7898eeebfe293a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9b0fa4d11e0486c8d7898eeebfe293a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9b0fa4d11e0486c8d7898eeebfe293a"}}, "title": "Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.", "authors": [{"family": "Wang", "given": "Jing", "initials": "J", "orcid": "0000-0002-3793-3264", "researcher": {"href": "https://publications.scilifelab.se/researcher/98818d7f0b9c48088fdb7109ba037f54.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Park", "given": "Eung-Jun", "initials": "EJ"}, {"family": "Liu", "given": "Jianquan", "initials": "J"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "29", "issue": "6", "pages": "1120-1136", "issn-l": "0962-1083"}, "abstract": "Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome-wide patterns of within- and between- species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the speciation process.", "doi": "10.1111/mec.15388", "pmid": "32068935", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GENBANK", "key": "PRJNA576115"}], "notes": [], "created": "2020-07-08T13:03:45.321Z", "modified": "2024-01-16T13:48:42.878Z"}, {"entity": "publication", "iuid": "5d45e246a4a448159af62be64061ffaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d45e246a4a448159af62be64061ffaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d45e246a4a448159af62be64061ffaa"}}, "title": "Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans.", "authors": [{"family": "Tzelepis", "given": "Georgios", "initials": "G"}, {"family": "Hod\u00e9n", "given": "Kristian Persson", "initials": "KP"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "\u00c5sman", "given": "Anna K M", "initials": "AKM"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2020-02-21", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "11", "issue": null, "pages": "252", "issn-l": "1664-302X"}, "abstract": "The potato late blight pathogen Phytophthora infestans has both an asexual and a sexual mode of reproduction. In Scandinavia, the pathogen is reproducing sexually on a regular basis, whereas clonal lineages dominate in other geographical regions. This study aimed at elucidating events or key genes underlying this difference in sexual behavior. First, the transcriptomes of eight strains, known as either clonal or sexual, were compared during early stages of mating. Principal component analysis (PCA) divided the samples in two clusters A and B and a clear grouping of the mating samples together with the A1 mating type parents was observed. Induction of genes encoding DNA adenine N6-methylation (6mA) methyl-transferases clearly showed a bias toward the cluster A. In contrast, the Avrblb2 effector gene family was highly induced in most of the mating samples and was associated with cluster B in the PCA, similarly to genes coding for acetyl-transferases, which play an important role in RXLR modification prior to secretion. Avrblb2 knock-down strains displayed a reduction in virulence and oospore formation, suggesting a role during the mating process. In conclusion, a number of gene candidates important for the reproductive processes were revealed. The results suggest a possible epigenetic influence and involvement of specific RXLR effectors in mating-related processes.", "doi": "10.3389/fmicb.2020.00252", "pmid": "32153537", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7046690"}], "notes": [], "created": "2020-07-08T13:04:13.663Z", "modified": "2021-11-10T12:53:51.325Z"}, {"entity": "publication", "iuid": "35806cca1dd04fef9c3505fa53346c1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35806cca1dd04fef9c3505fa53346c1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35806cca1dd04fef9c3505fa53346c1e"}}, "title": "Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Gill", "given": "Jacquelyn", "initials": "J"}, {"family": "Fisher", "given": "Daniel C", "initials": "DC"}, {"family": "Protopopov", "given": "Albert V", "initials": "AV"}, {"family": "Herridge", "given": "Victoria L", "initials": "VL"}, {"family": "Plotnikov", "given": "Valery", "initials": "V", "orcid": "0000-0002-4870-3499", "researcher": {"href": "https://publications.scilifelab.se/researcher/378b10136be74923bff019375f5d6c91.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "historical article", "published": "2020-02-21", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "84", "issn-l": "2399-3642"}, "abstract": "Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44-49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids.", "doi": "10.1038/s42003-020-0806-7", "pmid": "32081985", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0806-7"}, {"db": "pmc", "key": "PMC7035339"}], "notes": [], "created": "2020-07-08T13:04:57.570Z", "modified": "2024-01-16T13:48:42.909Z"}, {"entity": "publication", "iuid": "51f1cee219854f9f9ec98b890e43ad35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51f1cee219854f9f9ec98b890e43ad35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51f1cee219854f9f9ec98b890e43ad35"}}, "title": "Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry.", "authors": [{"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2020-02-18", "journal": {"title": "Front Oncol", "issn": "2234-943X", "volume": "10", "issue": null, "pages": "162", "issn-l": "2234-943X"}, "abstract": "Early-stage (I and II) ovarian carcinoma patients generally have good prognosis. Yet, some patients die earlier than expected. Thus, it is important to stratify early-stage patients into risk groups to identify those in need of more aggressive treatment regimens. The prognostic value of 29 histotype-specific biomarkers identified using RNA sequencing was evaluated for early-stage clear-cell (CCC), endometrioid (EC) and mucinous (MC) ovarian carcinomas (n = 112) using immunohistochemistry on tissue microarrays. Biomarkers with prognostic significance were further evaluated in an external ovarian carcinoma data set using the web-based Kaplan-Meier plotter tool. Here, we provide evidence of aberrant protein expression patterns and prognostic significance of 17 novel histotype-specific prognostic biomarkers [10 for CCC (ARPC2, CCT5, GNB1, KCTD10, NUP155, RPL13A, RPL37, SETD3, SMYD2, TRIO), three for EC (CECR1, KIF26B, PIK3CA), and four for MC (CHEK1, FOXM1, KIF23, PARPBP)], suggesting biological heterogeneity within the histotypes. Combined predictive models comprising the protein expression status of the validated CCC, EC and MC biomarkers together with established clinical markers (age, stage, CA125, ploidy) improved the predictive power in comparison with models containing established clinical markers alone, further strengthening the importance of the biomarkers in ovarian carcinoma. Further, even improved predictive powers were demonstrated when combining these models with our previously identified prognostic biomarkers PITHD1 (CCC) and GPR158 (MC). Moreover, the proteins demonstrated improved risk prediction of CCC-, EC-, and MC-associated ovarian carcinoma survival. The novel histotype-specific prognostic biomarkers may not only improve prognostication and patient stratification of early-stage ovarian carcinomas, but may also guide future clinical therapy decisions.", "doi": "10.3389/fonc.2020.00162", "pmid": "32133296", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7040170"}], "notes": [], "created": "2021-01-08T16:29:14.665Z", "modified": "2024-01-16T13:48:42.923Z"}, {"entity": "publication", "iuid": "0d1dc5ac35e34b5593a24d2634f4dbbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d1dc5ac35e34b5593a24d2634f4dbbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d1dc5ac35e34b5593a24d2634f4dbbe"}}, "title": "Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.", "authors": [{"family": "Dahl", "given": "Sara", "initials": "S", "orcid": "0000-0002-2120-2176", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ef8760a81624f4ca7619d077dab48e6.json"}}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Schr\u00f6der", "given": "Anna Katharina", "initials": "AK"}, {"family": "Wickstr\u00f6m", "given": "Ronny", "initials": "R"}, {"family": "Te\u00e4r Fahnehjelm", "given": "Kristina", "initials": "K"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2020-02-10", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "15", "issue": "2", "pages": "e0228622", "issn-l": "1932-6203"}, "abstract": "Optic nerve hypoplasia (ONH) is a congenital malformation with a reduced number of retinal ganglion cell axons in a thin optic nerve. It is a common cause of visual impairment in children and ONH is associated with neurodevelopmental disorders, pituitary hormone deficiencies, and brain malformations. In most cases, the aetiology is unknown, but both environmental factors and genetic causes have been described. This study aimed to identify genetic variants underlying ONH in a well-characterised cohort of individuals with ONH. We performed array comparative genomic hybridization and whole genome sequencing in 29 individuals with ONH. Rare variants were verified by Sanger sequencing and inheritance was assessed in parental samples. We identified 11 rare single nucleotide variants (SNVs) in ten individuals, including a homozygous variant in KIF7 (previously associated with Joubert syndrome), a heterozygous de novo variant in COL4A1 (previously described in an individual with porencephaly), and a homozygous variant in COL4A2. In addition, one individual harboured a heterozygous variant in OPA1 and a heterozygous variant in COL4A1, both were inherited and assessed as variants of unknown clinical significance. Finally, a heterozygous deletion of 341 kb involving exons 7-18 of SOX5 (associated with Lamb-Schaffer syndrome) was identified in one individual. The overall diagnostic yield of pathogenic or likely pathogenic variants in individuals with ONH using whole genome sequencing was 4/29 (14%). Our results show that there is a genetic heterogeneity in ONH and indicate that genetic causes of ONH are not rare. We conclude that genetic testing is valuable in a substantial proportion of the individuals with ONH, especially in cases with non-isolated ONH.", "doi": "10.1371/journal.pone.0228622", "pmid": "32040484", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-12114"}, {"db": "pmc", "key": "PMC7010252"}], "notes": [], "created": "2020-07-08T13:05:14.299Z", "modified": "2024-01-16T13:48:42.967Z"}, {"entity": "publication", "iuid": "2f662c22fce1474b9d17ade9e0181ceb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f662c22fce1474b9d17ade9e0181ceb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f662c22fce1474b9d17ade9e0181ceb"}}, "title": "Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).", "authors": [{"family": "Wang", "given": "Xi", "initials": "X"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}], "type": "journal article", "published": "2020-02-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "12", "issue": "2", "pages": "3803-3817", "issn-l": "1759-6653"}, "abstract": "Under the neutral theory, species with larger effective population size are expected to harbor higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin's paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere, and it consequently plays a major role in European forestry. Here, we use whole-genome resequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an corresponding enormous current population size, our analyses find that genetic diversity of P. abies is low across a number of populations (\u03c0 = 0.0049 in Central-Europe, \u03c0 = 0.0063 in Sweden-Norway, \u03c0 = 0.0063 in Finland). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterized by several reoccurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.", "doi": "10.1093/gbe/evaa005", "pmid": "31958121", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5709816"}, {"db": "pmc", "key": "PMC7046165"}], "notes": [], "created": "2021-01-08T16:29:08.731Z", "modified": "2024-01-16T13:48:42.975Z"}, {"entity": "publication", "iuid": "2629beeaf3fe4217aa50a38e5732a8f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2629beeaf3fe4217aa50a38e5732a8f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2629beeaf3fe4217aa50a38e5732a8f6"}}, "title": "The antimalarial drug amodiaquine stabilizes p53 through ribosome biogenesis stress, independently of its autophagy-inhibitory activity.", "authors": [{"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Zisi", "given": "Asimina", "initials": "A", "orcid": "0000-0002-4253-0275", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf82380ca6e4cd1985bc9dd23789539.json"}}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "Carreras-Puigvert", "given": "Jordi", "initials": "J"}, {"family": "Henriksson", "given": "Martin", "initials": "M"}, {"family": "H\u00fchn", "given": "Daniela", "initials": "D"}, {"family": "Watanabe", "given": "Kenji", "initials": "K"}, {"family": "Helleday", "given": "Thomas", "initials": "T"}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J"}], "type": "journal article", "published": "2020-02-00", "journal": {"volume": "27", "issn": "1476-5403", "issue": "2", "pages": "773-789", "title": "Cell Death Differ.", "issn-l": "1350-9047"}, "abstract": "Pharmacological inhibition of ribosome biogenesis is a promising avenue for cancer therapy. Herein, we report a novel activity of the FDA-approved antimalarial drug amodiaquine which inhibits rRNA transcription, a rate-limiting step for ribosome biogenesis, in a dose-dependent manner. Amodiaquine triggers degradation of the catalytic subunit of RNA polymerase I (Pol I), with ensuing RPL5/RPL11-dependent stabilization of p53. Pol I shutdown occurs in the absence of DNA damage and without the subsequent ATM-dependent inhibition of rRNA transcription. RNAseq analysis revealed mechanistic similarities of amodiaquine with BMH-21, the first-in-class Pol I inhibitor, and with chloroquine, the antimalarial analog of amodiaquine, with well-established autophagy-inhibitory activity. Interestingly, autophagy inhibition caused by amodiaquine is not involved in the inhibition of rRNA transcription, suggesting two independent anticancer mechanisms. In vitro, amodiaquine is more efficient than chloroquine in restraining the proliferation of human cell lines derived from colorectal carcinomas, a cancer type with predicted susceptibility to ribosome biogenesis stress. Taken together, our data reveal an unsuspected activity of a drug approved and used in the clinics for over 30 years, and provide rationale for repurposing amodiaquine in cancer therapy.", "doi": "10.1038/s41418-019-0387-5", "pmid": "31285544", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41418-019-0387-5"}, {"db": "pmc", "key": "PMC7205879"}], "notes": [], "created": "2019-11-28T13:50:15.354Z", "modified": "2025-10-17T13:04:28.370Z"}, {"entity": "publication", "iuid": "ee719b0f99754255b9e919a7e976953e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee719b0f99754255b9e919a7e976953e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee719b0f99754255b9e919a7e976953e"}}, "title": "Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.", "authors": [{"family": "Ekhteraei-Tousi", "given": "Samaneh", "initials": "S"}, {"family": "Lewerentz", "given": "Jacob", "initials": "J"}, {"family": "Larsson", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2020-01-30", "journal": {"title": "Cells", "issn": "2073-4409", "volume": "9", "issue": "2", "pages": "323", "issn-l": "2073-4409"}, "abstract": "Chromosome-specific regulatory mechanisms provide a model to understand the coordinated regulation of genes on entire chromosomes or on larger genomic regions. In fruit flies, two chromosome-wide systems have been characterized: The male-specific lethal (MSL) complex, which mediates dosage compensation and primarily acts on the male X-chromosome, and Painting of fourth (POF), which governs chromosome-specific regulation of genes located on the 4th chromosome. How targeting of one specific chromosome evolves is still not understood; but repeated sequences, in forms of satellites and transposable elements, are thought to facilitate the evolution of chromosome-specific targeting. The highly repetitive 1.688 satellite has been functionally connected to both these systems. Considering the rapid evolution and the necessarily constant adaptation of regulatory mechanisms, such as dosage compensation, we hypothesised that POF and/or 1.688 may still show traces of dosage-compensation functions. Here, we test this hypothesis by transcriptome analysis. We show that loss of Pof decreases not only chromosome 4 expression but also reduces the X-chromosome expression in males. The 1.688 repeat deletion, Zhr1 (Zygotic hybrid rescue), does not affect male dosage compensation detectably; however, Zhr1 in females causes a stimulatory effect on X-linked genes with a strong binding affinity to the MSL complex (genes close to high-affinity sites). Lack of pericentromeric 1.688 also affected 1.688 expression in trans and was linked to the differential expression of genes involved in eggshell formation. We discuss our results with reference to the connections between POF, the 1.688 satellite and dosage compensation, and the role of the 1.688 satellite in hybrid lethality.", "doi": "10.3390/cells9020323", "pmid": "32019091", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "cells9020323"}, {"db": "pmc", "key": "PMC7072490"}], "notes": [], "created": "2020-07-08T13:05:15.076Z", "modified": "2024-01-16T13:48:43.003Z"}, {"entity": "publication", "iuid": "18df90c9313348749d18bfcfc7334742", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18df90c9313348749d18bfcfc7334742.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18df90c9313348749d18bfcfc7334742"}}, "title": "Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.", "authors": [{"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "Bayfield", "given": "Oliver W", "initials": "OW", "orcid": "0000-0003-1421-7780", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb071bf951644667b670a0c00f869e46.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Antson", "given": "Alfred A", "initials": "AA", "orcid": "0000-0002-4533-3816", "researcher": {"href": "https://publications.scilifelab.se/researcher/42b5a7cd8d044d3298e8e93eb9af1a76.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2020-01-30", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "12", "issue": "2", "pages": "158", "issn-l": "1999-4915"}, "abstract": "Viruses in aquatic environments play a key role in microbial population dynamics and nutrient cycling. In particular, bacteria of the phylum Bacteriodetes are known to participate in recycling algal blooms. Studies of phage-host interactions involving this phylum are hence important to understand the processes shaping bacterial and viral communities in the ocean as well as nutrient cycling. In this study, we isolated and sequenced three strains of flavobacteria-LMO6, LMO9, LMO8-and 38 virulent phages infecting them. These phages represent 15 species, occupying three novel genera. Additionally, one temperate phage was induced from LMO6 and was found to be competent at infecting LMO9. Functions could be predicted for a limited number of phage genes, mainly representing roles in DNA replication and virus particle formation. No metabolic genes were detected. While the phages isolated on LMO8 could infect all three bacterial strains, the LMO6 and LMO9 phages could not infect LMO8. Of the phages isolated on LMO9, several showed a host-derived reduced efficiency of plating on LMO6, potentially due to differences in DNA methyltransferase genes. Overall, these phage-host systems contribute novel genetic information to our sequence databases and present valuable tools for the study of both virulent and temperate phages.", "doi": "10.3390/v12020158", "pmid": "32019073", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "v12020158"}, {"db": "pmc", "key": "PMC7077304"}], "notes": [], "created": "2020-07-08T13:05:17.299Z", "modified": "2024-01-16T13:48:43.010Z"}, {"entity": "publication", "iuid": "2327daa01a69409ebeaa040fe7f5fbd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3"}}, "title": "Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.", "authors": [{"family": "Garcia", "given": "Maxime", "initials": "M", "orcid": "0000-0003-2827-9261", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf9b1b223f04296adcb6bd091c548de.json"}}, {"family": "Juhos", "given": "Szilveszter", "initials": "S"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}], "type": "journal article", "published": "2020-01-29", "journal": {"volume": "9", "issn": "2046-1402", "issue": null, "pages": "63", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.", "doi": "10.12688/f1000research.16665.2", "pmid": "32269765", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7111497"}], "notes": [], "created": "2020-04-23T08:58:58.026Z", "modified": "2024-01-16T13:48:43.022Z"}, {"entity": "publication", "iuid": "a0852875f0e24bf78b3c291325fc9de9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0852875f0e24bf78b3c291325fc9de9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0852875f0e24bf78b3c291325fc9de9"}}, "title": "Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.", "authors": [{"family": "Buetti-Dinh", "given": "Antoine", "initials": "A", "orcid": "0000-0002-6469-0296", "researcher": {"href": "https://publications.scilifelab.se/researcher/071a99356d6f4650a6707dc84777a66c.json"}}, {"family": "Herold", "given": "Malte", "initials": "M", "orcid": "0000-0003-2627-0159", "researcher": {"href": "https://publications.scilifelab.se/researcher/70759c28794141fbb123901947534ec4.json"}}, {"family": "Christel", "given": "Stephan", "initials": "S", "orcid": "0000-0003-0021-2452", "researcher": {"href": "https://publications.scilifelab.se/researcher/9db0f79d5ee144308ccb724e51959bc8.json"}}, {"family": "El Hajjami", "given": "Mohamed", "initials": "M"}, {"family": "Delogu", "given": "Francesco", "initials": "F"}, {"family": "Ilie", "given": "Olga", "initials": "O"}, {"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0fa4b91d7384fda991fcda7c3df41be.json"}}, {"family": "Poetsch", "given": "Ansgar", "initials": "A"}, {"family": "Sand", "given": "Wolfgang", "initials": "W"}, {"family": "Vera", "given": "Mario", "initials": "M", "orcid": "0000-0002-1762-4421", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a9ade6aac4e45399d1e1207a8b58398.json"}}, {"family": "Pivkin", "given": "Igor V", "initials": "IV"}, {"family": "Friedman", "given": "Ran", "initials": "R", "orcid": "0000-0001-8696-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/aff68ae331c349e189a6ecf511823fc3.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2020-01-21", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "21", "issue": "1", "pages": "23", "issn-l": "1471-2105"}, "abstract": "Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications.\n\nWe performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation.\n\nThe structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context.\n\nThe combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.", "doi": "10.1186/s12859-019-3337-9", "pmid": "31964336", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-019-3337-9"}, {"db": "pmc", "key": "PMC6975020"}], "notes": [], "created": "2020-07-08T13:03:37.375Z", "modified": "2024-01-16T13:48:43.057Z"}, {"entity": "publication", "iuid": "798d0c199a87482abd2a408a2148a1ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/798d0c199a87482abd2a408a2148a1ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/798d0c199a87482abd2a408a2148a1ac"}}, "title": "A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice.", "authors": [{"family": "Purhonen", "given": "Janne", "initials": "J"}, {"family": "Grigorjev", "given": "Vladislav", "initials": "V"}, {"family": "Ekiert", "given": "Robert", "initials": "R", "orcid": "0000-0002-8879-0646", "researcher": {"href": "https://publications.scilifelab.se/researcher/18f5478e3272434f8e04014a4da545b5.json"}}, {"family": "Aho", "given": "Noora", "initials": "N"}, {"family": "Rajendran", "given": "Jayasimman", "initials": "J", "orcid": "0000-0003-3487-8260", "researcher": {"href": "https://publications.scilifelab.se/researcher/92dfb99f063c475086ad84783ab34716.json"}}, {"family": "Pietras", "given": "Rafa\u0142", "initials": "R", "orcid": "0000-0001-8424-6590", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f9c7e05c9284550ad49f0cc9237ad45.json"}}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K", "orcid": "0000-0002-2449-8283", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c36d2ff5111435aa23416cdfc359b2d.json"}}, {"family": "Wikstr\u00f6m", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7527-4415", "researcher": {"href": "https://publications.scilifelab.se/researcher/66d471fc1c914756ac37da41bb759da4.json"}}, {"family": "Sharma", "given": "Vivek", "initials": "V"}, {"family": "Osyczka", "given": "Artur", "initials": "A"}, {"family": "Fellman", "given": "Vineta", "initials": "V", "orcid": "0000-0002-1355-5633", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c2179b7025441f688426ab24abd390e.json"}}, {"family": "Kallij\u00e4rvi", "given": "Jukka", "initials": "J", "orcid": "0000-0003-3773-7025", "researcher": {"href": "https://publications.scilifelab.se/researcher/c592c2565d4f42efb54b3e6016968ddf.json"}}], "type": "journal article", "published": "2020-01-16", "journal": {"volume": "11", "issn": "2041-1723", "issue": "1", "pages": "322", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "We previously observed an unexpected fivefold (35 vs. 200 days) difference in the survival of respiratory chain complex III (CIII) deficient Bcs1lp.S78G mice between two congenic backgrounds. Here, we identify a spontaneous homoplasmic mtDNA variant (m.G14904A, mt-Cybp.D254N), affecting the CIII subunit cytochrome b (MT-CYB), in the background with short survival. We utilize maternal inheritance of mtDNA to confirm this as the causative variant and show that it further decreases the low CIII activity in Bcs1lp.S78G tissues to below survival threshold by 35 days of age. Molecular dynamics simulations predict D254N to restrict the flexibility of MT-CYB ef loop, potentially affecting RISP dynamics. In Rhodobacter cytochrome bc1 complex the equivalent substitution causes a kinetics defect with longer occupancy of RISP head domain towards the quinol oxidation site. These findings represent a unique case of spontaneous mitonuclear epistasis and highlight the role of mtDNA variation as modifier of mitochondrial disease phenotypes.", "doi": "10.1038/s41467-019-14201-2", "pmid": "31949167", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-14201-2"}, {"db": "pmc", "key": "PMC6965120"}], "notes": [], "created": "2020-02-03T09:00:33.293Z", "modified": "2021-11-10T12:44:51.374Z"}, {"entity": "publication", "iuid": "c982efa83ad042baaaa633f71d3b3cb9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c982efa83ad042baaaa633f71d3b3cb9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c982efa83ad042baaaa633f71d3b3cb9"}}, "title": "Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.", "authors": [{"family": "Rugiu", "given": "Luca", "initials": "L", "orcid": "0000-0002-9675-7168", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d411b99abcc4474aff904e43247fb7a.json"}}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Pereyra", "given": "Ricardo Tom\u00e1s", "initials": "RT"}, {"family": "Jormalainen", "given": "Veijo", "initials": "V"}], "type": "journal article", "published": "2020-01-13", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "42", "issn-l": "1471-2164"}, "abstract": "Rockweeds are among the most important foundation species of temperate rocky littoral shores. In the Baltic Sea, the rockweed Fucus vesiculosus is distributed along a decreasing salinity gradient from the North Atlantic entrance to the low-salinity regions in the north-eastern margins, thus, demonstrating a remarkable tolerance to hyposalinity. The underlying mechanisms for this tolerance are still poorly understood. Here, we exposed F. vesiculosus from two range-margin populations to the hyposaline (2.5 PSU - practical salinity unit) conditions that are projected to occur in the region by the end of this century as a result of climate change. We used transcriptome analysis (RNA-seq) to determine the gene expression patterns associated with hyposalinity acclimation, and examined the variation in these patterns between the sampled populations.\n\nHyposalinity induced different responses in the two populations: in one, only 26 genes were differentially expressed between salinity treatments, while the other population demonstrated up- or downregulation in 3072 genes. In the latter population, the projected future hyposalinity induced an acute response in terms of antioxidant production. Genes associated with membrane composition and structure were also heavily involved, with the upregulation of fatty acid and actin production, and the downregulation of ion channels and alginate pathways. Changes in gene expression patterns clearly indicated an inhibition of the photosynthetic machinery, with a consequent downregulation of carbohydrate production. Simultaneously, energy consumption increased, as revealed by the upregulation of genes associated with respiration and ATP synthesis. Overall, the genes that demonstrated the largest increase in expression were ribosomal proteins involved in translation pathways. The fixation rate of SNP:s was higher within genes responding to hyposalinity than elsewhere in the transcriptome.\n\nThe high fixation rate in the genes coding for salinity acclimation mechanisms implies strong selection for them. The among-population differentiation that we observed in the transcriptomic response to hyposalinity stress suggests that populations of F. vesiculosus may differ in their tolerance to future desalination, possibly as a result of local adaptation to salinity conditions within the Baltic Sea. These results emphasise the importance of considering interspecific genetic variation when evaluating the consequences of environmental change.", "doi": "10.1186/s12864-020-6470-y", "pmid": "31931708", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-6470-y"}, {"db": "pmc", "key": "PMC6958763"}], "notes": [], "created": "2020-07-08T13:03:42.198Z", "modified": "2024-01-16T13:48:43.072Z"}, {"entity": "publication", "iuid": "cae2c19d93fe471eac4b766e6643b20a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cae2c19d93fe471eac4b766e6643b20a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cae2c19d93fe471eac4b766e6643b20a"}}, "title": "Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines.", "authors": [{"family": "Lethin", "given": "Johanna", "initials": "J"}, {"family": "Shakil", "given": "Shahriar S M", "initials": "SSM"}, {"family": "Hassan", "given": "Sameer", "initials": "S"}, {"family": "Sirijovski", "given": "Nick", "initials": "N"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Olsson", "given": "Olof", "initials": "O"}, {"family": "Aronsson", "given": "Henrik", "initials": "H", "orcid": "0000-0003-4424-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/0227592dd1174af4a8a8dc39183b0f19.json"}}], "type": "journal article", "published": "2020-01-13", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "20", "issue": "1", "pages": "18", "issn-l": "1471-2229"}, "abstract": "Triticum aestivum (wheat) is one of the world's oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance.\n\nAfter titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0-30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested.\n\nThe mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming.", "doi": "10.1186/s12870-019-2137-8", "pmid": "31931695", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12870-019-2137-8"}, {"db": "pmc", "key": "PMC6958588"}], "notes": [], "created": "2020-07-08T13:03:36.627Z", "modified": "2024-01-16T13:48:43.079Z"}, {"entity": "publication", "iuid": "be5bf1b1f6ab471bbecf5c58227c4a16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be5bf1b1f6ab471bbecf5c58227c4a16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be5bf1b1f6ab471bbecf5c58227c4a16"}}, "title": "A regulatory role for CHD2 in myelopoiesis.", "authors": [{"family": "Shahin Varnoosfaderani", "given": "Farzaneh", "initials": "F"}, {"family": "Palau", "given": "Anna", "initials": "A"}, {"family": "Dong", "given": "Wenbo", "initials": "W", "orcid": "0000-0002-5209-4884", "researcher": {"href": "https://publications.scilifelab.se/researcher/81bd1bba109e48ab9e3c19d3c947bf82.json"}}, {"family": "Persson", "given": "Jenna", "initials": "J"}, {"family": "Durand-Dubief", "given": "Micka\u00ebl", "initials": "M", "orcid": "0000-0002-8556-4459", "researcher": {"href": "https://publications.scilifelab.se/researcher/85c11d5d8d94488aad3e77a84b89ff8d.json"}}, {"family": "Svensson", "given": "J Peter", "initials": "JP", "orcid": "0000-0002-5863-6250", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c226ba652024fdabbbf9203e1edb5d1.json"}}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2020-01-10", "journal": {"title": "Epigenetics", "issn": "1559-2308", "volume": "15", "issue": "6-7", "pages": "702-714", "issn-l": "1559-2294"}, "abstract": "The transcriptional program that dictates haematopoietic cell fate and differentiation requires an epigenetic regulatory and memory function, provided by a network of epigenetic factors that regulate DNA methylation, post-translational histone modifications and chromatin structure. Disturbed epigenetic regulation causes perturbations in the blood cell differentiation program that results in various types of haematopoietic disorders. Thus, accurate epigenetic regulation is essential for functional haematopoiesis. In this study, we used a CRISPR-Cas9 screening approach to identify new epigenetic regulators in myeloid differentiation. We designed a Chromatin-UMI CRISPR guide library targeting 1092 epigenetic regulators. Phorbol 12-myristate 13-acetate (PMA) treatment of the chronic myeloid leukaemia cell line K-562 was used as a megakaryocytic myeloid differentiation model. Both previously described developmental epigenetic regulators and novel factors were identified in our screen. In this study, we validated and characterized a role for the chromatin remodeller CHD2 in myeloid proliferation and megakaryocytic differentiation.", "doi": "10.1080/15592294.2019.1710913", "pmid": "31900031", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "CRISPR Functional Genomics": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC7574388"}], "notes": [], "created": "2020-01-20T10:22:28.949Z", "modified": "2024-01-16T13:48:43.086Z"}, {"entity": "publication", "iuid": "24e0c101ab3f49ac830c669e75aa8dfa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24e0c101ab3f49ac830c669e75aa8dfa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24e0c101ab3f49ac830c669e75aa8dfa"}}, "title": "Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.", "authors": [{"family": "Gelabert", "given": "Pere", "initials": "P"}, {"family": "Sandoval-Velasco", "given": "Marcela", "initials": "M"}, {"family": "Serres", "given": "Aitor", "initials": "A"}, {"family": "de Manuel", "given": "Marc", "initials": "M"}, {"family": "Renom", "given": "Pere", "initials": "P"}, {"family": "Margaryan", "given": "Ashot", "initials": "A"}, {"family": "Stiller", "given": "Josefin", "initials": "J"}, {"family": "de-Dios", "given": "Toni", "initials": "T"}, {"family": "Fang", "given": "Qi", "initials": "Q"}, {"family": "Feng", "given": "Shaohong", "initials": "S"}, {"family": "Ma\u00f1osa", "given": "Santi", "initials": "S"}, {"family": "Pacheco", "given": "George", "initials": "G"}, {"family": "Ferrando-Bernal", "given": "Manuel", "initials": "M"}, {"family": "Shi", "given": "Guolin", "initials": "G"}, {"family": "Hao", "given": "Fei", "initials": "F"}, {"family": "Chen", "given": "Xianqing", "initials": "X"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Navarro", "given": "Arcadi", "initials": "A"}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Marqu\u00e8s-Bonet", "given": "Tom\u00e0s", "initials": "T"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Antunes", "given": "Agostinho", "initials": "A"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Lalueza-Fox", "given": "Carles", "initials": "C"}], "type": "journal article", "published": "2020-01-06", "journal": {"volume": "30", "issn": "1879-0445", "issue": "1", "pages": "108-114.e5", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.", "doi": "10.1016/j.cub.2019.10.066", "pmid": "31839456", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(19)31438-1"}], "notes": [], "created": "2020-01-08T16:49:21.462Z", "modified": "2021-11-10T12:55:04.959Z"}, {"entity": "publication", "iuid": "b113002942174b6b8c2f67907d1d2182", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b113002942174b6b8c2f67907d1d2182.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b113002942174b6b8c2f67907d1d2182"}}, "title": "Discovery of Novel Sequences in 1,000 Swedish Genomes.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "M\u00e5rtensson", "given": "Gustaf", "initials": "G"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2020-01-01", "journal": {"volume": "37", "issn": "1537-1719", "issue": "1", "pages": "18-30", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Novel sequences (NSs), not present in the human reference genome, are abundant and remain largely unexplored. Here, we utilize de novo assembly to study NS in 1,000 Swedish individuals first sequenced as part of the SweGen project revealing a total of 46 Mb in 61,044 distinct contigs of sequences not present in GRCh38. The contigs were aligned to recently published catalogs of Icelandic and Pan-African NSs, as well as the chimpanzee genome, revealing a great diversity of shared sequences. Analyzing the positioning of NS across the chimpanzee genome, we find that 2,807 NS align confidently within 143 chimpanzee orthologs of human genes. Aligning the whole genome sequencing data to the chimpanzee genome, we discover ancestral NS common throughout the Swedish population. The NSs were searched for repeats and repeat elements: revealing a majority of repetitive sequence (56%), and enrichment of simple repeats (28%) and satellites (15%). Lastly, we align the unmappable reads of a subset of the thousand genomes data to our collection of NS, as well as the previously published Pan-African NS: revealing that both the Swedish and Pan-African NS are widespread, and that the Swedish NSs are largely a subset of the Pan-African NS. Overall, these results highlight the importance of creating a more diverse reference genome and illustrate that significant amounts of the NS may be of ancestral origin.", "doi": "10.1093/molbev/msz176", "pmid": "31560401", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5555682"}, {"db": "pmc", "key": "PMC6984370"}], "notes": [], "created": "2019-10-30T08:45:30.942Z", "modified": "2024-01-16T13:48:43.107Z"}, {"entity": "publication", "iuid": "1fad0065d94b468984935c5caf4d75ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fad0065d94b468984935c5caf4d75ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fad0065d94b468984935c5caf4d75ee"}}, "title": "Genome-wide signatures of environmental adaptation in European aspen (Populus tremula) under current and future climate conditions.", "authors": [{"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}], "type": "journal article", "published": "2020-01-00", "journal": {"volume": "13", "issn": "1752-4571", "issue": "1", "pages": "132-142", "title": "Evol Appl", "issn-l": "1752-4571"}, "abstract": "Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess local adaptation to current climate in European aspen (Populus tremula) by using environmental association analyses to identify genetic variants associated with two representative climate variables describing current day variation in temperature and precipitation. We also analysed patterns of genetic differentiation between southern and northern populations and observe that regions of high genetic differentiation are enriched for SNPs that are significantly associated with climate. Using variants associated with climate, we examined patterns of isolation by distance and environment and used spatial modelling to predict the geographic distribution of genomic variation in response to two scenarios of future climate change. We show that climate conditions at a northern reference site will correspond to climate conditions experienced by current day populations located 4-8 latitude degrees further south. By assessing the relationship between phenotypic traits and vegetative fitness, we also demonstrate that southern populations harbour genetic variation that likely would be adaptive further north under both climate change scenarios. Current day populations at the lagging edge of the distribution in Sweden can therefore serve as sources for introducing adaptive alleles onto northern populations, but the likelihood of this largely depends on naturally occurring levels of gene flow.", "doi": "10.1111/eva.12792", "pmid": "31892948", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA12792"}, {"db": "pmc", "key": "PMC6935590"}], "notes": [], "created": "2020-01-08T16:49:47.812Z", "modified": "2024-01-16T13:48:43.171Z"}, {"entity": "publication", "iuid": "2774e945362a4b97a34b9aeb3aea2f35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2774e945362a4b97a34b9aeb3aea2f35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2774e945362a4b97a34b9aeb3aea2f35"}}, "title": "A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver", "authors": [{"family": "Olsson Lindvall", "given": "Martina", "initials": "M"}, {"family": "Davila Lopez", "given": "Marcela", "initials": "M"}, {"family": "Klasson", "given": "Sofia", "initials": "S"}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Nilsson", "given": "Staffan", "initials": "S"}, {"family": "Stanne", "given": "Tara M", "initials": "TM"}, {"family": "Jern", "given": "Christina", "initials": "C"}], "type": "journal-article", "published": "2019-12-30", "journal": {"volume": "120", "issn": "0340-6245", "issue": "02", "pages": "229-242", "title": "Thromb. Haemost.", "issn-l": null}, "abstract": "Characterizing the relationship between genetic, epigenetic (e.g., deoxyribonucleic acid [DNA] methylation), and transcript variation could provide insights into mechanisms regulating hemostasis and potentially identify new drug targets. Several hemostatic factors are synthesized in the liver, yet high-resolution DNA methylation data from human liver tissue is currently lacking for these genes. Single-nucleotide polymorphisms (SNPs) can influence DNA methylation in cis which can affect gene expression. This can be analyzed through allele-specific methylation (ASM) experiments. We performed targeted genomic DNA- and bisulfite-sequencing of 35 hemostatic genes in human liver samples for SNP and DNA methylation analysis, respectively, and integrated the data for ASM determination. ASM-associated SNPs (ASM-SNPs) were tested for association to gene expression in liver using in-house generated ribonucleic acid-sequencing data. We then assessed whether ASM-SNPs associated with gene expression, plasma proteins, or other traits relevant for hemostasis using publicly available data. We identified 112 candidate ASM-SNPs. Of these, 68% were associated with expression of their respective genes in human liver or in other human tissues and 54% were associated with the respective plasma protein levels, activity, or other relevant hemostatic genome-wide association study traits such as venous thromboembolism, coronary artery disease, stroke, and warfarin dose maintenance. Our study provides the first detailed map of the DNA methylation landscape and ASM analysis of hemostatic genes in human liver tissue, and suggests that methylation regulated by genetic variants in cis may provide a mechanistic link between noncoding SNPs and variation observed in circulating hemostatic proteins, prothrombotic diseases, and drug response.", "doi": "10.1055/s-0039-3401824", "pmid": "31887778", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-01-07T14:28:03.996Z", "modified": "2024-01-16T13:48:43.243Z"}, {"entity": "publication", "iuid": "b58a481da1744ca8b371ca73d93972c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b58a481da1744ca8b371ca73d93972c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b58a481da1744ca8b371ca73d93972c6"}}, "title": "Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.", "authors": [{"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Hagen", "given": "Ingerid J", "initials": "IJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Sokolova", "given": "Natalia", "initials": "N"}, {"family": "Berteaux", "given": "Dominique", "initials": "D"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2019-12-23", "journal": {"volume": "374", "issn": "1471-2970", "issue": "1788", "pages": "20190212", "title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn-l": "0962-8436"}, "abstract": "Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'", "doi": "10.1098/rstb.2019.0212", "pmid": "31679495", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6863501"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4669517"}], "notes": [], "created": "2019-11-20T09:28:56.670Z", "modified": "2024-01-16T13:48:43.259Z"}, {"entity": "publication", "iuid": "e59ae9ad042b4b0c9a586a70c8502869", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e59ae9ad042b4b0c9a586a70c8502869.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e59ae9ad042b4b0c9a586a70c8502869"}}, "title": "Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers.", "authors": [{"family": "Arroyo M\u00fchr", "given": "Laila Sara", "initials": "LS"}, {"family": "Lagheden", "given": "Camilla", "initials": "C"}, {"family": "Eklund", "given": "Carina", "initials": "C"}, {"family": "Lei", "given": "Jiayao", "initials": "J"}, {"family": "Nordqvist-Kleppe", "given": "Sara", "initials": "S"}, {"family": "Spar\u00e9n", "given": "P\u00e4r", "initials": "P"}, {"family": "Sundstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Dillner", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2019-12-20", "journal": {"volume": null, "issn": "1465-2099", "issue": null, "title": "J. Gen. Virol.", "issn-l": "0022-1317"}, "abstract": "Introduction. Cervical cancer is caused by human papillomavirus (HPV), but some cases may test HPV-negative. We previously tested 2850 Swedish cases and found that 394/2850 (13.8 %) cases tested HPV DNA-negative by PCR. Sequencing is the most thorough method to assess HPV status.Aim.. We wished to assess whether deep sequencing might detect HPV sequences among these HPV-negative cervical cancer specimens, and to increase the likelihood of detecting transcriptionally active infections.Methodology. Out of the 2850 cancer cases, we sequenced a random sample of 92 HPV PCR-negative cervical cancers and 34 HPV PCR-positive cervical cancers. Four pools of blank blocks were sequenced as negative controls. To enrich for mRNA - a hallmark of active viral infection - the samples were extracted, reverse-transcribed, rRNA-depleted and then sequenced using the NovaSeq 6000 system (Illumina, USA). High-quality reads were aligned to the human genome and non-human reads were queried against HPV proteins.Results. We obtained a median of 23 million paired reads per sample. HPV was detected in 31/34 HPV PCR-positive cases. Among cases negative for HPV by PCR, 48/92 (52.2 %) contained HPV sequences, with HPV33 being the most commonly detected type among these (14/48 cases, 29.2 %). Comparison of the ratio of exon and intron sequences found that the sequenced material contained both DNA and RNA. Splice junctions were detected in 12 cases.Conclusion. Apparently, some cervical cancers contain HPV that is difficult to detect by PCR. Sequencing may be a helpful tool for additional quality assurance for HPV testing methods.", "doi": "10.1099/jgv.0.001374", "pmid": "31859615", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-08T16:49:45.687Z", "modified": "2020-01-21T13:56:16.567Z"}, {"entity": "publication", "iuid": "da6ca856685141ae9efbd6bfc317bff0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da6ca856685141ae9efbd6bfc317bff0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da6ca856685141ae9efbd6bfc317bff0"}}, "title": "A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Tebani", "given": "Abdellah", "initials": "A", "orcid": "0000-0002-8901-2678", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf47745ed3454f3c819cf6414f140ff0.json"}}, {"family": "Pou", "given": "Christian", "initials": "C", "orcid": "0000-0003-3932-788X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6015314c4c04ee08d7e4358cfb55b9f.json"}}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23dc2e614784017b08cb2d8f6b60ded.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal article", "published": "2019-12-20", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "366", "issue": "6472", "pages": null}, "abstract": "Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs.", "doi": "10.1126/science.aax9198", "pmid": "31857451", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "366/6472/eaax9198"}], "notes": [], "created": "2019-12-21T09:40:14.331Z", "modified": "2024-01-16T13:48:43.274Z"}, {"entity": "publication", "iuid": "15fab752b91e4f3889c3ea995c9c69c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15fab752b91e4f3889c3ea995c9c69c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15fab752b91e4f3889c3ea995c9c69c7"}}, "title": "A transposable element insertion is associated with an alternative life history strategy.", "authors": [{"family": "Woronik", "given": "Alyssa", "initials": "A"}, {"family": "Tunstr\u00f6m", "given": "Kalle", "initials": "K"}, {"family": "Perry", "given": "Michael W", "initials": "MW"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Stefanescu", "given": "Constanti", "initials": "C"}, {"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "MP"}, {"family": "Brattstr\u00f6m", "given": "Oskar", "initials": "O"}, {"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Lehmann", "given": "Philipp", "initials": "P"}, {"family": "K\u00e4kel\u00e4", "given": "Reijo", "initials": "R"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}], "type": "journal article", "published": "2019-12-17", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "5757", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Tradeoffs affect resource allocation during development and result in fitness consequences that drive the evolution of life history strategies. Yet despite their importance, we know little about the mechanisms underlying life history tradeoffs. Many species of Colias butterflies exhibit an alternative life history strategy (ALHS) where females divert resources from wing pigment synthesis to reproductive and somatic development. Due to this reallocation, a wing color polymorphism is associated with the ALHS: either yellow/orange or white. Here we map the locus associated with this ALHS in Colias crocea to a transposable element insertion located downstream of the Colias homolog of BarH-1, a homeobox transcription factor. Using CRISPR/Cas9 gene editing, antibody staining, and electron microscopy we find white-specific expression of BarH-1 suppresses the formation of pigment granules in wing scales and gives rise to white wing color. Lipid and transcriptome analyses reveal physiological differences associated with the ALHS. Together, these findings characterize a mechanism for a female-limited ALHS.", "doi": "10.1038/s41467-019-13596-2", "pmid": "31848330", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13596-2"}, {"db": "pmc", "key": "PMC6917731"}], "notes": [], "created": "2020-01-08T16:48:54.088Z", "modified": "2020-01-21T13:56:16.533Z"}, {"entity": "publication", "iuid": "e17e910899a9452fbd9c76292733652c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e17e910899a9452fbd9c76292733652c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e17e910899a9452fbd9c76292733652c"}}, "title": "NGS targeted screening of 100 Scandinavian patients with coronal synostosis.", "authors": [{"family": "Topa", "given": "Alexandra", "initials": "A"}, {"family": "Rohlin", "given": "Anna", "initials": "A"}, {"family": "Andersson", "given": "Mattias K", "initials": "MK"}, {"family": "Fehr", "given": "Andr\u00e9", "initials": "A"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Stenman", "given": "G\u00f6ran", "initials": "G"}, {"family": "K\u00f6lby", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2019-12-14", "journal": {"volume": null, "issn": "1552-4833", "issue": null, "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Craniosynostosis (CS), the premature closure of one or more cranial sutures, occurs both as part of a syndrome or in isolation (nonsyndromic form). Here, we have studied the prevalence and spectrum of genetic alterations associated with coronal suture closure in 100 Scandinavian patients treated at a single craniofacial unit. All patients were phenotypically assessed and analyzed with a custom-designed 63 gene NGS-panel. Most cases (78%) were syndromic forms of CS. Pathogenic and likely pathogenic variants explaining the phenotype were found in 80% of the families with syndromic CS and in 14% of those with nonsyndromic CS. Sixty-five percent of the families had mutations in the CS core genes FGFR2, TWIST1, FGFR3, TCF12, EFNB1, FGFR1, and POR. Five novel pathogenic/likely pathogenic variants in TWIST1, TCF12, and EFNB1 were identified. We also found novel variants in SPECC1L, IGF1R, and CYP26B1 with a possible modulator phenotypic effect. Our findings demonstrate that NGS targeted sequencing is a powerful tool to detect pathogenic mutations in patients with coronal CS and further emphasize the importance of thorough assessment of the patient's phenotype for reliable interpretation of the molecular findings. This is particularly important in patients with complex phenotypes and rare forms of CS.", "doi": "10.1002/ajmg.a.61427", "pmid": "31837199", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-08T16:48:52.551Z", "modified": "2020-01-21T13:56:16.518Z"}, {"entity": "publication", "iuid": "dbc92553ebbe4a27bb1181acdc5a493e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbc92553ebbe4a27bb1181acdc5a493e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbc92553ebbe4a27bb1181acdc5a493e"}}, "title": "BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.", "authors": [{"family": "Uebersch\u00e4r", "given": "Malin", "initials": "M"}, {"family": "Wang", "given": "Huazhen", "initials": "H"}, {"family": "Zhang", "given": "Chun", "initials": "C"}, {"family": "Kondo", "given": "Shu", "initials": "S"}, {"family": "Aoki", "given": "Tsutomu", "initials": "T"}, {"family": "Schedl", "given": "Paul", "initials": "P"}, {"family": "Lai", "given": "Eric C", "initials": "EC"}, {"family": "Wen", "given": "Jiayu", "initials": "J"}, {"family": "Dai", "given": "Qi", "initials": "Q"}], "type": "journal article", "published": "2019-12-13", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "5700", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The Drosophila genome encodes three BEN-solo proteins including Insensitive (Insv), Elba1 and Elba2 that possess activities in transcriptional repression and chromatin insulation. A fourth protein-Elba3-bridges Elba1 and Elba2 to form an ELBA complex. Here, we report comprehensive investigation of these proteins in Drosophila embryos. We assess common and distinct binding sites for Insv and ELBA and their genetic interdependencies. While Elba1 and Elba2 binding generally requires the ELBA complex, Elba3 can associate with chromatin independently of Elba1 and Elba2. We further demonstrate that ELBA collaborates with other insulators to regulate developmental patterning. Finally, we find that adjacent gene pairs separated by an ELBA bound sequence become less differentially expressed in ELBA mutants. Transgenic reporters confirm the insulating activity of ELBA- and Insv-bound sites. These findings define ELBA and Insv as general insulator proteins in Drosophila and demonstrate the functional importance of insulators to partition transcription units.", "doi": "10.1038/s41467-019-13558-8", "pmid": "31836703", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13558-8"}, {"db": "pmc", "key": "PMC6911014"}], "notes": [], "created": "2020-01-08T16:48:51.677Z", "modified": "2020-01-21T13:56:16.511Z"}, {"entity": "publication", "iuid": "f110ed0f92844e4cbd068a8671f9fee9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f110ed0f92844e4cbd068a8671f9fee9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f110ed0f92844e4cbd068a8671f9fee9"}}, "title": "A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.", "authors": [{"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Wu", "given": "Chenglin", "initials": "C"}, {"family": "F\u00fcrth", "given": "Daniel", "initials": "D"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X"}, {"family": "W\u00e4rdell", "given": "Eva", "initials": "E"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "\u00d6sterholm", "given": "Cecilia", "initials": "C"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "\u00c5kesson", "given": "Elisabet", "initials": "E"}, {"family": "Bergmann", "given": "Olaf", "initials": "O"}, {"family": "Bienko", "given": "Magda", "initials": "M", "orcid": "0000-0002-6499-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a983bc4595448be8b0f7487f17afa7d.json"}}, {"family": "M\u00e5nsson-Broberg", "given": "Agneta", "initials": "A"}, {"family": "Nilsson", "given": "Mats", "initials": "M"}, {"family": "Sylv\u00e9n", "given": "Christer", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2019-12-12", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674", "volume": "179", "issue": "7", "pages": "1647-1660.e19"}, "abstract": "The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.", "doi": "10.1016/j.cell.2019.11.025", "pmid": "31835037", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Advanced FISH Technologies": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "In Situ Sequencing": "Technology development"}, "xrefs": [{"db": "pii", "key": "S0092-8674(19)31282-6"}], "notes": [], "created": "2019-12-16T15:05:37.917Z", "modified": "2025-10-17T13:02:18.291Z"}, {"entity": "publication", "iuid": "63ec6f126e6a4e21a793a3b2389b0ecd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63ec6f126e6a4e21a793a3b2389b0ecd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63ec6f126e6a4e21a793a3b2389b0ecd"}}, "title": "Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.", "authors": [{"family": "Pineau", "given": "Charles", "initials": "C", "orcid": "0000-0002-7461-5433", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc849989e84465185d831c58b49e682.json"}}, {"family": "Hikmet", "given": "Feria", "initials": "F"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Chen", "given": "Shuqi", "initials": "S"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}], "type": "journal article", "published": "2019-12-06", "journal": {"volume": "18", "issn": "1535-3907", "issue": "12", "pages": "4215-4230", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "One of the most complex organs in the human body is the testis, where spermatogenesis takes place. This physiological process involves thousands of genes and proteins that are activated and repressed, making testis the organ with the highest number of tissue-specific genes. However, the function of a large proportion of the corresponding proteins remains unknown and testis harbors many missing proteins (MPs), defined as products of protein-coding genes that lack experimental mass spectrometry evidence. Here, an integrated omics approach was used for exploring the cell type-specific protein expression of genes with an elevated expression in testis. By combining genome-wide transcriptomics analysis with immunohistochemistry, more than 500 proteins with distinct testicular protein expression patterns were identified, and these were selected for in-depth characterization of their in situ expression in eight different testicular cell types. The cell type-specific protein expression patterns allowed us to identify six distinct clusters of expression at different stages of spermatogenesis. The analysis highlighted numerous poorly characterized proteins in each of these clusters whose expression overlapped with that of known proteins involved in spermatogenesis, including 85 proteins with an unknown function and 60 proteins that previously have been classified as MPs. Furthermore, we were able to characterize the in situ distribution of several proteins that previously lacked spatial information and cell type-specific expression within the testis. The testis elevated expression levels both at the RNA and protein levels suggest that these proteins are related to testis-specific functions. In summary, the study demonstrates the power of combining genome-wide transcriptomics analysis with antibody-based protein profiling to explore the cell type-specific expression of both well-known proteins and MPs. The analyzed proteins constitute important targets for further testis-specific research in male reproductive disorders.", "doi": "10.1021/acs.jproteome.9b00351", "pmid": "31429579", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-08T16:47:43.388Z", "modified": "2021-07-08T13:44:33.313Z"}, {"entity": "publication", "iuid": "5ca4516c48154d5b90ae351e07808ca9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ca4516c48154d5b90ae351e07808ca9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ca4516c48154d5b90ae351e07808ca9"}}, "title": "Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.", "authors": [{"family": "Ameen", "given": "Carly", "initials": "C"}, {"family": "Feuerborn", "given": "Tatiana R", "initials": "TR"}, {"family": "Brown", "given": "Sarah K", "initials": "SK"}, {"family": "Linderholm", "given": "Anna", "initials": "A"}, {"family": "Hulme-Beaman", "given": "Ardern", "initials": "A"}, {"family": "Lebrasseur", "given": "Oph\u00e9lie", "initials": "O"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Lounsberry", "given": "Zachary T", "initials": "ZT"}, {"family": "Lin", "given": "Audrey T", "initials": "AT"}, {"family": "Appelt", "given": "Martin", "initials": "M"}, {"family": "Bachmann", "given": "Lutz", "initials": "L"}, {"family": "Betts", "given": "Matthew", "initials": "M"}, {"family": "Britton", "given": "Kate", "initials": "K"}, {"family": "Darwent", "given": "John", "initials": "J"}, {"family": "Dietz", "given": "Rune", "initials": "R"}, {"family": "Fredholm", "given": "Merete", "initials": "M"}, {"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Goriunova", "given": "Olga I", "initials": "OI"}, {"family": "Gr\u00f8nnow", "given": "Bjarne", "initials": "B"}, {"family": "Haile", "given": "James", "initials": "J"}, {"family": "Hallsson", "given": "J\u00f3n Hallsteinn", "initials": "JH"}, {"family": "Harrison", "given": "Ramona", "initials": "R"}, {"family": "Heide-J\u00f8rgensen", "given": "Mads Peter", "initials": "MP"}, {"family": "Knecht", "given": "Rick", "initials": "R"}, {"family": "Losey", "given": "Robert J", "initials": "RJ"}, {"family": "Masson-MacLean", "given": "Edouard", "initials": "E"}, {"family": "McGovern", "given": "Thomas H", "initials": "TH"}, {"family": "McManus-Fry", "given": "Ellen", "initials": "E"}, {"family": "Meldgaard", "given": "Morten", "initials": "M"}, {"family": "Midtdal", "given": "\u00c5slaug", "initials": "\u00c5"}, {"family": "Moss", "given": "Madonna L", "initials": "ML"}, {"family": "Nikitin", "given": "Iurii G", "initials": "IG"}, {"family": "Nomokonova", "given": "Tatiana", "initials": "T"}, {"family": "P\u00e1lsd\u00f3ttir", "given": "Alb\u00edna Hulda", "initials": "AH"}, {"family": "Perri", "given": "Angela", "initials": "A"}, {"family": "Popov", "given": "Aleksandr N", "initials": "AN"}, {"family": "Rankin", "given": "Lisa", "initials": "L"}, {"family": "Reuther", "given": "Joshua D", "initials": "JD"}, {"family": "Sablin", "given": "Mikhail", "initials": "M"}, {"family": "Schmidt", "given": "Anne Lisbeth", "initials": "AL"}, {"family": "Shirar", "given": "Scott", "initials": "S"}, {"family": "Smiarowski", "given": "Konrad", "initials": "K"}, {"family": "Sonne", "given": "Christian", "initials": "C"}, {"family": "Stiner", "given": "Mary C", "initials": "MC"}, {"family": "Vasyukov", "given": "Mitya", "initials": "M"}, {"family": "West", "given": "Catherine F", "initials": "CF"}, {"family": "Ween", "given": "Gro Birgit", "initials": "GB"}, {"family": "Wennerberg", "given": "Sanne Eline", "initials": "SE"}, {"family": "Wiig", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Woollett", "given": "James", "initials": "J"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hansen", "given": "Anders J", "initials": "AJ"}, {"family": "P Gilbert", "given": "M Thomas", "initials": "MT"}, {"family": "Sacks", "given": "Benjamin N", "initials": "BN"}, {"family": "Frantz", "given": "Laurent", "initials": "L"}, {"family": "Larson", "given": "Greger", "initials": "G"}, {"family": "Dobney", "given": "Keith", "initials": "K"}, {"family": "Darwent", "given": "Christyann M", "initials": "CM"}, {"family": "Evin", "given": "Allowen", "initials": "A"}], "type": "journal article", "published": "2019-12-04", "journal": {"volume": "286", "issn": "1471-2954", "issue": "1916", "pages": "20191929", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.", "doi": "10.1098/rspb.2019.1929", "pmid": "31771471", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6939252"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4740998"}], "notes": [], "created": "2020-01-08T16:48:18.766Z", "modified": "2021-07-07T20:31:10.813Z"}, {"entity": "publication", "iuid": "9797ffcb4104436abf36713e3e05d177", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9797ffcb4104436abf36713e3e05d177.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9797ffcb4104436abf36713e3e05d177"}}, "title": "High throughput barcoding method for genome-scale phasing.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Frick", "given": "Tobias", "initials": "T"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2019-12-02", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "18116", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.", "doi": "10.1038/s41598-019-54446-x", "pmid": "31792271", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-54446-x"}, {"db": "pmc", "key": "PMC6889410"}], "notes": [], "created": "2020-01-08T16:49:20.740Z", "modified": "2021-07-07T15:18:57.764Z"}, {"entity": "publication", "iuid": "b8ce5be580cb4a538fb83f3a3a931972", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8ce5be580cb4a538fb83f3a3a931972.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8ce5be580cb4a538fb83f3a3a931972"}}, "title": "Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type", "authors": [{"family": "Franco", "given": "Irene", "initials": "I"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT"}, {"family": "Moggio", "given": "Aldo", "initials": "A"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Vrta\u010dnik", "given": "Peter", "initials": "P"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Norgren", "given": "Nina", "initials": "N"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Mas-Ponte", "given": "David", "initials": "D"}, {"family": "Nordstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Lundgren", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Stenvinkel", "given": "Peter", "initials": "P"}, {"family": "Wennberg", "given": "Lars", "initials": "L"}, {"family": "Supek", "given": "Fran", "initials": "F"}, {"family": "Eriksson", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "20", "issn": "1474-760X", "issue": "1", "pages": null, "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on specific processes active in different human tissues and their effect on the transition to cancer.\n\nTo analyze somatic mutation patterns, we compile a comprehensive genetic atlas of somatic mutations in healthy human cells. High-confidence variants are obtained from newly generated and publicly available whole genome DNA sequencing data from single non-cancer cells, clonally expanded in vitro. To enable a well-controlled comparison of different cell types, we obtain single genome data (92% mean coverage) from multi-organ biopsies from the same donors. These data show multiple cell types that are protected from mutagens and display a stereotyped mutation profile, despite their origin from different tissues. Conversely, the same tissue harbors cells with distinct mutation profiles associated to different differentiation states. Analyses of mutation rate in the coding and non-coding portions of the genome identify a cell type bearing a unique mutation pattern characterized by mutation enrichment in active chromatin, regulatory, and transcribed regions.\n\nOur analysis of normal cells from healthy donors identifies a somatic mutation landscape that enhances the risk of tumor transformation in a specific cell population from the kidney proximal tubule. This unique pattern is characterized by high rate of mutation accumulation during adult life and specific targeting of expressed genes and regulatory regions.", "doi": "10.1186/s13059-019-1892-z", "pmid": "31849330", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-18T12:48:17.823Z", "modified": "2024-01-16T13:48:43.366Z"}, {"entity": "publication", "iuid": "82de3f6315754e4e8a0a947da25358ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82de3f6315754e4e8a0a947da25358ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82de3f6315754e4e8a0a947da25358ce"}}, "title": "Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes", "authors": [{"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "Berglund", "given": "Fanny", "initials": "F"}, {"family": "Razavi", "given": "Mohammad", "initials": "M"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Dr\u00f6ge", "given": "Johannes", "initials": "J"}, {"family": "Samant", "given": "Sharvari", "initials": "S"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "7", "issn": "2049-2618", "issue": "1", "pages": null, "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases.\n\nShotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and bla RSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli.\n\nBy exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.", "doi": "10.1186/s40168-019-0710-x", "pmid": "31248462", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T15:38:29.244Z", "modified": "2020-01-21T13:56:15.476Z"}, {"entity": "publication", "iuid": "f95bdf8e170c4590b325788476b5774a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f95bdf8e170c4590b325788476b5774a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f95bdf8e170c4590b325788476b5774a"}}, "title": "PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding.", "authors": [{"family": "Kloth", "given": "Karen J", "initials": "KJ", "orcid": "0000-0002-0379-5473", "researcher": {"href": "https://publications.scilifelab.se/researcher/54e0bb41dc5b44f38cf4a88dcc7ff14b.json"}}, {"family": "Abreu", "given": "Ilka N", "initials": "IN", "orcid": "0000-0003-4728-0161", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb725d57dfe40588d386dafe2c58479.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Pet\u0159\u00edk", "given": "Ivan", "initials": "I"}, {"family": "Villard", "given": "Clo\u00e9", "initials": "C"}, {"family": "Str\u00f6m", "given": "Cecilia", "initials": "C"}, {"family": "Amini", "given": "Fariba", "initials": "F"}, {"family": "Nov\u00e1k", "given": "Ond\u0159ej", "initials": "O"}, {"family": "Moritz", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4258-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/95ad5b7fe48f42eda1328f54a385e097.json"}}, {"family": "Albrectsen", "given": "Benedicte R", "initials": "BR", "orcid": "0000-0002-9337-4540", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf822eff202b4547849f8a8a9d4efc02.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "181", "issn": "1532-2548", "issue": "4", "pages": "1704-1720", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": "The plant cell wall plays an important role in damage-associated molecular pattern-induced resistance to pathogens and herbivorous insects. Our current understanding of cell wall-mediated resistance is largely based on the degree of pectin methylesterification. However, little is known about the role of pectin acetylesterification in plant immunity. This study describes how one pectin-modifying enzyme, PECTIN ACETYLESTERASE 9 (PAE9), affects the Arabidopsis (Arabidopsis thaliana) transcriptome, secondary metabolome, and aphid performance. Electro-penetration graphs showed that Myzus persicae aphids established phloem feeding earlier on pae9 mutants. Whole-genome transcriptome analysis revealed a set of 56 differentially expressed genes (DEGs) between uninfested pae9-2 mutants and wild-type plants. The majority of the DEGs were enriched for biotic stress responses and down-regulated in the pae9-2 mutant, including PAD3 and IGMT2, involved in camalexin and indole glucosinolate biosynthesis, respectively. Relative quantification of more than 100 secondary metabolites revealed decreased levels of several compounds, including camalexin and oxylipins, in two independent pae9 mutants. In addition, absolute quantification of phytohormones showed that jasmonic acid (JA), jasmonoyl-Ile, salicylic acid, abscisic acid, and indole-3-acetic acid were compromised due to PAE9 loss of function. After aphid infestation, however, pae9 mutants increased their levels of camalexin, glucosinolates, and JA, and no long-term effects were observed on aphid fitness. Overall, these data show that PAE9 is required for constitutive up-regulation of defense-related compounds, but that it is not required for aphid-induced defenses. The signatures of phenolic antioxidants, phytoprostanes, and oxidative stress-related transcripts indicate that the processes underlying PAE9 activity involve oxidation-reduction reactions.", "doi": "10.1104/pp.19.00635", "pmid": "31551361", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "pp.19.00635"}, {"db": "pmc", "key": "PMC6878011"}], "notes": [], "created": "2020-01-07T15:46:12.838Z", "modified": "2025-10-17T13:03:17.046Z"}, {"entity": "publication", "iuid": "b1c8e445bafa421699e0ca5d311d02b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1c8e445bafa421699e0ca5d311d02b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1c8e445bafa421699e0ca5d311d02b9"}}, "title": "Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers", "authors": [{"family": "H\u00f6glund", "given": "Julia", "initials": "J"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Enroth", "given": "Stefan", "initials": "S"}, {"family": "Karlsson", "given": "Torgny", "initials": "T"}, {"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Genome-wide association studies (GWAS) have identified associations between thousands of common genetic variants and human traits. However, common variants usually explain a limited fraction of the heritability of a trait. A powerful resource for identifying trait-associated variants is whole genome sequencing (WGS) data in cohorts comprised of families or individuals from a limited geographical area. To evaluate the power of WGS compared to imputations, we performed GWAS on WGS data for 72 inflammatory biomarkers, in a kinship-structured cohort. When using WGS data, we identified 18 novel associations that were not detected when analyzing the same biomarkers with genotyped or imputed SNPs. Five of the novel top variants were low frequency variants with a minor allele frequency (MAF) of <5%. Our results suggest that, even when applying a GWAS approach, we gain power and precision using WGS data, presumably due to more accurate determination of genotypes. The lack of a comparable dataset for replication of our results is a limitation in our study. However, this further highlights that there is a need for more genetic epidemiological studies based on WGS data.", "doi": "10.1038/s41598-019-53111-7", "pmid": "31727947", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-29T12:36:47.798Z", "modified": "2024-01-16T13:48:43.415Z"}, {"entity": "publication", "iuid": "f443991f0cc64850a2b0e6cdc57400dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f443991f0cc64850a2b0e6cdc57400dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f443991f0cc64850a2b0e6cdc57400dd"}}, "title": "Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.", "authors": [{"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "Faria", "given": "Rui", "initials": "R"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Westram", "given": "Anja M", "initials": "AM"}, {"family": "Butlin", "given": "Roger K", "initials": "RK"}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "5", "issn": "2375-2548", "issue": "12", "pages": "eaav9963", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.", "doi": "10.1126/sciadv.aav9963", "pmid": "31840052", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "aav9963"}, {"db": "pmc", "key": "PMC6892616"}], "notes": [], "created": "2020-01-08T16:48:53.277Z", "modified": "2020-01-21T13:56:16.525Z"}, {"entity": "publication", "iuid": "eac1e35e9cc746989d7728764d6974cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eac1e35e9cc746989d7728764d6974cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eac1e35e9cc746989d7728764d6974cf"}}, "title": "Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing", "authors": [{"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Al Hakim", "given": "Ezeddin", "initials": "E"}, {"family": "Kindblom", "given": "Marie", "initials": "M"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Demirci", "given": "Ilke", "initials": "I"}, {"family": "Paterlini", "given": "Marta", "initials": "M"}, {"family": "Reu", "given": "Pedro", "initials": "P"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Michaelsson", "given": "Jakob", "initials": "J"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "20", "issn": "1474-760X", "issue": "1", "pages": null, "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.", "doi": "10.1186/s13059-019-1673-8", "pmid": "30935387", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-04-04T19:05:37.120Z", "modified": "2024-01-16T13:48:43.447Z"}, {"entity": "publication", "iuid": "bf44d9e6ac00420a8ce09fb1c3ed732f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf44d9e6ac00420a8ce09fb1c3ed732f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf44d9e6ac00420a8ce09fb1c3ed732f"}}, "title": "An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition.", "authors": [{"family": "Wessels", "given": "Bernard", "initials": "B"}, {"family": "Seyfferth", "given": "Carolin", "initials": "C"}, {"family": "Escamez", "given": "Sacha", "initials": "S"}, {"family": "Vain", "given": "Thomas", "initials": "T"}, {"family": "Antos", "given": "Kamil", "initials": "K"}, {"family": "Vahala", "given": "Jorma", "initials": "J"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Kangasj\u00e4rvi", "given": "Jaakko", "initials": "J"}, {"family": "Eder", "given": "Michaela", "initials": "M"}, {"family": "Felten", "given": "Judith", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2019-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "224", "issue": "4", "pages": "1585-1599"}, "abstract": "Differentiation of xylem elements involves cell expansion, secondary cell wall (SCW) deposition and programmed cell death. Transitions between these phases require strict spatiotemporal control. The function of Populus ERF139 (Potri.013G101100) in xylem differentiation was characterized in transgenic overexpression and dominant repressor lines of ERF139 in hybrid aspen (Populus tremula \u00d7 tremuloides). Xylem properties, SCW chemistry and downstream targets were analyzed in both types of transgenic trees using microscopy techniques, Fourier transform-infrared spectroscopy, pyrolysis-GC/MS, wet chemistry methods and RNA sequencing. Opposite phenotypes were observed in the secondary xylem vessel sizes and SCW chemistry in the two different types of transgenic trees, supporting the function of ERF139 in suppressing the radial expansion of vessel elements and stimulating accumulation of guaiacyl-type lignin and possibly also xylan. Comparative transcriptomics identified genes related to SCW biosynthesis (LAC5, LBD15, MYB86) and salt and drought stress-responsive genes (ANAC002, ABA1) as potential direct targets of ERF139. The phenotypes of the transgenic trees and the stem expression profiles of ERF139 potential target genes support the role of ERF139 as a transcriptional regulator of xylem cell expansion and SCW formation, possibly in response to osmotic changes of the cells.", "doi": "10.1111/nph.15960", "pmid": "31125440", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-02T17:19:34.055Z", "modified": "2022-04-01T15:13:21.877Z"}, {"entity": "publication", "iuid": "ab1a9e92b16c4435ad348245129368c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab1a9e92b16c4435ad348245129368c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab1a9e92b16c4435ad348245129368c5"}}, "title": "ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes", "authors": [{"family": "Bysani", "given": "Madhusudhan", "initials": "M"}, {"family": "Agren", "given": "Rasmus", "initials": "R"}, {"family": "Daveg\u00e5rdh", "given": "Cajsa", "initials": "C"}, {"family": "Volkov", "given": "Petr", "initials": "P"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "Ling", "given": "Charlotte", "initials": "C"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Impaired insulin secretion from pancreatic islets is a hallmark of type 2 diabetes (T2D). Altered chromatin structure may contribute to the disease. We therefore studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified 57,105 and 53,284 ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors, respectively. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific transcription factors (TFs), e.g. FOXA2, MAFB, NKX2.2, NKX6.1 and PDX1, bind. Islet ATAC-seq peaks overlap with 13 SNPs associated with T2D (e.g. rs7903146, rs2237897, rs757209, rs11708067 and rs878521 near TCF7L2, KCNQ1, HNF1B, ADCY5 and GCK, respectively) and with additional 67 SNPs in LD with known T2D SNPs (e.g. SNPs annotated to GIPR, KCNJ11, GLIS3, IGF2BP2, FTO and PPARG). There was enrichment of open chromatin regions near highly expressed genes in human islets. Moreover, 1,078 open chromatin peaks, annotated to 898 genes, differed in prevalence between diabetic and non-diabetic islet donors. Some of these peaks are annotated to candidate genes for T2D and islet dysfunction (e.g. HHEX, HMGA2, GLIS3, MTNR1B and PARK2) and some overlap with SNPs associated with T2D (e.g. rs3821943 near WFS1 and rs508419 near ANK1). Enhancer regions and motifs specific to key TFs including BACH2, FOXO1, FOXA2, NEUROD1, MAFA and PDX1 were enriched in differential islet ATAC-seq peaks of T2D versus non-diabetic donors. Our study provides new understanding into how T2D alters the chromatin landscape, and thereby accessibility for TFs and gene expression, in human pancreatic islets.", "doi": "10.1038/s41598-019-44076-8", "pmid": "31123324", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "GEO", "description": "ATAC-seq data", "key": "GSE129383"}], "notes": [], "created": "2019-06-18T10:42:51.751Z", "modified": "2020-01-21T13:56:17.683Z"}, {"entity": "publication", "iuid": "2022891d3217451b8ae7c76bc9132e3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2022891d3217451b8ae7c76bc9132e3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2022891d3217451b8ae7c76bc9132e3d"}}, "title": "A cell fitness selection model for neuronal survival during development", "authors": [{"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Wu", "given": "Haohao", "initials": "H"}, {"family": "Fontanet", "given": "Paula", "initials": "P"}, {"family": "Codeluppi", "given": "Simone", "initials": "S"}, {"family": "Akkuratova", "given": "Natalia", "initials": "N"}, {"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Xue-Franz\u00e9n", "given": "Yongtao", "initials": "Y"}, {"family": "Niederreither", "given": "Karen", "initials": "K"}, {"family": "Sharma", "given": "Anil", "initials": "A"}, {"family": "Da Silva", "given": "Fabio", "initials": "F"}, {"family": "Comai", "given": "Glenda", "initials": "G"}, {"family": "Agirman", "given": "Gulistan", "initials": "G"}, {"family": "Palumberi", "given": "Domenico", "initials": "D"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}, {"family": "Moqrich", "given": "Aziz", "initials": "A"}, {"family": "Schedl", "given": "Andreas", "initials": "A"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Hadjab", "given": "Saida", "initials": "S"}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Developmental cell death plays an important role in the construction of functional neural circuits. In vertebrates, the canonical view proposes a selection of the surviving neurons through stochastic competition for target-derived neurotrophic signals, implying an equal potential for neurons to compete. Here we show an alternative cell fitness selection of neurons that is defined by a specific neuronal heterogeneity code. Proprioceptive sensory neurons that will undergo cell death and those that will survive exhibit different molecular signatures that are regulated by retinoic acid and transcription factors, and are independent of the target and neurotrophins. These molecular features are genetically encoded, representing two distinct subgroups of neurons with contrasted functional maturation states and survival outcome. Thus, in this model, a heterogeneous code of intrinsic cell fitness in neighboring neurons provides differential competitive advantage resulting in the selection of cells with higher capacity to survive and functionally integrate into neural networks.", "doi": "10.1038/s41467-019-12119-3", "pmid": "31515492", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-09-27T09:40:06.695Z", "modified": "2024-01-16T13:48:43.462Z"}, {"entity": "publication", "iuid": "4554ee75529a430fa716fb26eec6f852", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4554ee75529a430fa716fb26eec6f852.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4554ee75529a430fa716fb26eec6f852"}}, "title": "A Spatiomolecular Map of the Striatum", "authors": [{"family": "M\u00e4rtin", "given": "Antje", "initials": "A"}, {"family": "Calvigioni", "given": "Daniela", "initials": "D"}, {"family": "Tzortzi", "given": "Ourania", "initials": "O"}, {"family": "Fuzik", "given": "Janos", "initials": "J"}, {"family": "W\u00e4rnberg", "given": "Emil", "initials": "E"}, {"family": "Meletis", "given": "Konstantinos", "initials": "K"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "29", "issn": "2211-1247", "issue": "13", "pages": "4320-4333.e5", "title": "Cell Rep", "issn-l": null}, "abstract": "The striatum is organized into two major outputs formed by striatal projection neuron (SPN) subtypes with distinct molecular identities. In addition, histochemical division into patch and matrix compartments represents an additional spatial organization, proposed to mirror a motor-motivation regionalization. To map the molecular diversity of patch versus matrix SPNs, we genetically labeled mu opioid receptor (Oprm1) expressing neurons and performed single-nucleus RNA sequencing. This allowed us to establish molecular definitions of patch, matrix, and exopatch SPNs, as well as identification of Col11a1+ striatonigral SPNs. At the tissue level, mapping the expression of candidate markers reveals organization of spatial domains, which are conserved in the non-human primate brain. The spatial markers are cell-type independent and instead represent a spatial code found across all SPNs within a spatial domain. The spatiomolecular map establishes a formal system for targeting and studying striatal subregions and SPNs subtypes, beyond the classical striatonigral and striatopallidal division.", "doi": "10.1016/j.celrep.2019.11.096", "pmid": "31875543", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2020-01-07T20:10:15.165Z", "modified": "2020-01-21T13:56:16.574Z"}, {"entity": "publication", "iuid": "2f3fc2505d90467ea15d6d7fd508de68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f3fc2505d90467ea15d6d7fd508de68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f3fc2505d90467ea15d6d7fd508de68"}}, "title": "Programmed DNA elimination of germline development genes in songbirds.", "authors": [{"family": "Kinsella", "given": "Cormac M", "initials": "CM"}, {"family": "Ruiz-Ruano", "given": "Francisco J", "initials": "FJ"}, {"family": "Dion-C\u00f4t\u00e9", "given": "Anne-Marie", "initials": "AM"}, {"family": "Charles", "given": "Alexander J", "initials": "AJ"}, {"family": "Gossmann", "given": "Toni I", "initials": "TI"}, {"family": "Cabrero", "given": "Josefa", "initials": "J"}, {"family": "Kappei", "given": "Dennis", "initials": "D"}, {"family": "Hemmings", "given": "Nicola", "initials": "N"}, {"family": "Simons", "given": "Mirre J P", "initials": "MJP"}, {"family": "Camacho", "given": "Juan Pedro M", "initials": "JPM"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2019-11-29", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "5468", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline-soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein level. Using comparative genomics, we show that genes have been added to the GRC over millions of years of evolution, with embryonic development genes bicc1 and trim71 dating to the ancestor of songbirds and dozens of other genes added very recently. The somatic elimination of this evolutionarily dynamic chromosome in songbirds implies a unique mechanism to minimise genetic conflict between germline and soma, relevant to antagonistic pleiotropy, an evolutionary process underlying ageing and sexual traits.", "doi": "10.1038/s41467-019-13427-4", "pmid": "31784533", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-13427-4"}, {"db": "pmc", "key": "PMC6884545"}], "notes": [], "created": "2020-01-08T16:48:20.466Z", "modified": "2020-01-21T13:56:16.488Z"}, {"entity": "publication", "iuid": "3e566b52c0814a2186badf96a7dcb3be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e566b52c0814a2186badf96a7dcb3be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e566b52c0814a2186badf96a7dcb3be"}}, "title": "The human secretome", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Karlsson", "given": "Max J", "initials": "MJ"}, {"family": "Hober", "given": "Andreas", "initials": "A"}, {"family": "Svensson", "given": "Anne Sophie", "initials": "AS"}, {"family": "Scheffel", "given": "Julia", "initials": "J"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Zhong", "given": "Wen", "initials": "W"}, {"family": "Tebani", "given": "Abdellah", "initials": "A"}, {"family": "Strandberg", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Berling", "given": "Anna", "initials": "A"}, {"family": "Ekblad", "given": "Siri", "initials": "S"}, {"family": "Dannemeyer", "given": "Melanie", "initials": "M"}, {"family": "Kanje", "given": "Sara", "initials": "S"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Volk", "given": "Anna Luisa", "initials": "AL"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "M\u00e5nberg", "given": "Anna", "initials": "A"}, {"family": "Dodig-Crnkovic", "given": "Tea", "initials": "T"}, {"family": "Pin", "given": "Elisa", "initials": "E"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "H\u00e4ussler", "given": "Ragna S", "initials": "RS"}, {"family": "Hong", "given": "Mun Gwan", "initials": "MG"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Vuu", "given": "Jimmy", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Emil", "initials": "E"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Robinson", "given": "Jonathan", "initials": "J"}, {"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Sullivan", "given": "Devin", "initials": "D"}, {"family": "Thul", "given": "Peter", "initials": "P"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gummesson", "given": "Anders", "initials": "A"}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal-article", "published": "2019-11-26", "journal": {"title": "Sci. Signal.", "issn": "1945-0877", "issn-l": "1945-0877", "volume": "12", "issue": "609", "pages": "eaaz0274"}, "abstract": "The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.", "doi": "10.1126/scisignal.aaz0274", "pmid": "31772123", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Spatial Proteomics": "Collaborative", "Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-03T08:34:48.430Z", "modified": "2021-12-09T13:59:58.034Z"}, {"entity": "publication", "iuid": "962c83aa1b6e49929f0e95cf57715c1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/962c83aa1b6e49929f0e95cf57715c1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/962c83aa1b6e49929f0e95cf57715c1f"}}, "title": "Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.", "authors": [{"family": "Stiller", "given": "Christiane", "initials": "C"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "Frick", "given": "Tobias", "initials": "T"}, {"family": "Westerlund", "given": "Kristina", "initials": "K"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}, {"family": "Karlstr\u00f6m", "given": "Amelie Eriksson", "initials": "AE"}], "type": "journal article", "published": "2019-11-20", "journal": {"volume": "30", "issn": "1520-4812", "issue": "11", "pages": "2790-2798", "title": "Bioconjug. Chem.", "issn-l": "1043-1802"}, "abstract": "Antibody-DNA conjugates are powerful tools for DNA-assisted protein analysis. Growing usage of these methods demands efficient production of high-quality conjugates. We developed an easy and fast synthesis route yielding covalent antibody-DNA conjugates with a defined conjugation site and low batch-to-batch variability. We utilize the Z domain from protein A, containing the unnatural amino acid 4-benzoylphenylalanine (BPA) for photoaffinity labeling of the antibodies' Fc region. Z( xBPA) domains are C-terminally modified with triple-glycine (G3)-modified DNA-oligonucleotides via enzymatic Sortase A coupling. We show reliable modification of the most commonly used IgG's. To prove our conjugates' functionality, we detected antibody-antigen binding events in an assay called Droplet Barcode Sequencing for Protein analysis (DBS-Pro). It confirms not only retained functionality for both conjugate parts but also the potential of using DBS-Pro for quantifying protein abundances. As intermediates are easily storable and our approach is modular, it offers a convenient strategy for screening various antibody-DNA conjugates using the same starting material.", "doi": "10.1021/acs.bioconjchem.9b00548", "pmid": "31609586", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-02T16:53:05.851Z", "modified": "2024-01-16T13:48:43.497Z"}, {"entity": "publication", "iuid": "e7838bf1f3a949b698f6596c64c84c3f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7838bf1f3a949b698f6596c64c84c3f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7838bf1f3a949b698f6596c64c84c3f"}}, "title": "Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).", "authors": [{"family": "Apuli", "given": "Rami-Petteri", "initials": "RP"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}], "type": "journal article", "published": "2019-11-19", "journal": {"volume": null, "issn": "2160-1836", "issue": null, "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.", "doi": "10.1534/g3.119.400504", "pmid": "31744900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "g3.119.400504"}], "notes": [], "created": "2019-12-02T17:21:22.039Z", "modified": "2024-01-16T13:48:43.504Z"}, {"entity": "publication", "iuid": "e156232b4736436ba989d23fbc9d6ef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e156232b4736436ba989d23fbc9d6ef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e156232b4736436ba989d23fbc9d6ef1"}}, "title": "Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.", "authors": [{"family": "Panula", "given": "Sarita", "initials": "S"}, {"family": "Kurek", "given": "Magdalena", "initials": "M"}, {"family": "Kumar", "given": "Pankaj", "initials": "P"}, {"family": "Albalushi", "given": "Halima", "initials": "H"}, {"family": "Padrell S\u00e1nchez", "given": "Sara", "initials": "S"}, {"family": "Damdimopoulou", "given": "Pauliina", "initials": "P"}, {"family": "Olofsson", "given": "Jan I", "initials": "JI"}, {"family": "Hovatta", "given": "Outi", "initials": "O"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}, {"family": "Stukenborg", "given": "Jan-Bernd", "initials": "JB"}], "type": "journal article", "published": "2019-11-19", "journal": {"volume": null, "issn": "1460-2350", "issue": null, "title": "Hum. Reprod.", "issn-l": "0268-1161"}, "abstract": "Does the X chromosome inactivation (XCI) of Klinefelter syndrome (KS)-derived human induced pluripotent stem cells (hiPSCs) correspond to female human pluripotent stem cells (hPSCs) and reflect the KS genotype?\n\nOur results demonstrate for the first time that KS-derived hiPSCs show similar XCI behavior to female hPSCs in culture and show biological relevance to KS genotype-related clinical features.\n\nSo far, assessment of XCI of KS-derived hiPSCs was based on H3K27me3 staining and X-inactive specific transcript gene expression disregarding the at least three XCI states (XaXi with XIST coating, XaXi lacking XIST coating, and XaXe (partially eroded XCI)) that female hPSCs display in culture.\n\nThe study used hiPSC lines generated from two azoospermic patients with KS and included two healthy male (HM) and one healthy female donor.\n\nIn this study, we derived hiPSCs by reprograming fibroblasts with episomal plasmids and applying laminin 521 as culture substrate. hiPSCs were characterized by karyotyping, immunocytochemistry, immunohistochemistry, quantitative PCR, teratoma formation, and embryoid body differentiation. XCI and KS hiPSC relevance were assessed by whole genome transcriptomics analysis and immunocytochemistry plus FISH of KS, HM and female fibroblast, and their hiPSC derivatives.\n\nApplying whole genome transcriptomics analysis, we could identify differentially expressed genes (DEGs) between KS and HM donors with enrichment in gene ontology terms associated with fertility, cardiovascular development, ossification, and brain development, all associated with KS genotype-related clinical features. Furthermore, XCI analysis based on transcriptomics data, RNA FISH, and H3K27me3 staining revealed variable XCI states of KS hiPSCs similar to female hiPSCs, showing either normal (XaXi) or eroded (XaXe) XCI. KS hiPSCs with normal XCI showed nevertheless upregulated X-linked genes involved in nervous system development as well as synaptic transmission, supporting the potential use of KS-derived hiPSCs as an in vitro model for KS.\n\nDetailed clinical information for patients included in this study was not available. Although a correlation between DEGs and the KS genotype could be observed, the biological relevance of these cells has to be confirmed with further experiments. In addition, karyotype analysis for two hiPSC lines was performed at passage 12 but not repeated at a later passage. Nevertheless, since all XCI experiments for those lines were performed between passage 11 and 15 the authors expect no karyotypic changes for those experiments.\n\nAs KS patients have variable clinical phenotypes that are influenced by the grade of aneuploidy, mosaicism, origin of the X chromosome, and XCI 'escapee' genes, which vary not only among individuals but also among different tissues within the same individual, differentiated KS hiPSCs could be used for a better understanding of KS pathogenesis.\n\nThis study was supported by grants from the Knut and Alice Wallenberg Foundation (2016.0121 and 2015.0096), Ming Wai Lau Centre for Reparative Medicine (2-343/2016), Ragnar S\u00f6derberg Foundation (M67/13), Swedish Research Council (2013-32485-100360-69), the Centre for Innovative Medicine (2-388/2016-40), Kronprinsessan Lovisas F\u00f6rening F\u00f6r Barnasjukv\u00e5rd/Stiftelsen Axel Tielmans Minnesfond, Samariten Foundation, Jonasson Center at the Royal Institute of Technology, Sweden, and Initial Training Network Marie Curie Program 'Growsperm' (EU-FP7-PEOPLE-2013-ITN 603568). The authors declare no conflicts of interest.", "doi": "10.1093/humrep/dez134", "pmid": "31743397", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5621184"}], "notes": [], "created": "2019-12-02T17:21:20.650Z", "modified": "2024-01-16T13:48:43.511Z"}, {"entity": "publication", "iuid": "3441bbe4bc7b42078a3475a299853b75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3441bbe4bc7b42078a3475a299853b75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3441bbe4bc7b42078a3475a299853b75"}}, "title": "Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.", "authors": [{"family": "Zanni", "given": "Giulia", "initials": "G"}, {"family": "Goto", "given": "Shinobu", "initials": "S"}, {"family": "Fragopoulou", "given": "Adamantia F", "initials": "AF"}, {"family": "Gaudenzi", "given": "Giulia", "initials": "G"}, {"family": "Naidoo", "given": "Vinogran", "initials": "V"}, {"family": "Di Martino", "given": "Elena", "initials": "E"}, {"family": "Levy", "given": "Gabriel", "initials": "G"}, {"family": "Dominguez", "given": "Cecilia A", "initials": "CA"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Cedazo-Minguez", "given": "Angel", "initials": "A"}, {"family": "Merino-Serrais", "given": "Paula", "initials": "P"}, {"family": "Stamatakis", "given": "Antonios", "initials": "A"}, {"family": "Hermanson", "given": "Ola", "initials": "O"}, {"family": "Blomgren", "given": "Klas", "initials": "K"}], "type": "journal article", "published": "2019-11-14", "journal": {"volume": null, "issn": "1476-5578", "issue": null, "pages": null, "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "Cranial radiotherapy in children has detrimental effects on cognition, mood, and social competence in young cancer survivors. Treatments harnessing hippocampal neurogenesis are currently of great relevance in this context. Lithium, a well-known mood stabilizer, has both neuroprotective, pro-neurogenic as well as antitumor effects, and in the current study we introduced lithium treatment 4 weeks after irradiation. Female mice received a single 4 Gy whole-brain radiation dose on postnatal day (PND) 21 and were randomized to 0.24% Li2CO 3 chow or normal chow from PND 49 to 77. Hippocampal neurogenesis was assessed on PND 77, 91, and 105. We found that lithium treatment had a pro-proliferative effect on neural progenitors, but neuronal integration occurred only after it was discontinued. Also, the treatment ameliorated deficits in spatial learning and memory retention observed in irradiated mice. Gene expression profiling and DNA methylation analysis identified two novel factors related to the observed effects, Tppp, associated with microtubule stabilization, and GAD2/65, associated with neuronal signaling. Our results show that lithium treatment reverses irradiation-induced loss of hippocampal neurogenesis and cognitive impairment even when introduced long after the injury. We propose that lithium treatment should be intermittent in order to first make neural progenitors proliferate and then, upon discontinuation, allow them to differentiate. Our findings suggest that pharmacological treatment of cognitive so-called late effects in childhood cancer survivors is possible.", "doi": "10.1038/s41380-019-0584-0", "pmid": "31723242", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41380-019-0584-0"}], "notes": [], "created": "2019-12-02T17:21:21.364Z", "modified": "2024-01-16T13:48:43.525Z"}, {"entity": "publication", "iuid": "c3696d7ec9684a9d947af102e6b2c93a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3696d7ec9684a9d947af102e6b2c93a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3696d7ec9684a9d947af102e6b2c93a"}}, "title": "Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions.", "authors": [{"family": "Al-Farsi", "given": "Hissa M", "initials": "HM"}, {"family": "Al-Adwani", "given": "Salma", "initials": "S"}, {"family": "Ahmed", "given": "Sultan", "initials": "S"}, {"family": "Vogt", "given": "Carmen", "initials": "C"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Leber", "given": "Anna", "initials": "A"}, {"family": "Al-Jardani", "given": "Amina", "initials": "A"}, {"family": "Al-Azri", "given": "Saleh", "initials": "S"}, {"family": "Al-Muharmi", "given": "Zakariya", "initials": "Z"}, {"family": "Toprak", "given": "Muhammet S", "initials": "MS"}, {"family": "Giske", "given": "Christian G", "initials": "CG"}, {"family": "Bergman", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2019-11-14", "journal": {"volume": "10", "issn": "1664-302X", "issue": null, "pages": "2632", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Colistin is a polypeptide antibiotic drug that targets lipopolysaccharides in the outer membrane of Gram-negative bacteria. Inactivation of the mgrB-gene is a common mechanism behind colistin-resistance in Klebsiella pneumoniae (Kpn). Since colistin is a cyclic polypeptide, it may exhibit cross-resistance with the antimicrobial peptide LL-37, and with other innate effector mechanisms, but previous results are inconclusive.\n\nTo study potential cross-resistance between colistin and LL-37, as well as with other innate effector mechanisms, and to compare virulence of colistin-resistant and susceptible Kpn strains.\n\nCarbapenemase-producing Kpn from Oman ( n = 17) were subjected to antimicrobial susceptibility testing and whole genome sequencing. Susceptibility to colistin and LL-37 was studied. The surface charge was determined by zeta-potential measurements and the morphology of treated bacteria was analyzed with electron microscopy. Bacterial survival was assessed in human whole blood and serum, as well as in a zebrafish infection-model.\n\nGenome-analysis revealed insertion-sequences in the mgrB gene, as a cause of colistin resistance in 8/17 isolates. Colistin-resistant (Col-R) isolates were found to be more resistant to LL-37 compared to colistin-susceptible (Col-S) isolates, but only at concentrations \u226550 \u03bcg/ml. There was no significant difference in surface charge between the isolates. The morphological changes were similar in both Col-R and Col-S isolates after exposure to LL-37. Finally, no survival difference between the Col-R and Col-S isolates was observed in whole blood or serum, or in zebrafish embryos.\n\nCross-resistance between colistin and LL-37 was observed at elevated concentrations of LL-37. However, Col-R and Col-S isolates exhibited similar survival in serum and whole blood, and in a zebrafish infection-model, suggesting that cross-resistance most likely play a limited role during physiological conditions. However, it cannot be ruled out that the observed cross-resistance could be relevant in conditions where LL-37 levels reach high concentrations, such as during infection or inflammation.", "doi": "10.3389/fmicb.2019.02632", "pmid": "31803163", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6870453"}], "notes": [], "created": "2020-01-08T16:48:50.186Z", "modified": "2020-01-21T13:56:16.503Z"}, {"entity": "publication", "iuid": "5b59dfa32e5f440fa3619f3f00d31b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b59dfa32e5f440fa3619f3f00d31b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b59dfa32e5f440fa3619f3f00d31b21"}}, "title": "Carnivores, competition and genetic connectivity in the Anthropocene.", "authors": [{"family": "Creel", "given": "Scott", "initials": "S"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}, {"family": "Becker", "given": "Matthew", "initials": "M"}, {"family": "Simukonda", "given": "Chuma", "initials": "C"}, {"family": "Norman", "given": "Anita", "initials": "A"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Chifunte", "given": "Clive", "initials": "C"}], "type": "journal article", "published": "2019-11-08", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "16339", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Current extinction rates are comparable to five prior mass extinctions in the earth's history, and are strongly affected by human activities that have modified more than half of the earth's terrestrial surface. Increasing human activity restricts animal movements and isolates formerly connected populations, a particular concern for the conservation of large carnivores, but no prior research has used high throughput sequencing in a standardized manner to examine genetic connectivity for multiple species of large carnivores and multiple ecosystems. Here, we used RAD SNP genotypes to test for differences in connectivity between multiple ecosystems for African wild dogs (Lycaon pictus) and lions (Panthera leo), and to test correlations between genetic distance, geographic distance and landscape resistance due to human activity. We found weaker connectivity, a stronger correlation between genetic distance and geographic distance, and a stronger correlation between genetic distance and landscape resistance for lions than for wild dogs, and propose a new hypothesis that adaptations to interspecific competition may help to explain differences in vulnerability to isolation by humans.", "doi": "10.1038/s41598-019-52904-0", "pmid": "31705017", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-52904-0"}, {"db": "pmc", "key": "PMC6841969"}], "notes": [], "created": "2019-12-02T17:21:18.825Z", "modified": "2020-01-21T13:56:15.790Z"}, {"entity": "publication", "iuid": "fe4601405ded493f93c9a5be716c5c06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe4601405ded493f93c9a5be716c5c06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe4601405ded493f93c9a5be716c5c06"}}, "title": "From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.", "authors": [{"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Bjerin", "given": "Olof", "initials": "O"}, {"family": "Gustavsson", "given": "Peter", "initials": "P"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Georgii-Hemming", "given": "Patrik", "initials": "P"}, {"family": "Iwarsson", "given": "Erik", "initials": "E"}, {"family": "Johansson-Soller", "given": "Maria", "initials": "M"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Norling", "given": "Ameli", "initials": "A"}, {"family": "Sahlin", "given": "Ellika", "initials": "E"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Ygberg", "given": "Sofia", "initials": "S"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2019-11-07", "journal": {"volume": "11", "issn": "1756-994X", "issue": "1", "pages": "68", "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": "Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test.\n\nWe analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure.\n\nFirst, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data. Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively.\n\nThe overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.", "doi": "10.1186/s13073-019-0675-1", "pmid": "31694722", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s13073-019-0675-1"}, {"db": "pmc", "key": "PMC6836550"}], "notes": [], "created": "2019-11-21T13:21:06.171Z", "modified": "2024-01-16T13:48:43.561Z"}, {"entity": "publication", "iuid": "0a0d2e6459924588ac1a114168b121b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a0d2e6459924588ac1a114168b121b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a0d2e6459924588ac1a114168b121b5"}}, "title": "Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Asmala", "given": "Eero", "initials": "E"}, {"family": "Carstensen", "given": "Jacob", "initials": "J"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2019-11-07", "journal": {"volume": "10", "issn": "1664-302X", "issue": null, "pages": "2579", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.", "doi": "10.3389/fmicb.2019.02579", "pmid": "31787958", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6854034"}], "notes": [], "created": "2020-01-08T16:48:21.213Z", "modified": "2020-01-21T13:56:16.495Z"}, {"entity": "publication", "iuid": "fda3631ee6eb40dab32f8a6239a4f7b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fda3631ee6eb40dab32f8a6239a4f7b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fda3631ee6eb40dab32f8a6239a4f7b8"}}, "title": "Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.", "authors": [{"family": "Marquina", "given": "Daniel", "initials": "D"}, {"family": "Esparza-Salas", "given": "Rodrigo", "initials": "R"}, {"family": "Roslin", "given": "Tomas", "initials": "T"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2019-11-00", "journal": {"volume": "19", "issn": "1755-0998", "issue": "6", "pages": "1516-1530", "title": "Mol Ecol Resour", "issn-l": "1755-098X"}, "abstract": "DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers - COI and 16S - and three different sampling methods: (a) homogenized Malaise trap samples (homogenate), (b) preservative ethanol from the same samples, and (c) soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is significantly different from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol while strong and large taxa are overrepresented in homogenate. For soil samples, highly degenerate COI primers pick up large amounts of nontarget DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in molecular operational taxonomic unit (MOTU) content was found between the trap and the soil samples. Our results demonstrate that none of the tested sampling approaches is satisfactory on its own. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.", "doi": "10.1111/1755-0998.13071", "pmid": "31379089", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6899807"}], "notes": [], "created": "2020-01-08T16:47:40.630Z", "modified": "2020-01-21T13:56:16.358Z"}, {"entity": "publication", "iuid": "f8ad8e9980a54d9caeff5a105bd9b6a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8ad8e9980a54d9caeff5a105bd9b6a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8ad8e9980a54d9caeff5a105bd9b6a2"}}, "title": "Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.", "authors": [{"family": "Saremi", "given": "Nedda F", "initials": "NF"}, {"family": "Supple", "given": "Megan A", "initials": "MA"}, {"family": "Byrne", "given": "Ashley", "initials": "A"}, {"family": "Cahill", "given": "James A", "initials": "JA"}, {"family": "Coutinho", "given": "Luiz Lehmann", "initials": "LL"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Figueir\u00f3", "given": "Henrique V", "initials": "HV"}, {"family": "Johnson", "given": "Warren E", "initials": "WE"}, {"family": "Milne", "given": "Heather J", "initials": "HJ"}, {"family": "O'Brien", "given": "Stephen J", "initials": "SJ"}, {"family": "O'Connell", "given": "Brendan", "initials": "B"}, {"family": "Onorato", "given": "David P", "initials": "DP"}, {"family": "Riley", "given": "Seth P D", "initials": "SPD"}, {"family": "Sikich", "given": "Jeff A", "initials": "JA"}, {"family": "Stahler", "given": "Daniel R", "initials": "DR"}, {"family": "Villela", "given": "Priscilla Marqui Schmidt", "initials": "PMS"}, {"family": "Vollmers", "given": "Christopher", "initials": "C"}, {"family": "Wayne", "given": "Robert K", "initials": "RK"}, {"family": "Eizirik", "given": "Eduardo", "initials": "E"}, {"family": "Corbett-Detig", "given": "Russell B", "initials": "RB"}, {"family": "Green", "given": "Richard E", "initials": "RE"}, {"family": "Wilmers", "given": "Christopher C", "initials": "CC"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}], "type": "journal article", "published": "2019-10-18", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4769", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.", "doi": "10.1038/s41467-019-12741-1", "pmid": "31628318", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-12741-1"}, {"db": "pmc", "key": "PMC6800433"}], "notes": [], "created": "2019-12-02T16:53:08.735Z", "modified": "2021-07-07T20:31:10.946Z"}, {"entity": "publication", "iuid": "3ad5f96bf6154c73b5c68111c7ffe880", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ad5f96bf6154c73b5c68111c7ffe880.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ad5f96bf6154c73b5c68111c7ffe880"}}, "title": "Whole-genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation", "authors": [{"family": "Paulsson", "given": "Johan O", "initials": "JO"}, {"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "Wang", "given": "Na", "initials": "N"}, {"family": "Stenman", "given": "Adam", "initials": "A"}, {"family": "Crona", "given": "Joakim", "initials": "J"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Ghaderi", "given": "Mehran", "initials": "M"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Zedenius", "given": "Jan", "initials": "J"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC"}], "type": "journal-article", "published": "2019-10-17", "journal": {"volume": null, "issn": "0022-3417", "issue": null, "pages": null, "title": "J. Pathol", "issn-l": "0022-3417"}, "abstract": "The genetics underlying thyroid cancer dedifferentiation is only partly understood and has not yet been characterised using comprehensive pan-genomic analyses. We investigated a unique case with synchronous follicular thyroid carcinoma (FTC), poorly differentiated thyroid carcinoma (PDTC), and anaplastic thyroid carcinoma (ATC), as well as regional lymph node metastases from the PDTC and ATC from a single patient using whole-genome sequencing (WGS). The FTC displayed mutations in CALR, RB1, and MSH2, and the PDTC exhibited mutations in TP53, DROSHA, APC, TERT, and additional DNA repair genes - associated with an immense increase in sub-clonal somatic mutations. All components displayed an overrepresentation of C>T transitions with associated microsatellite instability (MSI) in the PDTC and ATC, with borderline MSI in the FTC. Clonality analyses pinpointed a shared ancestral clone enriched for mutations in TP53-associated regulation of DNA repair and identified important sub-clones for each tumour component already present in the corresponding preceding lesion. This genomic characterisation of the natural progression of thyroid cancer reveals several novel genes of interest for future studies. Moreover, the findings support the theory of a stepwise dedifferentiation process and suggest that defects in DNA repair could play an important role in the clonal evolution of thyroid cancer. \u00a9 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.", "doi": "10.1002/path.5359", "pmid": "31621921", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T14:49:24.669Z", "modified": "2024-01-16T13:48:43.669Z"}, {"entity": "publication", "iuid": "f8f7e1aa81ab4c7ab893a61f6c326981", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8f7e1aa81ab4c7ab893a61f6c326981.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8f7e1aa81ab4c7ab893a61f6c326981"}}, "title": "Microbe-host interplay in atopic dermatitis and psoriasis.", "authors": [{"family": "Fyhrquist", "given": "Nanna", "initials": "N"}, {"family": "Muirhead", "given": "Gareth", "initials": "G"}, {"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S"}, {"family": "Jeanmougin", "given": "Marine", "initials": "M"}, {"family": "Olah", "given": "Peter", "initials": "P"}, {"family": "Skoog", "given": "Tiina", "initials": "T"}, {"family": "Jules-Clement", "given": "Gerome", "initials": "G"}, {"family": "Feld", "given": "Micha", "initials": "M"}, {"family": "Barrientos-Somarribas", "given": "Mauricio", "initials": "M"}, {"family": "Sinkko", "given": "Hanna", "initials": "H"}, {"family": "van den Bogaard", "given": "Ellen H", "initials": "EH"}, {"family": "Zeeuwen", "given": "Patrick L J M", "initials": "PLJM"}, {"family": "Rikken", "given": "Gijs", "initials": "G"}, {"family": "Schalkwijk", "given": "Joost", "initials": "J"}, {"family": "Niehues", "given": "Hanna", "initials": "H"}, {"family": "D\u00e4ubener", "given": "Walter", "initials": "W"}, {"family": "Eller", "given": "Silvia Kathrin", "initials": "SK"}, {"family": "Alexander", "given": "Helen", "initials": "H"}, {"family": "Pennino", "given": "Davide", "initials": "D"}, {"family": "Suomela", "given": "Sari", "initials": "S"}, {"family": "Tessas", "given": "Ioannis", "initials": "I"}, {"family": "Lybeck", "given": "Emilia", "initials": "E"}, {"family": "Baran", "given": "Anna M", "initials": "AM"}, {"family": "Darban", "given": "Hamid", "initials": "H"}, {"family": "Gangwar", "given": "Roopesh Singh", "initials": "RS"}, {"family": "Gerstel", "given": "Ulrich", "initials": "U"}, {"family": "Jahn", "given": "Katharina", "initials": "K"}, {"family": "Karisola", "given": "Piia", "initials": "P"}, {"family": "Yan", "given": "Lee", "initials": "L"}, {"family": "Hansmann", "given": "Britta", "initials": "B"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Meller", "given": "Stephan", "initials": "S"}, {"family": "Bylesj\u00f6", "given": "Max", "initials": "M"}, {"family": "Hup\u00e9", "given": "Philippe", "initials": "P"}, {"family": "Levi-Schaffer", "given": "Francesca", "initials": "F"}, {"family": "Greco", "given": "Dario", "initials": "D"}, {"family": "Ranki", "given": "Annamari", "initials": "A"}, {"family": "Schr\u00f6der", "given": "Jens M", "initials": "JM"}, {"family": "Barker", "given": "Jonathan", "initials": "J"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Tsoka", "given": "Sophia", "initials": "S"}, {"family": "Lauerma", "given": "Antti", "initials": "A"}, {"family": "Soumelis", "given": "Vassili", "initials": "V"}, {"family": "Nestle", "given": "Frank O", "initials": "FO"}, {"family": "Homey", "given": "Bernhard", "initials": "B"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Alenius", "given": "Harri", "initials": "H"}], "type": "journal article", "published": "2019-10-16", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "4703", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Despite recent advances in understanding microbial diversity in skin homeostasis, the relevance of microbial dysbiosis in inflammatory disease is poorly understood. Here we perform a comparative analysis of skin microbial communities coupled to global patterns of cutaneous gene expression in patients with atopic dermatitis or psoriasis. The skin microbiota is analysed by 16S amplicon or whole genome sequencing and the skin transcriptome by microarrays, followed by integration of the data layers. We find that atopic dermatitis and psoriasis can be classified by distinct microbes, which differ from healthy volunteers microbiome composition. Atopic dermatitis is dominated by a single microbe (Staphylococcus aureus), and associated with a disease relevant host transcriptomic signature enriched for skin barrier function, tryptophan metabolism and immune activation. In contrast, psoriasis is characterized by co-occurring communities of microbes with weak associations with disease related gene expression. Our work provides a basis for biomarker discovery and targeted therapies in skin dysbiosis.", "doi": "10.1038/s41467-019-12253-y", "pmid": "31619666", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-12253-y"}, {"db": "pmc", "key": "PMC6795799"}], "notes": [], "created": "2019-12-02T16:50:28.663Z", "modified": "2024-01-16T13:48:43.676Z"}, {"entity": "publication", "iuid": "03a8b4f010b64f98b90e3af194d3c9ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03a8b4f010b64f98b90e3af194d3c9ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03a8b4f010b64f98b90e3af194d3c9ff"}}, "title": "Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.", "authors": [{"family": "H\u00f6gfors-R\u00f6nnholm", "given": "Eva", "initials": "E"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Brambilla", "given": "Diego", "initials": "D"}, {"family": "Huntemann", "given": "Marcel", "initials": "M"}, {"family": "Clum", "given": "Alicia", "initials": "A"}, {"family": "Foster", "given": "Brian", "initials": "B"}, {"family": "Foster", "given": "Bryce", "initials": "B"}, {"family": "Roux", "given": "Simon", "initials": "S"}, {"family": "Palaniappan", "given": "Krishnaveni", "initials": "K"}, {"family": "Varghese", "given": "Neha", "initials": "N"}, {"family": "Mukherjee", "given": "Supratim", "initials": "S"}, {"family": "Reddy", "given": "T B K", "initials": "TBK"}, {"family": "Daum", "given": "Chris", "initials": "C"}, {"family": "Copeland", "given": "Alex", "initials": "A"}, {"family": "Chen", "given": "I-Min A", "initials": "IA"}, {"family": "Ivanova", "given": "Natalia N", "initials": "NN"}, {"family": "Kyrpides", "given": "Nikos C", "initials": "NC"}, {"family": "Harmon-Smith", "given": "Miranda", "initials": "M"}, {"family": "Eloe-Fadrosh", "given": "Emiley A", "initials": "EA"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Engblom", "given": "Sten", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2019-10-16", "journal": {"volume": "6", "issn": "2052-4463", "issue": "1", "pages": "207", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.", "doi": "10.1038/s41597-019-0222-3", "pmid": "31619684", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41597-019-0222-3"}, {"db": "pmc", "key": "PMC6795848"}], "notes": [], "created": "2020-01-08T16:48:16.453Z", "modified": "2020-01-21T13:56:16.447Z"}, {"entity": "publication", "iuid": "17ab6ae7353b461ab314603a3d7cf0e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17ab6ae7353b461ab314603a3d7cf0e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17ab6ae7353b461ab314603a3d7cf0e1"}}, "title": "Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.", "authors": [{"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Dahl", "given": "Martin", "initials": "M"}, {"family": "Deyanova", "given": "Diana", "initials": "D"}, {"family": "Lyimo", "given": "Liberatus D", "initials": "LD"}, {"family": "Bik", "given": "Holly M", "initials": "HM"}, {"family": "Schuelke", "given": "Taruna", "initials": "T"}, {"family": "Pereira", "given": "Tiago Jos\u00e9", "initials": "TJ"}, {"family": "Bj\u00f6rk", "given": "Mats", "initials": "M"}, {"family": "Creer", "given": "Simon", "initials": "S"}, {"family": "Gullstr\u00f6m", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-10-04", "journal": {"volume": "2", "issn": "2399-3642", "issue": null, "pages": "362", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Ecological interactions between aquatic plants and sediment communities can shape the structure and function of natural systems. Currently, we do not fully understand how seagrass habitat degradation impacts the biodiversity of belowground sediment communities. Here, we evaluated indirect effects of disturbance of seagrass meadows on meiobenthic community composition, with a five-month in situ experiment in a tropical seagrass meadow. Disturbance was created by reducing light availability (two levels of shading), and by mimicking grazing events (two levels) to assess impacts on meiobenthic diversity using high-throughput sequencing of 18S rRNA amplicons. Both shading and simulated grazing had an effect on meiobenthic community structure, mediated by seagrass-associated biotic drivers and sediment abiotic variables. Additionally, shading substantially altered the trophic structure of the nematode community. Our findings show that degradation of seagrass meadows can alter benthic community structure in coastal areas with potential impacts to ecosystem functions mediated by meiobenthos in marine sediments.", "doi": "10.1038/s42003-019-0610-4", "pmid": "31602411", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "610"}, {"db": "pmc", "key": "PMC6778119"}], "notes": [], "created": "2019-12-02T17:20:31.307Z", "modified": "2024-01-16T13:48:43.707Z"}, {"entity": "publication", "iuid": "a9e29ea237a646e788a4a310df3e47a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9e29ea237a646e788a4a310df3e47a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9e29ea237a646e788a4a310df3e47a7"}}, "title": "Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee.", "authors": [{"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Kapheim", "given": "Karen M", "initials": "KM"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal article", "published": "2019-10-01", "journal": {"volume": "36", "issn": "1537-1719", "issue": "10", "pages": "2277-2291", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Social insect genomes exhibit the highest rates of crossing over observed in plants and animals. The evolutionary causes of these extreme rates are unknown. Insight can be gained by comparing recombination rate variation across the genomes of related social and solitary insects. Here, we compare the genomic recombination landscape of the highly social honey bee, Apis mellifera, with the solitary alfalfa leafcutter bee, Megachile rotundata, by analyzing patterns of linkage disequilibrium in population-scale genome sequencing data. We infer that average recombination rates are extremely elevated in A. mellifera compared with M. rotundata. However, our results indicate that similar factors control the distribution of crossovers in the genomes of both species. Recombination rate is significantly reduced in coding regions in both species, with genes inferred to be germline methylated having particularly low rates. Genes with worker-biased patterns of expression in A. mellifera and their orthologs in M. rotundata have higher than average recombination rates in both species, suggesting that selection for higher diversity in genes involved in worker caste functions in social taxa is not the explanation for these elevated rates. Furthermore, we find no evidence that recombination has modulated the efficacy of selection among genes during bee evolution, which does not support the hypothesis that high recombination rates facilitated positive selection for new functions in social insects. Our results indicate that the evolution of sociality in insects likely entailed selection on modifiers that increased recombination rates genome wide, but that the genomic recombination landscape is determined by the same factors.", "doi": "10.1093/molbev/msz130", "pmid": "31143942", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "5505446"}], "notes": [], "created": "2020-01-08T16:47:18.422Z", "modified": "2020-01-21T13:56:16.309Z"}, {"entity": "publication", "iuid": "5bf650cb4a7f4b749b28c33ca56fdda5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5bf650cb4a7f4b749b28c33ca56fdda5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5bf650cb4a7f4b749b28c33ca56fdda5"}}, "title": "Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2019-10-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "10", "pages": "2875-2886", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.", "doi": "10.1093/gbe/evz212", "pmid": "31580421", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5580498"}, {"db": "pmc", "key": "PMC6795238"}], "notes": [], "created": "2019-12-02T17:20:06.547Z", "modified": "2024-01-16T13:48:43.736Z"}, {"entity": "publication", "iuid": "1480cd1fc76041efbf481e1e78910244", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1480cd1fc76041efbf481e1e78910244.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1480cd1fc76041efbf481e1e78910244"}}, "title": "High-definition spatial transcriptomics for in situ tissue profiling.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Eraslan", "given": "G\u00f6kcen", "initials": "G", "orcid": "0000-0001-9579-2909", "researcher": {"href": "https://publications.scilifelab.se/researcher/71e9cd3199cf4f1eaa0d1855332b6c48.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Klughammer", "given": "Johanna", "initials": "J", "orcid": "0000-0002-3628-9278", "researcher": {"href": "https://publications.scilifelab.se/researcher/333aaa1cbef442fc975ed9e75506f5ae.json"}}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4393e30947441519e7ab28fccb9bc3a.json"}}, {"family": "Schapiro", "given": "Denis", "initials": "D"}, {"family": "\u00c4ij\u00f6", "given": "Tarmo", "initials": "T", "orcid": "0000-0002-3008-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb8806f1f3464220b432068f535f8fa1.json"}}, {"family": "Bonneau", "given": "Richard", "initials": "R"}, {"family": "Bergenstr\u00e5hle", "given": "Ludvig", "initials": "L", "orcid": "0000-0002-5108-4481", "researcher": {"href": "https://publications.scilifelab.se/researcher/98234e5e06c241879f6f986ded3ab6f9.json"}}, {"family": "Navarro", "given": "Jos\u00e9 Fernand\u00e9z", "initials": "JF", "orcid": "0000-0002-4035-5258", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d0277bfd8b14cd996b4443998d8eff2.json"}}, {"family": "Gould", "given": "Joshua", "initials": "J", "orcid": "0000-0001-9581-5461", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7e6e620c1e0400589dc890aa8b5b693.json"}}, {"family": "Griffin", "given": "Gabriel K", "initials": "GK", "orcid": "0000-0002-4042-6757", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcad3f88b9b440d491198312d6ab44ab.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Ronaghi", "given": "Mostafa", "initials": "M"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Regev", "given": "Aviv", "initials": "A"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL", "orcid": "0000-0002-2207-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ea50cf03c6748c086846c3a28882979.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "16", "issn": "1548-7105", "issue": "10", "pages": "987-990", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-\u03bcm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.", "doi": "10.1038/s41592-019-0548-y", "pmid": "31501547", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41592-019-0548-y"}, {"db": "pmc", "key": "PMC6765407"}, {"db": "mid", "key": "NIHMS1536533"}], "notes": [], "created": "2019-12-02T16:50:31.747Z", "modified": "2024-01-16T13:48:43.751Z"}, {"entity": "publication", "iuid": "107f1491ed634c06952f61f4e99dc42b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/107f1491ed634c06952f61f4e99dc42b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/107f1491ed634c06952f61f4e99dc42b"}}, "title": "Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.", "authors": [{"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Warmuth", "given": "Vera M", "initials": "VM"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Aliabadian", "given": "Mansour", "initials": "M"}, {"family": "F\u00f6rschler", "given": "Marc", "initials": "M"}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Ewels", "given": "Phil", "initials": "P"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Schielzeth", "given": "Holger", "initials": "H"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Burri", "given": "Reto", "initials": "R"}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "139", "issn": "1095-9513", "issue": null, "pages": "106568", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.", "doi": "10.1016/j.ympev.2019.106568", "pmid": "31349102", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(19)30221-0"}], "notes": [], "created": "2019-12-02T17:22:51.880Z", "modified": "2024-01-16T13:48:43.760Z"}, {"entity": "publication", "iuid": "88ca69fe4ed541d0ad898f7f989c34b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88ca69fe4ed541d0ad898f7f989c34b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88ca69fe4ed541d0ad898f7f989c34b0"}}, "title": "Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.", "authors": [{"family": "Cappellini", "given": "Enrico", "initials": "E"}, {"family": "Welker", "given": "Frido", "initials": "F"}, {"family": "Pandolfi", "given": "Luca", "initials": "L"}, {"family": "Ramos-Madrigal", "given": "Jazm\u00edn", "initials": "J"}, {"family": "Samodova", "given": "Diana", "initials": "D"}, {"family": "R\u00fcther", "given": "Patrick L", "initials": "PL"}, {"family": "Fotakis", "given": "Anna K", "initials": "AK"}, {"family": "Lyon", "given": "David", "initials": "D"}, {"family": "Moreno-Mayar", "given": "J V\u00edctor", "initials": "JV"}, {"family": "Bukhsianidze", "given": "Maia", "initials": "M"}, {"family": "Rakownikow Jersie-Christensen", "given": "Rosa", "initials": "R"}, {"family": "Mackie", "given": "Meaghan", "initials": "M"}, {"family": "Ginolhac", "given": "Aur\u00e9lien", "initials": "A"}, {"family": "Ferring", "given": "Reid", "initials": "R"}, {"family": "Tappen", "given": "Martha", "initials": "M"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Dickinson", "given": "Marc R", "initials": "MR"}, {"family": "Stafford", "given": "Thomas W", "initials": "TW"}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Moodley", "given": "Yoshan", "initials": "Y"}, {"family": "Agusti", "given": "Jordi", "initials": "J"}, {"family": "Kahlke", "given": "Ralf-Dietrich", "initials": "RD"}, {"family": "Kiladze", "given": "Gocha", "initials": "G"}, {"family": "Mart\u00ednez-Navarro", "given": "Bienvenido", "initials": "B"}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Sandoval Velasco", "given": "Marcela", "initials": "M"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Kelstrup", "given": "Christian D", "initials": "CD"}, {"family": "Allentoft", "given": "Morten E", "initials": "ME"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Penkman", "given": "Kirsty", "initials": "K"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Rook", "given": "Lorenzo", "initials": "L"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Olsen", "given": "Jesper V", "initials": "JV"}, {"family": "Lordkipanidze", "given": "David", "initials": "D"}, {"family": "Willerslev", "given": "Eske", "initials": "E"}], "type": "historical article", "published": "2019-10-00", "journal": {"volume": "574", "issn": "1476-4687", "issue": "7776", "pages": "103-107", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.", "doi": "10.1038/s41586-019-1555-y", "pmid": "31511700", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-019-1555-y"}, {"db": "pmc", "key": "PMC6894936"}, {"db": "mid", "key": "EMS84015"}], "notes": [], "created": "2019-12-02T16:53:09.503Z", "modified": "2021-07-07T20:31:10.850Z"}, {"entity": "publication", "iuid": "e6a1e270d26b4a0ab8775ae1c8a28632", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6a1e270d26b4a0ab8775ae1c8a28632.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6a1e270d26b4a0ab8775ae1c8a28632"}}, "title": "Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.", "authors": [{"family": "Mesmar", "given": "Fahmi", "initials": "F"}, {"family": "Dai", "given": "Bingbing", "initials": "B"}, {"family": "Ibrahim", "given": "Ahmed", "initials": "A"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Jafferali", "given": "Mohammed Hakim", "initials": "MH"}, {"family": "Jose Augustine", "given": "Jithesh", "initials": "J"}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Kang", "given": "Ya'an", "initials": "Y"}, {"family": "Zhao", "given": "Yang", "initials": "Y"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Kim", "given": "Michael", "initials": "M"}, {"family": "Lin", "given": "Chin-Yo", "initials": "C"}, {"family": "Berkenstam", "given": "Anders", "initials": "A"}, {"family": "Fleming", "given": "Jason", "initials": "J"}, {"family": "Williams", "given": "Cecilia", "initials": "C"}], "type": "journal article", "published": "2019-09-30", "journal": {"volume": null, "issn": "2045-7634", "issue": null, "pages": null, "title": "Cancer Med", "issn-l": "2045-7634"}, "abstract": "Despite advances in cancer therapeutics, pancreatic cancer remains difficult to treat and often develops resistance to chemotherapies. We have evaluated a bioavailable genistein analogue, AXP107-11 which has completed phase Ib clinical trial, as an approach to sensitize tumor cells to chemotherapy. Using organotypic cultures of 14 patient-derived xenografts (PDX) of pancreatic ductal adenocarcinoma, we found that addition of AXP107-11 indeed sensitized 57% of cases to gemcitabine treatment. Results were validated using PDX models in vivo. Further, RNA-Seq from responsive and unresponsive tumors proposed a 41-gene treatment-predictive signature. Functional and molecular assays were performed in cell lines and demonstrated that the effect was synergistic. Transcriptome analysis indicated activation of G-protein-coupled estrogen receptor (GPER1) as the main underlying mechanism of action, which was corroborated using GPER1-selective agonists and antagonists. GPER1 expression in pancreatic tumors was indicative of survival, and our study proposes that activation of GPER1 may constitute a new avenue for pancreatic cancer therapeutics.", "doi": "10.1002/cam4.2581", "pmid": "31568691", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-02T17:20:33.691Z", "modified": "2024-01-16T13:48:43.797Z"}, {"entity": "publication", "iuid": "364977e412bd4a06b3b41e15769ebbf7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/364977e412bd4a06b3b41e15769ebbf7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/364977e412bd4a06b3b41e15769ebbf7"}}, "title": "Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Knapp", "given": "Michael", "initials": "M", "orcid": "0000-0002-0937-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b51a33edaea4bcf965b51daf13749c2.json"}}, {"family": "Kardailsky", "given": "Olga", "initials": "O"}, {"family": "Robertson", "given": "Bruce C", "initials": "BC", "orcid": "0000-0002-5348-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/765ee347a5f04b29b28a17f14f707231.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2019-09-27", "journal": {"volume": "15", "issn": "1744-957X", "issue": "9", "pages": "20190491", "title": "Biol. Lett.", "issn-l": "1744-9561"}, "abstract": "Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia (Heteralocha acutirostris) and South Island k\u014dkako (Callaeas cinereus). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island k\u014dkako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Ma\u014dri may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island k\u014dkako.", "doi": "10.1098/rsbl.2019.0491", "pmid": "31480938", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6769136"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4638131"}], "notes": [], "created": "2019-12-02T16:53:10.262Z", "modified": "2024-01-16T13:48:43.814Z"}, {"entity": "publication", "iuid": "798b7b8d4ca548f582ea788351fdd5ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/798b7b8d4ca548f582ea788351fdd5ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/798b7b8d4ca548f582ea788351fdd5ea"}}, "title": "Translational offsetting as a mode of estrogen receptor \u03b1-dependent regulation of gene expression.", "authors": [{"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Kusnadi", "given": "Eric P", "initials": "EP"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Rebello", "given": "Richard J", "initials": "RJ"}, {"family": "Leibovitch", "given": "Matthew", "initials": "M"}, {"family": "Ristau", "given": "Johannes", "initials": "J"}, {"family": "Chen", "given": "Shan", "initials": "S"}, {"family": "Lawrence", "given": "Mitchell G", "initials": "MG"}, {"family": "Szkop", "given": "Krzysztof J", "initials": "KJ"}, {"family": "Samreen", "given": "Baila", "initials": "B"}, {"family": "Balanathan", "given": "Preetika", "initials": "P"}, {"family": "Rapino", "given": "Francesca", "initials": "F"}, {"family": "Close", "given": "Pierre", "initials": "P"}, {"family": "Bukczynska", "given": "Patricia", "initials": "P"}, {"family": "Scharmann", "given": "Karin", "initials": "K"}, {"family": "Takizawa", "given": "Itsuhiro", "initials": "I"}, {"family": "Risbridger", "given": "Gail P", "initials": "GP"}, {"family": "Selth", "given": "Luke A", "initials": "LA"}, {"family": "Leidel", "given": "Sebastian A", "initials": "SA"}, {"family": "Lin", "given": "Qishan", "initials": "Q"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Furic", "given": "Luc", "initials": "L"}], "type": "journal article", "published": "2019-09-26", "journal": {"volume": null, "issn": "1460-2075", "issue": null, "pages": "e101323", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "Estrogen receptor alpha (ER\u03b1) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ER\u03b1 on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ER\u03b1 coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ER\u03b1 largely manifest as \"translational offsetting\" of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome association, are reduced following ER\u03b1 depletion lack features which limit translation efficiency including structured 5'UTRs and miRNA target sites. In contrast, mRNAs induced upon ER\u03b1 depletion whose polysome association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ER\u03b1 regulates levels of U34-modifying enzymes and thereby controls levels of U34-modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ER\u03b1-dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.", "doi": "10.15252/embj.2018101323", "pmid": "31556460", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "GEO", "key": "GSE120917"}, {"db": "GEO", "key": "GSE107590"}, {"db": "GEO", "key": "GSE117569"}, {"db": "GEO", "key": "GSE35428"}, {"db": "GEO", "key": "GSE104399"}, {"db": "GEO", "key": "GSE72249"}], "notes": [], "created": "2019-12-02T16:53:07.915Z", "modified": "2020-01-21T13:56:15.553Z"}, {"entity": "publication", "iuid": "4709badbd0ff4384bde2d08fb256b773", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4709badbd0ff4384bde2d08fb256b773.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4709badbd0ff4384bde2d08fb256b773"}}, "title": "Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.", "authors": [{"family": "Seyfferth", "given": "Carolin", "initials": "C"}, {"family": "Wessels", "given": "Bernard A", "initials": "BA"}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Love", "given": "Jonathan W", "initials": "JW"}, {"family": "R\u00fcggeberg", "given": "Markus", "initials": "M"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Vain", "given": "Thomas", "initials": "T"}, {"family": "Antos", "given": "Kamil", "initials": "K"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Felten", "given": "Judith", "initials": "J"}], "type": "journal article", "published": "2019-09-26", "journal": {"volume": "10", "issn": "1664-462X", "issue": null, "pages": "1101", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Tension wood (TW) in hybrid aspen trees forms on the upper side of displaced stems to generate a strain that leads to uplifting of the stem. TW is characterized by increased cambial growth, reduced vessel frequency and diameter, and the presence of gelatinous, cellulose-rich (G-)fibers with its microfibrils oriented parallel to the fiber cell axis. Knowledge remains limited about the molecular regulators required for the development of this special xylem tissue with its characteristic morphological, anatomical, and chemical features. In this study, we use transgenic, ethylene-insensitive (ETI) hybrid aspen trees together with time-lapse imaging to show that functional ethylene signaling is required for full uplifting of inclined stems. X-ray diffraction and Raman microspectroscopy of TW in ETI trees indicate that, although G-fibers form, the cellulose microfibril angle in the G-fiber S-layer is decreased, and the chemical composition of S- and G-layers is altered than in wild-type TW. The characteristic asymmetric growth and reduction of vessel density is suppressed during TW formation in ETI trees. A genome-wide transcriptome profiling reveals ethylene-dependent genes in TW, related to cell division, cell wall composition, vessel differentiation, microtubule orientation, and hormone crosstalk. Our results demonstrate that ethylene regulates transcriptional responses related to the amount of G-fiber formation and their properties (chemistry and cellulose microfibril angle) during TW formation. The quantitative and qualitative changes in G-fibers are likely to contribute to uplifting of stems that are displaced from their original position.", "doi": "10.3389/fpls.2019.01101", "pmid": "31611886", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6775489"}], "notes": [], "created": "2019-12-02T16:50:54.206Z", "modified": "2020-01-21T13:56:15.400Z"}, {"entity": "publication", "iuid": "cc8ef53f4f054306bc95e1504f86646c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc8ef53f4f054306bc95e1504f86646c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc8ef53f4f054306bc95e1504f86646c"}}, "title": "Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.", "authors": [{"family": "Masser", "given": "Anna E", "initials": "AE"}, {"family": "Kang", "given": "Wenjing", "initials": "W"}, {"family": "Roy", "given": "Joydeep", "initials": "J"}, {"family": "Mohanakrishnan Kaimal", "given": "Jayasankar", "initials": "J"}, {"family": "Quintana-Cordero", "given": "Jany", "initials": "J"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Andr\u00e9asson", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2019-09-25", "journal": {"volume": "8", "issn": "2050-084X", "issue": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "Hsf1 is an ancient transcription factor that responds to protein folding stress by inducing the heat-shock response (HSR) that restore perturbed proteostasis. Hsp70 chaperones negatively regulate the activity of Hsf1 via stress-responsive mechanisms that are poorly understood. Here, we have reconstituted budding yeast Hsf1-Hsp70 activation complexes and find that surplus Hsp70 inhibits Hsf1 DNA-binding activity. Hsp70 binds Hsf1 via its canonical substrate binding domain and Hsp70 regulates Hsf1 DNA-binding activity. During heat shock, Hsp70 is out-titrated by misfolded proteins derived from ongoing translation in the cytosol. Pushing the boundaries of the regulatory system unveils a genetic hyperstress program that is triggered by proteostasis collapse and involves an enlarged Hsf1 regulon. The findings demonstrate how an apparently simple chaperone-titration mechanism produces diversified transcriptional output in response to distinct stress loads.", "doi": "10.7554/eLife.47791", "pmid": "31552827", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "47791"}, {"db": "pmc", "key": "PMC6779467"}, {"db": "GEO", "key": "GSE78136"}], "notes": [], "created": "2019-12-02T17:19:37.154Z", "modified": "2024-01-16T13:48:43.822Z"}, {"entity": "publication", "iuid": "9cf391ad464e47f79d7b9e7f0c5c446b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cf391ad464e47f79d7b9e7f0c5c446b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cf391ad464e47f79d7b9e7f0c5c446b"}}, "title": "Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.", "authors": [{"family": "J\u00e4rviaho", "given": "Tekla", "initials": "T"}, {"family": "Bang", "given": "Benedicte", "initials": "B"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Moilanen", "given": "Jukka", "initials": "J"}, {"family": "M\u00f6tt\u00f6nen", "given": "Merja", "initials": "M"}, {"family": "Smith", "given": "C I Edvard", "initials": "CIE"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Niinim\u00e4ki", "given": "Riitta", "initials": "R"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "journal article", "published": "2019-09-24", "journal": {"volume": "3", "issn": "2473-9537", "issue": "18", "pages": "2722-2731", "title": "Blood Adv", "issn-l": "2473-9529"}, "abstract": "Pathogenic germline variants in \r\n                ETV6 have been associated with familial predisposition to thrombocytopenia and hematological malignancies, predominantly childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL). In addition, overrepresentation of a high hyperdiploid subtype and older age at diagnosis have been reported among sporadic BCP-ALL cases with germline variants in ETV6 We studied a family with 2 second-degree relatives who developed childhood high hyperdiploid BCP-ALL at ages 8 and 12 years, respectively. A constitutional balanced reciprocal translocation t(12;14)(p13.2;q23.1) was discovered in both patients by routine karyotyping at diagnosis and, subsequently, in 7 healthy family members who had not experienced hematological malignancies. No carriers had thrombocytopenia. Whole-genome sequencing confirmed the translocation, resulting in 2 actively transcribed but nonfunctional fusion genes, causing heterozygous loss and consequently monoallelic expression of ETV6 Whole-genome sequencing analysis of the affected female subjects' leukemia excluded additional somatic aberrations in ETV6 and RTN1 as well as shared somatic variants in other genes. Expression studies, performed to confirm decreased expression of ETV6, were not conclusive. We suggest that germline aberrations resulting in monoallelic expression of ETV6 contribute to leukemia susceptibility, whereas more severe functional deficiency of ETV6 is required for developing THC5. To our knowledge, this report is the first of a constitutional translocation disrupting ETV6 causing predisposition to childhood ALL.", "doi": "10.1182/bloodadvances.2018028795", "pmid": "31519648", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "bloodadvances.2018028795"}], "notes": [], "created": "2019-09-16T11:35:19.734Z", "modified": "2024-01-16T13:48:43.828Z"}, {"entity": "publication", "iuid": "4ef332e06ff64b6ba3af3338ba56cfe7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ef332e06ff64b6ba3af3338ba56cfe7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ef332e06ff64b6ba3af3338ba56cfe7"}}, "title": "Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186.", "authors": [{"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Shahsavani", "given": "Mansoureh", "initials": "M"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Breeuwsma", "given": "Nicole", "initials": "N"}, {"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Jin", "given": "Zhe", "initials": "Z"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "B"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Birnir", "given": "Bryndis", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Falk", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-09-24", "journal": {"volume": "10", "issn": "1664-8021", "issue": null, "pages": "896", "title": "Front Genet", "issn-l": "1664-8021"}, "abstract": "The etiology of hereditary ataxia syndromes is heterogeneous, and the mechanisms underlying these disorders are often unknown. Here, we utilized exome sequencing in two siblings with progressive ataxia and muscular weakness and identified a novel homozygous splice mutation (c.3020-1G > A) in neurofascin ( NFASC). In RNA extracted from fibroblasts, we showed that the mutation resulted in inframe skipping of exon 26, with a deprived expression of the full-length transcript that corresponds to NFASC isoform NF186. To further investigate the disease mechanisms, we reprogrammed fibroblasts from one affected sibling to induced pluripotent stem cells, directed them to neuroepithelial stem cells and finally differentiated to neurons. In early neurogenesis, differentiating cells with selective depletion of the NF186 isoform showed significantly reduced neurite outgrowth as well as fewer emerging neurites. Furthermore, whole-cell patch-clamp recordings of patient-derived neuronal cells revealed a lower threshold for openings, indicating altered Na+ channel kinetics, suggesting a lower threshold for openings as compared to neuronal cells without the NFASC mutation. Taken together, our results suggest that loss of the full-length NFASC isoform NF186 causes perturbed neurogenesis and impaired neuronal biophysical properties resulting in a novel early-onset autosomal recessive ataxia syndrome.", "doi": "10.3389/fgene.2019.00896", "pmid": "31608123", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6769111"}], "notes": [], "created": "2019-11-25T10:48:12.834Z", "modified": "2024-01-16T13:48:43.854Z"}, {"entity": "publication", "iuid": "07f2754f16ba4cc3b84e181f3e9f800b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07f2754f16ba4cc3b84e181f3e9f800b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07f2754f16ba4cc3b84e181f3e9f800b"}}, "title": "Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341.", "authors": [{"family": "Nilsson", "given": "E", "initials": "E"}, {"family": "Li", "given": "K", "initials": "K"}, {"family": "Fridlund", "given": "J", "initials": "J"}, {"family": "\u0160ul\u010dius", "given": "S", "initials": "S"}, {"family": "Bunse", "given": "C", "initials": "C"}, {"family": "Karlsson", "given": "C M G", "initials": "CMG"}, {"family": "Lindh", "given": "M", "initials": "M"}, {"family": "Lundin", "given": "D", "initials": "D"}, {"family": "Pinhassi", "given": "J", "initials": "J"}, {"family": "Holmfeldt", "given": "K", "initials": "K"}], "type": "journal article", "published": "2019-09-15", "journal": {"volume": "85", "issn": "1098-5336", "issue": "18", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Knowledge in aquatic virology has been greatly improved by culture-independent methods, yet there is still a critical need for isolating novel phages to identify the large proportion of \"unknowns\" that dominate metagenomes and for detailed analyses of phage-host interactions. Here, 54 phages infecting Rheinheimera sp. strain BAL341 (Gammaproteobacteria) were isolated from Baltic Sea seawater and characterized through genome content analysis and comparative genomics. The phages showed a myovirus-like morphology and belonged to a novel genus, for which we propose the name Barbavirus All phages had similar genome sizes and numbers of genes (80 to 84 kb; 134 to 145 genes), and based on average nucleotide identity and genome BLAST distance phylogeny, the phages were divided into five species. The phages possessed several genes involved in metabolic processes and host signaling, such as genes encoding ribonucleotide reductase and thymidylate synthase, phoH, and mazG One species had additional metabolic genes involved in pyridine nucleotide salvage, possibly providing a fitness advantage by further increasing the phages' replication efficiency. Recruitment of viral metagenomic reads (25 Baltic Sea viral metagenomes from 2012 to 2015) to the phage genomes showed pronounced seasonal variations, with increased relative abundances of barba phages in August and September synchronized with peaks in host abundances, as shown by 16S rRNA gene amplicon sequencing. Overall, this study provides detailed information regarding genetic diversity, phage-host interactions, and temporal dynamics of an ecologically important aquatic phage-host system.IMPORTANCE Phages are important in aquatic ecosystems as they influence their microbial hosts through lysis, gene transfer, transcriptional regulation, and expression of phage metabolic genes. Still, there is limited knowledge of how phages interact with their hosts, especially at fine scales. Here, a Rheinheimera phage-host system constituting highly similar phages infecting one host strain is presented. This relatively limited diversity has previously been seen only when smaller numbers of phages have been isolated and points toward ecological constraints affecting the Rheinheimera phage diversity. The variation of metabolic genes among the species points toward various fitness advantages, opening up possibilities for future hypothesis testing. Phage-host dynamics monitored over several years point toward recurring \"kill-the-winner\" oscillations and an ecological niche fulfilled by this system in the Baltic Sea. Identifying and quantifying ecological dynamics of such phage-host model systems in situ allow us to understand and study the influence of phages on aquatic ecosystems.", "doi": "10.1128/AEM.01003-19", "pmid": "31324626", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "AEM.01003-19"}, {"db": "pmc", "key": "PMC6715854"}], "notes": [], "created": "2019-12-02T16:50:57.126Z", "modified": "2024-01-16T13:48:43.878Z"}, {"entity": "publication", "iuid": "b3dbc0d472f941ad813234e064e3b453", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b3dbc0d472f941ad813234e064e3b453.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b3dbc0d472f941ad813234e064e3b453"}}, "title": "A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection.", "authors": [{"family": "Poux", "given": "Candice", "initials": "C"}, {"family": "Dondalska", "given": "Aleksandra", "initials": "A"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "P\u00e5lsson", "given": "Sandra", "initials": "S"}, {"family": "Contreras", "given": "Vanessa", "initials": "V"}, {"family": "Arasa", "given": "Claudia", "initials": "C"}, {"family": "J\u00e4rver", "given": "Peter", "initials": "P"}, {"family": "Albert", "given": "Jan", "initials": "J"}, {"family": "Busse", "given": "David C", "initials": "DC"}, {"family": "LeGrand", "given": "Roger", "initials": "R"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Tregoning", "given": "John S", "initials": "JS"}, {"family": "Spetz", "given": "Anna-Lena", "initials": "AL"}], "type": "journal article", "published": "2019-09-12", "journal": {"volume": "10", "issn": "1664-3224", "issue": null, "pages": "2161", "title": "Front Immunol", "issn-l": "1664-3224"}, "abstract": "The initiation of an immune response is dependent on the activation and maturation of dendritic cells after sensing pathogen associated molecular patterns by pattern recognition receptors. However, the response needs to be balanced as excessive pro-inflammatory cytokine production in response to viral or stress-induced pattern recognition receptor signaling has been associated with severe influenza A virus (IAV) infection. Here, we use an inhibitor of Toll-like receptor (TLR)3, a single-stranded oligonucleotide (ssON) with the capacity to inhibit certain endocytic routes, or a TLR3 agonist (synthetic double-stranded RNA PolyI:C), to evaluate modulation of innate responses during H1N1 IAV infection. Since IAV utilizes cellular endocytic machinery for viral entry, we also assessed ssON's capacity to affect IAV infection. We first show that IAV infected human monocyte-derived dendritic cells (MoDC) were unable to up-regulate the co-stimulatory molecules CD80 and CD86 required for T cell activation. Exogenous TLR3 stimulation did not overcome the IAV-mediated inhibition of co-stimulatory molecule expression in MoDC. However, TLR3 stimulation using PolyI:C led to an augmented pro-inflammatory cytokine response. We reveal that ssON effectively inhibited PolyI:C-mediated pro-inflammatory cytokine production in MoDC, notably, ssON treatment maintained an interferon response induced by IAV infection. Accordingly, RNAseq analyses revealed robust up-regulation of interferon-stimulated genes in IAV cultures treated with ssON. We next measured reduced IAV production in MoDC treated with ssON and found a length requirement for its anti-viral activity, which overlapped with its capacity to inhibit uptake of PolyI:C. Hence, in cases wherein an overreacting TLR3 activation contributes to IAV pathogenesis, ssON can reduce this signaling pathway. Furthermore, concomitant treatment with ssON and IAV infection in mice resulted in maintained weight and reduced viral load in the lungs. Therefore, extracellular ssON provides a mechanism for immune regulation of TLR3-mediated responses and suppression of IAV infection in vitro and in vivo in mice.", "doi": "10.3389/fimmu.2019.02161", "pmid": "31572376", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6751283"}], "notes": [], "created": "2019-12-02T16:50:30.980Z", "modified": "2021-07-08T13:26:08.297Z"}, {"entity": "publication", "iuid": "491ea2e58f9b43aab2ff3c4ae660f809", "links": {"self": {"href": "https://publications.scilifelab.se/publication/491ea2e58f9b43aab2ff3c4ae660f809.json"}, "display": {"href": "https://publications.scilifelab.se/publication/491ea2e58f9b43aab2ff3c4ae660f809"}}, "title": "Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status.", "authors": [{"family": "Das", "given": "Ishani", "initials": "I"}, {"family": "Wilhelm", "given": "Margareta", "initials": "M"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "Franco Marquez", "given": "Rodolfo", "initials": "R"}, {"family": "Costa Svedman", "given": "Fernanda", "initials": "F"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Egyh\u00e0zi Brage", "given": "Suzanne", "initials": "S"}], "type": "journal article", "published": "2019-09-10", "journal": {"volume": "10", "issn": "2041-4889", "issue": "9", "pages": "663", "title": "Cell Death Dis", "issn-l": "2041-4889"}, "abstract": "Current treatment modalities for disseminated cutaneous malignant melanoma (CMM) improve survival; however, relapses are common. A number of receptor tyrosine kinases (RTKs) including EGFR and MET have been reported to be involved in CMM metastasis and in the development of resistance to therapy, targeting the mitogen-activated protein kinase (MAPK pathway). IHC analysis showed that patients with higher MET protein expression had a significantly shorter overall survival. In addition, silencing of MET caused an upregulation of EGFR and p-AKT, which was abrogated by concomitant silencing of MET and EGFR in CMM cells resistant to MAPK-targeting drugs. We therefore explored novel treatment strategies using clinically approved drugs afatinib (ERBB family inhibitor) and crizotinib (MET inhibitor), to simultaneously block MET and ERBB family RTKs. The effects of the combination were assessed in cell culture and spheroid models using established CMM and patient-derived short-term cell lines, and an in vivo xenograft mouse model. The combination had a synergistic effect, promoting cell death, concomitant with a potent downregulation of migratory and invasive capacity independent of their BRAF/NRAS mutational status. Furthermore, the combination attenuated tumor growth rate, as ascertained by the significant reduction of Ki67 expression and induced DNA damage in vivo. Importantly, this combination therapy had minimal therapy-related toxicity in mice. Lastly, the cell cycle G2 checkpoint kinase WEE1 and the RTK IGF1R, non-canonical targets, were altered upon exposure to the combination. Knockdown of WEE1 abrogated the combination-mediated effects on cell migration and proliferation in BRAF mutant BRAF inhibitor-sensitive cells, whereas WEE1 silencing alone inhibited cell migration in NRAS mutant cells. In summary, our results show that afatinib and crizotinib in combination is a promising alternative targeted therapy option for CMM patients, irrespective of BRAF/NRAS mutational status, as well as for cases where resistance has developed towards BRAF inhibitors.", "doi": "10.1038/s41419-019-1875-8", "pmid": "31506424", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41419-019-1875-8"}, {"db": "pmc", "key": "PMC6737096"}], "notes": [], "created": "2019-09-24T12:55:08.033Z", "modified": "2020-01-21T13:56:16.409Z"}, {"entity": "publication", "iuid": "c3ecd75f65d14557b9a425f70937c824", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3ecd75f65d14557b9a425f70937c824.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3ecd75f65d14557b9a425f70937c824"}}, "title": "Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.", "authors": [{"family": "Pederson", "given": "Eric R A", "initials": "ERA"}, {"family": "Warshan", "given": "Denis", "initials": "D"}, {"family": "Rasmussen", "given": "Ulla", "initials": "U"}], "type": "journal article", "published": "2019-09-04", "journal": {"volume": "9", "issn": "2160-1836", "issue": "9", "pages": "2791-2797", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "The pleurocarpous feather moss Pleurozium schreberi is a ubiquitous moss species which plays a fundamental role in many terrestrial ecosystems, for instance within the boreal forest, the Earth's largest terrestrial biome, this species plays a significant role in driving ecosystem nitrogen and carbon inputs and fluxes. By hosting dinitrogen (N2)-fixing cyanobacteria, the moss-cyanobacteria symbiosis constitutes the main nitrogen input into the ecosystem and by the high productivity and the low decomposability of the moss litter, Pschreberi contributes significantly to build-up soil organic matter, and therefore long-term C sequestration. Knowledge on P. schreberi genome will facilitate the development of 'omics' and system's biology approaches to gain a more complete understanding of the physiology and ecological adaptation of the moss and the mechanisms underpinning the establishment of the symbiosis. Here we present the de novo assembly and annotation of P. schreberi genome that will help investigating these questions. The sequencing was performed using the HiSeq X platform with Illumina paired-end and mate-pair libraries prepared with CTAB extracted DNA. In total, the assembled genome was approximately 318 Mb, while repetitive elements account for 28.42% of the genome and 15,992 protein-coding genes were predicted from the genome, of which 84.23% have been functionally annotated. We anticipate that the genomic data generated will constitute a significant resource to study ecological and evolutionary genomics of P. schreberi, and will be valuable for evo-devo investigations as well as our understanding of the evolution of land plants by providing the genome of a pleurocarpous moss.", "doi": "10.1534/g3.119.400279", "pmid": "31285273", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.119.400279"}, {"db": "pmc", "key": "PMC6723128"}, {"db": "figshare", "key": "10.6084/m9.figshare.7775951"}], "notes": [], "created": "2019-12-02T17:20:52.764Z", "modified": "2020-01-21T13:56:17.674Z"}, {"entity": "publication", "iuid": "23c6366116a74e7aa39971ef231b62b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23c6366116a74e7aa39971ef231b62b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23c6366116a74e7aa39971ef231b62b0"}}, "title": "Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.", "authors": [{"family": "H\u00f6\u00f6k", "given": "Lars", "initials": "L"}, {"family": "Leal", "given": "Luis", "initials": "L"}, {"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "9", "pages": "2633-2652", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "In species with genetic sex determination, dosage compensation can evolve to equal expression levels of sex-linked and autosomal genes. Current knowledge about dosage compensation has mainly been derived from male-heterogametic (XX/XY) model organisms, whereas less is understood about the process in female-heterogametic systems (ZZ/ZW). In moths and butterflies, downregulation of Z-linked expression in males (ZZ) to match the expression level in females (ZW) is often observed. However, little is known about the underlying regulatory mechanisms, or if dosage compensation patterns vary across ontogenetic stages. In this study, we assessed dynamics of Z-linked and autosomal expression levels across developmental stages in the wood white (Leptidea sinapis). We found that although expression of Z-linked genes in general was reduced compared with autosomal genes, dosage compensation was actually complete for some categories of genes, in particular sex-biased genes, but equalization in females was constrained to a narrower gene set. We also observed a noticeable convergence in Z-linked expression between males and females after correcting for sex-biased genes. Sex-biased expression increased successively across developmental stages, and male-biased genes were enriched on the Z-chromosome. Finally, all five core genes associated with the ribonucleoprotein dosage compensation complex male-specific lethal were detected in adult females, in correspondence with a reduction in the expression difference between autosomes and the single Z-chromosome. We show that tuning of gene dosage is multilayered in Lepidoptera and argue that expression balance across chromosomal classes may predominantly be driven by enrichment of male-biased genes on the Z-chromosome and cooption of available dosage regulators.", "doi": "10.1093/gbe/evz176", "pmid": "31400207", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5545957"}, {"db": "pmc", "key": "PMC6761951"}], "notes": [], "created": "2019-12-02T17:20:07.341Z", "modified": "2024-01-16T13:48:43.918Z"}, {"entity": "publication", "iuid": "ad7e8afe165f4fd99bfc66e5e703cfa8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad7e8afe165f4fd99bfc66e5e703cfa8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad7e8afe165f4fd99bfc66e5e703cfa8"}}, "title": "Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.", "authors": [{"family": "Happel", "given": "Elisabeth M", "initials": "EM"}, {"family": "Markussen", "given": "Trine", "initials": "T"}, {"family": "Teikari", "given": "Jonna E", "initials": "JE"}, {"family": "Huchaiah", "given": "Vimala", "initials": "V"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Sivonen", "given": "Kaarina", "initials": "K"}, {"family": "Middelboe", "given": "Mathias", "initials": "M"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "95", "issn": "1574-6941", "issue": "9", "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": "Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.", "doi": "10.1093/femsec/fiz123", "pmid": "31397876", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "5545591"}], "notes": [], "created": "2020-01-08T16:47:41.318Z", "modified": "2020-01-21T13:56:16.366Z"}, {"entity": "publication", "iuid": "7c3a03180e554fe084cc0db9a6737b7c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c3a03180e554fe084cc0db9a6737b7c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c3a03180e554fe084cc0db9a6737b7c"}}, "title": "Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.", "authors": [{"family": "Morais", "given": "Erica B", "initials": "EB"}, {"family": "Sch\u00f6nenberger", "given": "J\u00fcrg", "initials": "J"}, {"family": "Conti", "given": "Elena", "initials": "E"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}, {"family": "Sz\u00f6v\u00e9nyi", "given": "P\u00e9ter", "initials": "P"}], "type": "journal article", "published": "2019-09-00", "journal": {"volume": "7", "issn": "2168-0450", "issue": "9", "pages": "e11290", "title": "Appl Plant Sci", "issn-l": "2168-0450"}, "abstract": "Information on orthologous groups of genes, their sequence variability, and annotation is required for project design in phylogenetic reconstruction. This resource is unavailable for the flowering plant family Acanthaceae (>4000 species).\n\nWe compared transcriptome sequences spanning the extant diversity of Acanthaceae in order to provide a set of orthologous low-copy nuclear genes and assess their utility for reconstructing phylogenetic relationships within this group of plants.\n\nWe present new transcriptome assemblies for eight species representing all major clades of Acanthaceae. The assemblies of five of these species are entirely based on new sequence data. Of these five species, three are from subfamilies for which no genomic resources were previously available (Nelsonioideae and Thunbergioideae). These five new transcriptomes are more complete than all others from public databases. Furthermore, we provide alignments with sequence information, annotation, and statistics for potential phylogenetic utility of 1619 orthologous low-copy nuclear markers.\n\nOur method of inferring assemblies from multiple pooled tissue samples delivers more complete transcriptomes than any available ones from Acanthaceae. We make available to the community new resources (e.g., sequence information, variability, and annotation of orthologous low-copy nuclear genes) that will help phylogenetic reconstruction in Acanthaceae.", "doi": "10.1002/aps3.11290", "pmid": "31572631", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "APS311290"}, {"db": "pmc", "key": "PMC6764435"}], "notes": [], "created": "2020-01-08T16:48:15.613Z", "modified": "2020-01-21T13:56:16.436Z"}, {"entity": "publication", "iuid": "d05046c85a1e4f1ca7defccbb1420945", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d05046c85a1e4f1ca7defccbb1420945.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d05046c85a1e4f1ca7defccbb1420945"}}, "title": "Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.", "authors": [{"family": "Karlsson", "given": "Christofer M G", "initials": "CMG"}, {"family": "Cerro-G\u00e1lvez", "given": "Elena", "initials": "E"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Karlsson", "given": "Camilla", "initials": "C"}, {"family": "Vila-Costa", "given": "Maria", "initials": "M"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2019-09-00", "journal": {"volume": "12", "issn": "1751-7915", "issue": "5", "pages": "892-906", "title": "Microb Biotechnol", "issn-l": "1751-7915"}, "abstract": "Organic pollutants (OPs) are critically toxic, bioaccumulative and globally widespread. Moreover, several OPs negatively influence aquatic wildlife. Although bacteria are major drivers of the ocean carbon cycle and the turnover of vital elements, there is limited knowledge of OP effects on heterotrophic bacterioplankton. We therefore investigated growth and gene expression responses of the Baltic Sea model bacterium Rheinheimera sp. BAL341 to environmentally relevant concentrations of distinct classes of OPs in 2-h incubation experiments. During exponential growth, exposure to a mix of polycyclic aromatic hydrocarbons, alkanes and organophosphate esters (denoted MIX) resulted in a significant decrease (between 9% and 18%) in bacterial abundance and production compared with controls. In contrast, combined exposure to perfluorooctanesulfonic acids and perfluorooctanoic acids (denoted PFAS) had no significant effect on growth. Nevertheless, MIX and PFAS exposures both induced significant shifts in gene expression profiles compared with controls in exponential growth. This involved several functional metabolism categories (e.g. stress response and fatty acids metabolism), some of which were pollutant-specific (e.g. phosphate acquisition and alkane-1 monooxygenase genes). In stationary phase, only two genes in the MIX treatment were significantly differentially expressed. The substantial direct influence of OPs on metabolism during bacterial growth suggests that widespread OPs could severely alter biogeochemical processes governed by bacterioplankton.", "doi": "10.1111/1751-7915.13441", "pmid": "31270938", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6680617"}, {"db": "GENBANK", "key": "KM586890"}], "notes": [], "created": "2019-12-02T16:52:24.485Z", "modified": "2024-01-16T13:48:43.965Z"}, {"entity": "publication", "iuid": "2a5e3e148f1049dbb785459de68467cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a5e3e148f1049dbb785459de68467cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a5e3e148f1049dbb785459de68467cd"}}, "title": "MiDRM pol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors.", "authors": [{"family": "Aralaguppe", "given": "Shambhu G", "initials": "SG"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Ashokkumar", "given": "Manickam", "initials": "M"}, {"family": "Kumar", "given": "Milner M", "initials": "MM"}, {"family": "Hanna", "given": "Luke Elizabeth", "initials": "LE"}, {"family": "Amogne", "given": "Wondwossen", "initials": "W"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U"}], "type": "journal article", "published": "2019-08-30", "journal": {"volume": "11", "issn": "1999-4915", "issue": "9", "title": "Viruses", "issn-l": "1999-4915"}, "abstract": "The detection of drug resistance mutations (DRMs) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high-throughput sequencing (HTS) data lack at most diagnostic laboratories. Thus, we have proposed a new pipeline, MiDRM pol, to quantify DRM from the HIV-1 pol region. The gag-vpu region of 87 plasma samples from HIV-infected individuals from three cohorts was amplified and sequenced by Illumina HiSeq2500. The sequence reads were adapter-trimmed, followed by analysis using in-house scripts. Samples from Swedish and Ethiopian cohorts were also sequenced by Sanger sequencing. The pipeline was validated against the online tool PASeq (Polymorphism Analysis by Sequencing). Based on an error rate of <1%, a value of >1% was set as reliable to consider a minor variant. Both pipelines detected the mutations in the dominant viral populations, while discrepancies were observed in minor viral populations. In five HIV-1 subtype C samples, minor mutations were detected at the <5% level by MiDRMpol but not by PASeq. MiDRMpol is a computationally as well as labor efficient bioinformatics pipeline for the detection of DRM from HTS data. It identifies minor viral populations (<20%) of DRMs. Our method can be incorporated into large-scale surveillance of HIV-1 DRM.", "doi": "10.3390/v11090806", "pmid": "31480341", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "v11090806"}, {"db": "pmc", "key": "PMC6784143"}], "notes": [], "created": "2020-01-08T16:47:44.108Z", "modified": "2020-01-21T13:56:16.401Z"}, {"entity": "publication", "iuid": "283a394561d1464badcf897ff572100c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/283a394561d1464badcf897ff572100c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/283a394561d1464badcf897ff572100c"}}, "title": "DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology.", "authors": [{"family": "L\u00e1zaro-Ib\u00e1\u00f1ez", "given": "Elisa", "initials": "E"}, {"family": "L\u00e4sser", "given": "Cecilia", "initials": "C"}, {"family": "Shelke", "given": "Ganesh Vilas", "initials": "GV"}, {"family": "Crescitelli", "given": "Rossella", "initials": "R"}, {"family": "Jang", "given": "Su Chul", "initials": "SC"}, {"family": "Cvjetkovic", "given": "Aleksander", "initials": "A"}, {"family": "Garc\u00eda-Rodr\u00edguez", "given": "Ana\u00eds", "initials": "A"}, {"family": "L\u00f6tvall", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2019-08-27", "journal": {"volume": "8", "issn": "2001-3078", "issue": "1", "pages": "1656993", "title": "J Extracell Vesicles", "issn-l": "2001-3078"}, "abstract": "Extracellular vesicles have the capacity to transfer lipids, proteins, and nucleic acids between cells, thereby influencing the recipient cell's phenotype. While the role of RNAs in EVs has been extensively studied, the function of DNA remains elusive. Here, we distinguished novel heterogeneous subpopulations of small extracellular vesicles (sEVs) based on their DNA content and topology. Low- and high-density sEV subsets from a human mast cell line (HMC-1) and an erythroleukemic cell line (TF-1) were separated using high-resolution iodixanol density gradients to discriminate the nature of the DNA cargo of the sEVs. Paired comparisons of the sEV-associated DNA and RNA molecules showed that RNA was more abundant than DNA and that most of the DNA was present in the high-density fractions, demonstrating that sEV subpopulations have different DNA content. DNA was predominately localised on the outside or surface of sEVs, with only a small portion being protected from enzymatic degradation. Whole-genome sequencing identified DNA fragments spanning all chromosomes and mitochondrial DNA when sEVs were analysed in bulk. Our work contributes to the understanding of how DNA is associated with sEVs and thus provides direction for distinguishing subtypes of EVs based on their DNA cargo and topology.", "doi": "10.1080/20013078.2019.1656993", "pmid": "31497265", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "1656993"}, {"db": "pmc", "key": "PMC6719264"}], "notes": [], "created": "2019-12-02T17:20:34.874Z", "modified": "2021-05-24T15:37:29.263Z"}, {"entity": "publication", "iuid": "03e1d400d72c4ecdb3a49ed132d7ef7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03e1d400d72c4ecdb3a49ed132d7ef7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03e1d400d72c4ecdb3a49ed132d7ef7a"}}, "title": "Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.", "authors": [{"family": "Marquardt", "given": "Nicole", "initials": "N"}, {"family": "Kek\u00e4l\u00e4inen", "given": "Eliisa", "initials": "E"}, {"family": "Chen", "given": "Puran", "initials": "P"}, {"family": "Lourda", "given": "Magda", "initials": "M"}, {"family": "Wilson", "given": "Jennifer N", "initials": "JN"}, {"family": "Scharenberg", "given": "Marlena", "initials": "M"}, {"family": "Bergman", "given": "Per", "initials": "P"}, {"family": "Al-Ameri", "given": "Mamdoh", "initials": "M"}, {"family": "H\u00e5rd", "given": "Joanna", "initials": "J"}, {"family": "Mold", "given": "Jeffrey E", "initials": "JE"}, {"family": "Ljunggren", "given": "Hans-Gustaf", "initials": "HG"}, {"family": "Micha\u00eblsson", "given": "Jakob", "initials": "J"}], "type": "journal article", "published": "2019-08-26", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3841", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Human lung tissue-resident NK cells (trNK cells) are likely to play an important role in host responses towards viral infections, inflammatory conditions and cancer. However, detailed insights into these cells are still largely lacking. Here we show, using RNA sequencing and flow cytometry-based analyses, that subsets of human lung CD69 +CD16- NK cells display hallmarks of tissue-residency, including high expression of CD49a, CD103, and ZNF683, and reduced expression of SELL, S1PR5, and KLF2/3. CD49a+CD16- NK cells are functionally competent, and produce IFN-\u03b3, TNF, MIP-1\u03b2, and GM-CSF. After stimulation with IL-15, they upregulate perforin, granzyme B, and Ki67 to a similar degree as CD49a-CD16- NK cells. Comparing datasets from trNK cells in human lung and bone marrow with tissue-resident memory CD8+ T cells identifies core genes co-regulated either by tissue-residency, cell-type or location. Together, our data indicate that human lung trNK cells have distinct features, likely regulating their function in barrier immunity.", "doi": "10.1038/s41467-019-11632-9", "pmid": "31451696", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11632-9"}, {"db": "pmc", "key": "PMC6710242"}], "notes": [], "created": "2019-12-02T16:52:30.576Z", "modified": "2020-01-21T13:56:15.499Z"}, {"entity": "publication", "iuid": "ddacb29df4184d21903954634a557d81", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddacb29df4184d21903954634a557d81.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddacb29df4184d21903954634a557d81"}}, "title": "Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.", "authors": [{"family": "Fernandes", "given": "Sunjay Jude", "initials": "SJ"}, {"family": "Morikawa", "given": "Hiromasa", "initials": "H"}, {"family": "Ewing", "given": "Ewoud", "initials": "E"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Joshi", "given": "Rubin Narayan", "initials": "RN"}, {"family": "Lagani", "given": "Vincenzo", "initials": "V"}, {"family": "Karathanasis", "given": "Nestoras", "initials": "N"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Planell", "given": "Nuria", "initials": "N"}, {"family": "Schmidt", "given": "Angelika", "initials": "A"}, {"family": "Tsamardinos", "given": "Ioannis", "initials": "I"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}], "type": "journal article", "published": "2019-08-19", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "11996", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Multiple Sclerosis (MS) is an autoimmune disease of the central nervous system with prominent neurodegenerative components. The triggering and progression of MS is associated with transcriptional and epigenetic alterations in several tissues, including peripheral blood. The combined influence of transcriptional and epigenetic changes associated with MS has not been assessed in the same individuals. Here we generated paired transcriptomic (RNA-seq) and DNA methylation (Illumina 450 K array) profiles of CD4+ and CD8+ T cells (CD4, CD8), using clinically accessible blood from healthy donors and MS patients in the initial relapsing-remitting and subsequent secondary-progressive stage. By integrating the output of a differential expression test with a permutation-based non-parametric combination methodology, we identified 149 differentially expressed (DE) genes in both CD4 and CD8 cells collected from MS patients. Moreover, by leveraging the methylation-dependent regulation of gene expression, we identified the gene SH3YL1, which displayed significant correlated expression and methylation changes in MS patients. Importantly, silencing of SH3YL1 in primary human CD4 cells demonstrated its influence on T cell activation. Collectively, our strategy based on paired sampling of several cell-types provides a novel approach to increase sensitivity for identifying shared mechanisms altered in CD4 and CD8 cells of relevance in MS in small sized clinical materials.", "doi": "10.1038/s41598-019-48493-7", "pmid": "31427643", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-48493-7"}, {"db": "pmc", "key": "PMC6700160"}], "notes": [], "created": "2020-01-08T16:47:42.719Z", "modified": "2020-01-21T13:56:16.382Z"}, {"entity": "publication", "iuid": "51496652ca9c45089d691dd80150a288", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51496652ca9c45089d691dd80150a288.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51496652ca9c45089d691dd80150a288"}}, "title": "Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2019-08-13", "journal": {"volume": "10", "issn": "2150-7511", "issue": "4", "title": "MBio", "issn-l": null}, "abstract": "Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two \"modern marine\" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic \"thoroughly mixed\" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or \"geogases.\"IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.", "doi": "10.1128/mBio.01470-19", "pmid": "31409677", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "mBio.01470-19"}, {"db": "pmc", "key": "PMC6692508"}], "notes": [], "created": "2020-01-08T16:47:42.034Z", "modified": "2020-01-21T13:56:16.374Z"}, {"entity": "publication", "iuid": "4c24079e980f4d5a92a0cefe7b18f5ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c24079e980f4d5a92a0cefe7b18f5ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c24079e980f4d5a92a0cefe7b18f5ef"}}, "title": "PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.", "authors": [{"family": "Costa", "given": "T\u00e2nia D F", "initials": "TDF"}, {"family": "Zhuang", "given": "Ting", "initials": "T"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Turco", "given": "Emilia", "initials": "E"}, {"family": "Olofsson", "given": "Helene", "initials": "H"}, {"family": "Masia-Balague", "given": "Miriam", "initials": "M"}, {"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Rabieifar", "given": "Parisa", "initials": "P"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "Kuiper", "given": "Raoul", "initials": "R"}, {"family": "Sj\u00f6lund", "given": "Jonas", "initials": "J"}, {"family": "Spiess", "given": "Matthias", "initials": "M"}, {"family": "Hern\u00e1ndez-Varas", "given": "Pablo", "initials": "P"}, {"family": "Rabenhorst", "given": "Uta", "initials": "U"}, {"family": "Roswall", "given": "Pernilla", "initials": "P"}, {"family": "Ma", "given": "Ran", "initials": "R"}, {"family": "Gong", "given": "Xiaowei", "initials": "X"}, {"family": "Hartman", "given": "Johan", "initials": "J"}, {"family": "Pietras", "given": "Kristian", "initials": "K"}, {"family": "Adams", "given": "Peter D", "initials": "PD"}, {"family": "Defilippi", "given": "Paola", "initials": "P"}, {"family": "Str\u00f6mblad", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2019-08-09", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "3589", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Overcoming cellular growth restriction, including the evasion of cellular senescence, is a hallmark of cancer. We report that PAK4 is overexpressed in all human breast cancer subtypes and associated with poor patient outcome. In mice, MMTV-PAK4 overexpression promotes spontaneous mammary cancer, while PAK4 gene depletion delays MMTV-PyMT driven tumors. Importantly, PAK4 prevents senescence-like growth arrest in breast cancer cells in vitro, in vivo and ex vivo, but is not needed in non-immortalized cells, while PAK4 overexpression in untransformed human mammary epithelial cells abrogates H-RAS-V12-induced senescence. Mechanistically, a PAK4 - RELB - C/EBP\u03b2 axis controls the senescence-like growth arrest and a PAK4 phosphorylation residue (RELB-Ser151) is critical for RELB-DNA interaction, transcriptional activity and expression of the senescence regulator C/EBP\u03b2. These findings establish PAK4 as a promoter of breast cancer that can overcome oncogene-induced senescence and reveal a selective vulnerability of cancer to PAK4 inhibition.", "doi": "10.1038/s41467-019-11510-4", "pmid": "31399573", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-11510-4"}, {"db": "pmc", "key": "PMC6689091"}], "notes": [], "created": "2019-12-02T16:53:04.441Z", "modified": "2020-01-21T13:56:15.526Z"}, {"entity": "publication", "iuid": "e63038cec18447a5b11525315a03bc11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e63038cec18447a5b11525315a03bc11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e63038cec18447a5b11525315a03bc11"}}, "title": "Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal-article", "published": "2019-08-08", "journal": {"volume": "28", "issn": "0962-1083", "issue": "6", "pages": "3756-3770", "title": "Mol Ecol", "issn-l": "0962-1083"}, "abstract": "Genome scans in recently separated species can inform on molecular mechanisms and evolutionary processes driving divergence. Large-scale polymorphism data from multiple species pairs are also key to investigate the repeatability of divergence-whether radiations tend to show parallel responses to similar selection pressures and/or underlying molecular forces. Here, we used whole-genome resequencing data from six wood white (Leptidea sp.) butterfly populations, representing three closely related species with karyomorph variation, to infer the species' demographic history and characterize patterns of genomic diversity and differentiation. The analyses supported previously established species relationships, and there was no evidence for postdivergence gene flow. We identified significant intraspecific genetic structure, in particular between karyomorph extremes in the wood white (L. sinapis)-a species with a remarkable chromosome number cline across the distribution range. The genomic landscapes of differentiation were erratic, and outlier regions were narrow and dispersed. Highly differentiated (F ST ) regions generally had low genetic diversity (\u03b8\u03c0 ), but increased absolute divergence (DXY ) and excess of rare frequency variants (low Tajima's D). A minority of differentiation peaks were shared across species and population comparisons. However, highly differentiated regions contained genes with overrepresented functions related to metabolism, response to stimulus and cellular processes, indicating recurrent directional selection on a specific set of traits in all comparisons. In contrast to the majority of genome scans in recently diverged lineages, our data suggest that divergence landscapes in Leptidea have been shaped by directional selection and genetic drift rather than stable recombination landscapes and/or introgression.", "doi": "10.1111/mec.15188", "pmid": "31325366", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "ENA", "description": "Leptidea DNA sequence reads, genome assembly and genotype calls", "key": "PRJEB21838"}], "notes": [], "created": "2019-08-14T08:50:31.009Z", "modified": "2024-01-16T13:48:44.002Z"}, {"entity": "publication", "iuid": "6ee1dea8abaa4575a6b072aa9941b46f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ee1dea8abaa4575a6b072aa9941b46f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ee1dea8abaa4575a6b072aa9941b46f"}}, "title": "Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.", "authors": [{"family": "Herlemann", "given": "D P R", "initials": "DPR"}, {"family": "Markert", "given": "S", "initials": "S"}, {"family": "Meeske", "given": "C", "initials": "C"}, {"family": "Andersson", "given": "A F", "initials": "AF"}, {"family": "de Bruijn", "given": "I", "initials": "I"}, {"family": "Hentschker", "given": "C", "initials": "C"}, {"family": "Unfried", "given": "F", "initials": "F"}, {"family": "Becher", "given": "D", "initials": "D"}, {"family": "J\u00fcrgens", "given": "K", "initials": "K"}, {"family": "Schweder", "given": "T", "initials": "T"}], "type": "journal article", "published": "2019-08-01", "journal": {"volume": "85", "issn": "1098-5336", "issue": "15", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, how the incubation itself challenges complex bacterial communities is thus far unknown. In this study, metaproteomic profiling, 16S rRNA gene analyses, and cell counts were combined to evaluate bacterial communities derived from marine, mesohaline, and oligohaline conditions after long-term batch incubations. Early in the experiment, the three bacterial communities were highly diverse and differed significantly in their compositions. Manipulation of the enclosures with terrigenous dissolved organic carbon resulted in notable differences compared to the control enclosures at this early phase of the experiment. However, after 55 days, bacterial communities in the manipulated and the control enclosures under marine and mesohaline conditions were all dominated by gammaproteobacterium Spongiibacter In the oligohaline enclosures, actinobacterial cluster I of the hgc group (hgc-I) remained abundant in the late phase of the incubation. Metaproteome analyses suggested that the ability to use outer membrane-based internal energy stores, in addition to the previously described grazing resistance, may enable the gammaproteobacterium Spongiibacter to prevail in long-time incubations. Under oligohaline conditions, the utilization of external recalcitrant carbon appeared to be more important (hgc-I). Enclosure experiments with complex natural microbial communities are important tools to investigate the effects of manipulations. However, species-specific properties, such as individual carbon storage strategies, can cause manipulation-independent effects and need to be considered when interpreting results from enclosures.IMPORTANCE In microbial ecology, enclosure studies are often used to investigate the effect of single environmental factors on complex bacterial communities. However, in addition to the manipulation, unintended effects (\"bottle effect\") may occur due to the enclosure itself. In this study, we analyzed the bacterial communities that originated from three different salinities of the Baltic Sea, comparing their compositions and physiological activities both at the early stage and after 55 days of incubation. Our results suggested that internal carbon storage strategies impact the success of certain bacterial species, independent of the experimental manipulation. Thus, while enclosure experiments remain valid tools in environmental research, microbial community composition shifts must be critically followed. This investigation of the metaproteome during long-term batch enclosures expanded our current understanding of the so-called \"bottle effect,\" which is well known to occur during enclosure experiments.", "doi": "10.1128/AEM.00825-19", "pmid": "31152013", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "AEM.00825-19"}, {"db": "pmc", "key": "PMC6643244"}], "notes": [], "created": "2020-01-08T16:47:19.262Z", "modified": "2020-01-21T13:56:16.319Z"}, {"entity": "publication", "iuid": "ea231e9b47b0493a9cbb3de5d7dcb992", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea231e9b47b0493a9cbb3de5d7dcb992.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea231e9b47b0493a9cbb3de5d7dcb992"}}, "title": "Gene Flow in the M\u00fcllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves).", "authors": [{"family": "Garg", "given": "Kritika M", "initials": "KM"}, {"family": "Sam", "given": "Katerina", "initials": "K"}, {"family": "Chattopadhyay", "given": "Balaji", "initials": "B"}, {"family": "Sadanandan", "given": "Keren R", "initials": "KR"}, {"family": "Koane", "given": "Bonny", "initials": "B"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}], "type": "journal article", "published": "2019-08-01", "journal": {"volume": "11", "issn": "1759-6653", "issue": "8", "pages": "2332-2343", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "M\u00fcllerian mimicry rings are remarkable symbiotic species assemblages in which multiple members share a similar phenotype. However, their evolutionary origin remains poorly understood. Although gene flow among species has been shown to generate mimetic patterns in some Heliconius butterflies, mimicry is believed to be due to true convergence without gene flow in many other cases. We investigated the evolutionary history of multiple members of a passerine mimicry ring in the poisonous Papuan pitohuis. Previous phylogenetic evidence indicates that the aposematic coloration shared by many, but not all, members of this genus is ancestral and has only been retained by members of the mimicry ring. Using a newly assembled genome and thousands of genomic DNA markers, we demonstrate gene flow from the hooded pitohui (Pitohui dichrous) into the southern variable pitohui (Pitohui uropygialis), consistent with shared patterns of aposematic coloration. The vicinity of putatively introgressed loci is significantly enriched for genes that are important in melanin pigment expression and toxin resistance, suggesting that gene flow may have been instrumental in the sharing of plumage patterns and toxicity. These results indicate that interspecies gene flow may be a more general mechanism in generating mimicry rings than hitherto appreciated.", "doi": "10.1093/gbe/evz168", "pmid": "31418795", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "5550337"}, {"db": "pmc", "key": "PMC6735254"}], "notes": [], "created": "2019-12-02T17:20:02.909Z", "modified": "2020-01-21T13:56:15.637Z"}, {"entity": "publication", "iuid": "ff45e6aec7a34cc583c6229238538107", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff45e6aec7a34cc583c6229238538107.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff45e6aec7a34cc583c6229238538107"}}, "title": "Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.", "authors": [{"family": "Ringh", "given": "Mikael V", "initials": "MV"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Breeze", "given": "Charles E", "initials": "CE"}, {"family": "Sj\u00f6holm", "given": "Louise K", "initials": "LK"}, {"family": "Slavec", "given": "Lara", "initials": "L"}, {"family": "Kullberg", "given": "Susanna", "initials": "S"}, {"family": "Wahlstr\u00f6m", "given": "Jan", "initials": "J"}, {"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Brynedal", "given": "Boel", "initials": "B"}, {"family": "Liu", "given": "Yun", "initials": "Y"}, {"family": "Almgren", "given": "Malin", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "\u00d6ckinger", "given": "Johan", "initials": "J"}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "46", "issn": "2352-3964", "issue": null, "pages": "290-304", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "While smoking is known to associate with development of multiple diseases, the underlying mechanisms are still poorly understood. Tobacco smoking can modify the chemical integrity of DNA leading to changes in transcriptional activity, partly through an altered epigenetic state. We aimed to investigate the impact of smoking on lung cells collected from bronchoalveolar lavage (BAL).\n\nWe profiled changes in DNA methylation (5mC) and its oxidised form hydroxymethylation (5hmC) using conventional bisulphite (BS) treatment and oxidative bisulphite treatment with Illumina Infinium MethylationEPIC BeadChip, and examined gene expression by RNA-seq in healthy smokers.\n\nWe identified 1667 total 5mC\u202f+\u202f5hmC, 1756 5mC and 67 5hmC differentially methylated positions (DMPs) between smokers and non-smokers (FDR-adjusted P <.05, absolute \u0394\u03b2 >0.15). Both 5mC DMPs and to a lesser extent 5mC\u202f+\u202f5hmC were predominantly hypomethylated. In contrast, almost all 5hmC DMPs were hypermethylated, supporting the hypothesis that smoking-associated oxidative stress can lead to DNA demethylation, via the established sequential oxidation of which 5hmC is the first step. While we confirmed differential methylation of previously reported smoking-associated 5mC\u202f+\u202f5hmC CpGs using former generations of BeadChips in alveolar macrophages, the large majority of identified DMPs, 5mC\u202f+\u202f5hmC (1639/1667), 5mC (1738/1756), and 5hmC (67/67), have not been previously reported. Most of these novel smoking-associating sites are specific to the EPIC BeadChip and, interestingly, many of them are associated to FANTOM5 enhancers. Transcriptional changes affecting 633 transcripts were consistent with DNA methylation profiles and converged to alteration of genes involved in migration, signalling and inflammatory response of immune cells.\n\nCollectively, these findings suggest that tobacco smoke exposure epigenetically modifies BAL cells, possibly involving a continuous active demethylation and subsequent increased activity of inflammatory processes in the lungs. FUND: The study was supported by the Swedish Research Council, the Swedish Heart-Lung Foundation, the Stockholm County Council (ALF), the King Gustav's and Queen Victoria's Freemasons' Foundation, Knut and Alice Wallenberg Foundation, Neuro Sweden, and the Swedish MS foundation.", "doi": "10.1016/j.ebiom.2019.07.006", "pmid": "31303497", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(19)30441-4"}, {"db": "pmc", "key": "PMC6710853"}], "notes": [], "created": "2019-09-17T16:24:25.920Z", "modified": "2024-01-16T13:48:44.009Z"}, {"entity": "publication", "iuid": "c95da5e9ba1841f4802e429f0e0a9b0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c95da5e9ba1841f4802e429f0e0a9b0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c95da5e9ba1841f4802e429f0e0a9b0e"}}, "title": "Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.", "authors": [{"family": "Kawakami", "given": "Takeshi", "initials": "T"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wintermantel", "given": "Dimitry", "initials": "D"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR"}, {"family": "Allsopp", "given": "Mike", "initials": "M"}, {"family": "Rundl\u00f6f", "given": "Maj", "initials": "M"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "212", "issn": "1943-2631", "issue": "4", "pages": "1101-1119", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": "Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary causes of this are not known. Here, we estimate rates of crossovers and gene conversions in 22 colonies of the honeybee, Apis mellifera, and 9 colonies of the bumblebee, Bombus terrestris, using direct sequencing of 299 haploid drone offspring. We confirm that both species have extremely elevated crossover rates, with higher rates measured in the highly eusocial honeybee than the primitively social bumblebee. There are also significant differences in recombination rate between subspecies of honeybee. There is substantial variation in genome-wide recombination rate between individuals of both A. mellifera and B. terrestris and the distribution of these rates overlap between species. A large proportion of interindividual variation in recombination rate is heritable, which indicates the presence of variation in trans-acting factors that influence recombination genome-wide. We infer that levels of crossover interference are significantly lower in honeybees compared to bumblebees, which may be one mechanism that contributes to higher recombination rates in honeybees. We also find a significant increase in recombination rate with distance from the centromere, mirrored by methylation differences. We detect a strong transmission bias due to GC-biased gene conversion associated with noncrossover gene conversions. Our results shed light on the mechanistic causes of extreme rates of recombination in social insects and the genetic architecture of recombination rate variation.", "doi": "10.1534/genetics.119.302008", "pmid": "31152071", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "genetics.119.302008"}, {"db": "pmc", "key": "PMC6707477"}], "notes": [], "created": "2020-01-08T16:47:38.438Z", "modified": "2020-01-21T13:56:16.327Z"}, {"entity": "publication", "iuid": "c9b9056d2a364bd58ef14fbb2031fa66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9b9056d2a364bd58ef14fbb2031fa66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9b9056d2a364bd58ef14fbb2031fa66"}}, "title": "Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Raymond", "given": "Caroline", "initials": "C"}, {"family": "Sommer", "given": "Christian", "initials": "C"}, {"family": "Gunnarsson", "given": "Jonas S", "initials": "JS"}, {"family": "Creer", "given": "Simon", "initials": "S"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "28", "issn": "1365-294X", "issue": "16", "pages": "3813-3829", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on-going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high-throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna-macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services.", "doi": "10.1111/mec.15179", "pmid": "31332853", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6852176"}, {"db": "GENBANK", "key": "PRJNA497177"}], "notes": [], "created": "2019-12-02T17:20:32.087Z", "modified": "2024-01-16T13:48:44.016Z"}, {"entity": "publication", "iuid": "983ea2c3052b425c903696a9faff59e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/983ea2c3052b425c903696a9faff59e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/983ea2c3052b425c903696a9faff59e9"}}, "title": "Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades", "authors": [{"family": "Hiltunen", "given": "Markus", "initials": "M"}, {"family": "Grudzinska-Sterno", "given": "Magdalena", "initials": "M"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Ryberg", "given": "Martin", "initials": "M"}, {"family": "Johannesson", "given": "Hanna", "initials": "H"}], "type": "journal-article", "published": "2019-08-00", "journal": {"volume": "29", "issn": "0960-9822", "issue": "16", "pages": "2758-2765.e6", "title": "Current Biology", "issn-l": "0960-9822"}, "abstract": "Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and re-sequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 \u00d7 10 -12 mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.", "doi": "10.1016/j.cub.2019.07.025", "pmid": "31402298", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-11-25T14:43:11.225Z", "modified": "2024-01-16T13:48:44.031Z"}, {"entity": "publication", "iuid": "f0b61c7f79764e5b80784ea748d8ef40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0b61c7f79764e5b80784ea748d8ef40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0b61c7f79764e5b80784ea748d8ef40"}}, "title": "Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.", "authors": [{"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Ringdahl", "given": "Jenny", "initials": "J"}, {"family": "Bryant", "given": "Patrick", "initials": "P"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "27", "issn": "1476-5438", "issue": "8", "pages": "1286-1295", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Colorectal cancer (CRC) is one of the major cancer types in the western world including Sweden. However, known genetic risk factors could only explain a limited part of heritability of the disease. Moreover, colon and rectal cancers are habitually discussed as one entity, colorectal cancer, although different carcinogenesis has been recognized. A genome-wide linkage scan in 32 colon- and 56 rectal cancer families from Sweden was performed based on 475 non-FAP/HNPCC patients genotyped using SNP arrays. A maximum HLOD of 2.50 at locus 6p21.1-p12.1 and a HLOD of 2.56 at 18p11.2 was obtained for colon and rectal cancer families, respectively. Exome sequencing over the regions of interest in 12 patients from six families identified 22 and 25 candidate risk variants for colon and rectal cancer, respectively. Haplotype association analysis in the two regions was carried out between additional 477 familial CRC cases and 4780 controls and suggested candidate haplotypes possibly associated with CRC risk. This study suggested two new linkage regions for colon cancer and rectal cancer with candidate predisposing variants. Further studies are required to elucidate the pathogenic mechanism of these regions and to pinpoint the causative genes.", "doi": "10.1038/s41431-019-0388-3", "pmid": "30952955", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-019-0388-3"}], "notes": [], "created": "2019-08-13T12:15:30.342Z", "modified": "2024-01-16T13:48:44.038Z"}, {"entity": "publication", "iuid": "d6f918844e414eaeb4553498ba65c32b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6f918844e414eaeb4553498ba65c32b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6f918844e414eaeb4553498ba65c32b"}}, "title": "Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells", "authors": [{"family": "Samudyata", "given": "", "initials": ""}, {"family": "Amaral", "given": "Paulo P", "initials": "PP"}, {"family": "Engstr\u00f6m", "given": "P\u00e4r G", "initials": "PG", "orcid": "0000-0001-5265-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce330ec225f4a8595932d092ab8c8d1.json"}}, {"family": "Robson", "given": "Samuel C", "initials": "SC"}, {"family": "Nielsen", "given": "Michael L", "initials": "ML"}, {"family": "Kouzarides", "given": "Tony", "initials": "T"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal-article", "published": "2019-08-00", "journal": {"volume": "381", "issn": "0014-4827", "issue": "1", "pages": "129-138", "title": "Experimental Cell Research", "issn-l": "0014-4827"}, "abstract": "Sox2 is a master transcriptional regulator of embryonic development. In this study, we determined the protein interactome of Sox2 in the chromatin and nucleoplasm of mouse embryonic stem (mES) cells. Apart from canonical interactions with pluripotency-regulating transcription factors, we identified interactions with several chromatin modulators, including members of the heterochromatin protein 1 (HP1) family, suggesting a role for Sox2 in chromatin-mediated transcriptional repression. Sox2 was also found to interact with RNA binding proteins (RBPs), including proteins involved in RNA processing. RNA immunoprecipitation followed by sequencing revealed that Sox2 associates with different messenger RNAs, as well as small nucleolar RNA Snord34 and the non-coding RNA 7SK. 7SK has been shown to regulate transcription at gene regulatory regions, which could suggest a functional interaction with Sox2 for chromatin recruitment. Nevertheless, we found no evidence of Sox2 modulating recruitment of 7SK to chromatin when examining 7SK chromatin occupancy by Chromatin Isolation by RNA Purification (ChIRP) in Sox2 depleted mES cells. In addition, knockdown of 7SK in mES cells did not lead to any change in Sox2 occupancy at 7SK-regulated genes. Thus, our results show that Sox2 extensively interacts with RBPs, and suggest that Sox2 and 7SK co-exist in a ribonucleoprotein complex whose function is not to regulate chromatin recruitment, but could rather regulate other processes in the nucleoplasm.", "doi": "10.1016/j.yexcr.2019.05.006", "pmid": "31077711", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4827(19)30239-3"}, {"db": "pmc", "key": "PMC6994247"}, {"db": "mid", "key": "EMS85623"}], "notes": [], "created": "2020-01-08T16:47:16.254Z", "modified": "2021-06-16T15:35:27.434Z"}, {"entity": "publication", "iuid": "73c7a8f90169436ca5c05231b2b6c117", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73c7a8f90169436ca5c05231b2b6c117.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73c7a8f90169436ca5c05231b2b6c117"}}, "title": "Early activating somatic PIK3CA mutations promote ectopic muscle development and upper limb overgrowth.", "authors": [{"family": "Frisk", "given": "Sofia", "initials": "S"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Blaszczyk", "given": "Izabela", "initials": "I"}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Herm", "given": "Bettina", "initials": "B"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Laurell", "given": "Tobias", "initials": "T"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "96", "issn": "1399-0004", "issue": "2", "pages": "118-125", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": "PIK3CA-related overgrowth spectrum is a group of rare genetic disorders with asymmetric overgrowth caused by somatic mosaic PIK3CA mutations. Here, we report clinical data and molecular findings from two patients with congenital muscular upper limb overgrowth and aberrant anatomy. During debulking surgery, numerous ectopic muscles were found in the upper limbs of the patients. DNA sequencing, followed by digital polymerase chain reaction, was performed on DNA extracted from biopsies from hypertrophic ectopic muscles and identified the somatic mosaic PIK3CA hotspot mutations c.3140A > G, p.(His1047Arg) and c.1624G > A, p.(Glu542Lys) in a male (patient 1) and a female (patient 2) patient, respectively. Patient 1 had four ectopic muscles and unilateral isolated muscular overgrowth while patient 2 had 13 ectopic muscles and bilateral isolated muscular overgrowth of both upper limbs, indicating that her mutation occurred at early pre-somitic mesoderm state. The finding of PIK3CA mutations in ectopic muscles highlights the importance of PIK3CA in cell fate in early human embryonic development. Moreover, our findings provide evidence that the disease phenotype depends on the timing of PIK3CA mutagenesis during embryogenesis and confirm the diagnostic entity PIK3CA-related muscular overgrowth with ectopic accessory muscles.", "doi": "10.1111/cge.13543", "pmid": "30919936", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6851821"}], "notes": [], "created": "2020-01-08T16:49:48.590Z", "modified": "2020-01-21T13:56:16.589Z"}, {"entity": "publication", "iuid": "bdf43e4350f94e0fa35e85f047beebfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bdf43e4350f94e0fa35e85f047beebfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bdf43e4350f94e0fa35e85f047beebfd"}}, "title": "Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.", "authors": [{"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Marki", "given": "Petter Zahl", "initials": "PZ"}, {"family": "Joseph", "given": "Leo", "initials": "L"}, {"family": "Sangster", "given": "George", "initials": "G"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "137", "issn": "1095-9513", "issue": null, "pages": "200-209", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "Old World orioles (Oriolidae) are medium-sized passerine birds confined largely to forested areas of Africa, Eurasia and Australasia. We present a new complete molecular (mtDNA) subspecies level phylogeny of the Oriolidae including all 113 taxa (35 species) together with a backbone phylogeny of 19 taxa from the main Oriolus clades based on (i) 21 nuclear genes, (ii) whole mito-genomes, and (iii) genome-wide ultraconserved elements. We use this phylogeny to assess systematic relationships and the biogeographical history of this avian family. Furthermore, we use morphological measurements to investigate the relationship between size and shape axes and upstream or back-colonization of this extensive island region from Asia. We show that several subspecies or groups of subspecies may warrant species rank and we find a continental example of two morphologically distinct species (O. mellianus/O. traillii) being genetically (mtDNA) very similar. Biogeographically, we confirm previous findings that members of the Oriolidae originated in Australo-Papua. Dispersal out of this area took place around 15 Mya to southeast Asia and Africa, and from Africa to the Palearctic followed by recolonization of the Indonesian and Philippine island region during the Plio-Pleistocene. Recolonisation of the Indonesian and Philippine islands coincided with an increase in body size, which may have facilitated the ability to co-exist with other congenerics.", "doi": "10.1016/j.ympev.2019.03.015", "pmid": "30914395", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(18)30644-4"}], "notes": [], "created": "2019-12-02T17:20:04.316Z", "modified": "2024-01-16T13:48:44.053Z"}, {"entity": "publication", "iuid": "5c9953b09c434d1db69cbddfecc37360", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c9953b09c434d1db69cbddfecc37360.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c9953b09c434d1db69cbddfecc37360"}}, "title": "31\u00b0 South: The physiology of adaptation to arid conditions in a passerine bird.", "authors": [{"family": "Ribeiro", "given": "\u00c2ngela M", "initials": "\u00c2M"}, {"family": "Puetz", "given": "Lara", "initials": "L"}, {"family": "Pattinson", "given": "Nicholas B", "initials": "NB"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "da Fonseca", "given": "Rute R", "initials": "RR"}, {"family": "Smit", "given": "Ben", "initials": "B"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2019-08-00", "journal": {"volume": "28", "issn": "1365-294X", "issue": "16", "pages": "3709-3721", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub-robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.", "doi": "10.1111/mec.15176", "pmid": "31291502", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "GENBANK", "key": "PRJNA492976"}], "notes": [], "created": "2019-12-02T17:19:30.443Z", "modified": "2021-07-07T20:31:10.807Z"}, {"entity": "publication", "iuid": "764f6d2c025b4c0abd3ffeddeef83720", "links": {"self": {"href": "https://publications.scilifelab.se/publication/764f6d2c025b4c0abd3ffeddeef83720.json"}, "display": {"href": "https://publications.scilifelab.se/publication/764f6d2c025b4c0abd3ffeddeef83720"}}, "title": "Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts.", "authors": [{"family": "Saini", "given": "Amarjit", "initials": "A"}, {"family": "Bj\u00f6rkhem-Bergman", "given": "Linda", "initials": "L"}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Lilja", "given": "Mats", "initials": "M"}, {"family": "Melin", "given": "Michael", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Olsson", "given": "Karl", "initials": "K"}, {"family": "Ekstr\u00f6m", "given": "Lena", "initials": "L"}, {"family": "Bergman", "given": "Peter", "initials": "P"}, {"family": "Altun", "given": "Mikael", "initials": "M"}, {"family": "Rullman", "given": "Eric", "initials": "E"}, {"family": "Gustafsson", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2019-07-29", "journal": {"volume": "8", "issn": "2049-3614", "issue": "7", "pages": "1070-1081", "title": "Endocr Connect", "issn-l": "2049-3614"}, "abstract": "The CC-genotype of the VDR polymorphism TaqI rs731236 has previously been associated with a higher risk of developing myopathy compared to TT-carriers. However, the mechanistic role of this polymorphism in skeletal muscle is not well defined. The effects of vitamin D on patients genotyped for the VDR polymorphism TaqI rs731236, comparing CC and TT-carriers were evaluated. Primary human myoblasts isolated from 4 CC-carriers were compared with myoblasts isolated from 4 TT-carriers and treated with vitamin D in vitro. A dose-dependent inhibitory effect on myoblast proliferation and differentiation was observed concurrent with modifications of key myogenic regulatory factors. RNA-sequencing revealed a Vitamin D dose-response gene signature enriched with a higher number of VDR-responsive elements (VDREs) per gene. Interestingly, the greater the expression of muscle differentiation markers in myoblasts the more pronounced was the Vitamin D-mediated response to suppress genes associated with myogenic fusion and myotube formation. This novel finding provides a mechanistic explanation to the inconsistency regarding previous reports of the role of vitamin D in myoblast differentiation. No effects in myoblast proliferation, differentiation or gene expression were related to CC vs. TT carriers. Our findings suggest that the VDR polymorphism TaqI rs731236 comparing CC vs. TT carriers did not influence the effects of vitamin D on primary human myoblasts and that vitamin D inhibits myoblast proliferation and differentiation through key regulators of cell cycle progression. Future studies need to employ strategies to identify the primary responses of vitamin D that drive the cellular response towards quiescence.", "doi": "10.1530/EC-19-0194", "pmid": "31252402", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EC-19-0194"}, {"db": "pmc", "key": "PMC6652245"}], "notes": [], "created": "2019-12-02T16:52:31.370Z", "modified": "2024-01-16T13:48:44.086Z"}, {"entity": "publication", "iuid": "0b0d84d71da8411a974593d2c45402ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b0d84d71da8411a974593d2c45402ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b0d84d71da8411a974593d2c45402ca"}}, "title": "Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.", "authors": [{"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Qu", "given": "Yanhua", "initials": "Y"}, {"family": "Rasmussen", "given": "Pamela C", "initials": "PC"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-07-24", "journal": {"volume": "19", "issn": "1471-2148", "issue": "1", "pages": "151", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex.\n\nWe generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade.\n\nWe found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, \"stepping-stone\" dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea.", "doi": "10.1186/s12862-019-1481-5", "pmid": "31340765", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-019-1481-5"}, {"db": "pmc", "key": "PMC6657069"}], "notes": [], "created": "2019-12-02T17:20:03.644Z", "modified": "2020-01-21T13:56:15.644Z"}, {"entity": "publication", "iuid": "944a0db828b548448d06f8a67b9c9c2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/944a0db828b548448d06f8a67b9c9c2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/944a0db828b548448d06f8a67b9c9c2a"}}, "title": "Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.", "authors": [{"family": "Wallander", "given": "Karin", "initials": "K"}, {"family": "Liu", "given": "Wen", "initials": "W"}, {"family": "von Holst", "given": "Susanna", "initials": "S"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "Forsberg", "given": "Anna", "initials": "A"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2019-07-23", "journal": {"volume": null, "issn": "1098-2264", "issue": null, "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "Colorectal cancer (CRC), prostate cancer (PrC), and gastric cancer (GC) are common worldwide, and the incidence is to a certain extent dependent on genetics. We have recently shown that in families with more than one case of CRC, the risk of other malignancies is increased. We therefore suggested the presence of not yet described CRC syndromes. In this study, we have searched for genetic susceptibility loci for potential cancer syndromes involving CRC combined with PrC and/or GC. We have performed SNP (single-nucleotide polymorphism)-based linkage analyses in 45 families with CRC, PrC, and GC. In the regions with suggested linkage, we performed exome and association haplotype analyses. Five loci generated a high logarithm of odds (HLOD) score >2, suggestive of linkage, in chromosome bands 1q31-32, 1q24-25, 6q25-26, 18p11-q11, and Xp11. Exome analysis detected no potential pathogenic sequence variants. The haplotype association study showed that one of the top five haplotypes with the lowest P value in the chromosome band 6q25 interestingly was found in the family which contributed the most to the increased HLOD at that locus. This study supports a suggested hereditary cancer syndrome involving CRC and PrC and indicates a location at 6q25. The impact of this locus needs to be confirmed in additional studies.", "doi": "10.1002/gcc.22786", "pmid": "31334572", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-08-13T12:15:28.354Z", "modified": "2024-01-16T13:48:44.111Z"}, {"entity": "publication", "iuid": "b4353b41d96846f6990c57429e83b248", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4353b41d96846f6990c57429e83b248.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4353b41d96846f6990c57429e83b248"}}, "title": "Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.", "authors": [{"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Garc\u00eda-Gil", "given": "M Rosario", "initials": "MR"}], "type": "journal article", "published": "2019-07-05", "journal": {"volume": "14", "issn": "1932-6203", "issue": "7", "pages": "e0219272", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Plant life cycle begins with germination of seed below the ground. This is followed by seedling's development in the dark: skotomorphogenesis; and then a light-mediated growth: photomorphogenesis. After germination, hypocotyl grows rapidly to reach the sun, which involves elongation of shoot at the expense of root and cotyledons. Upon reaching ground level, seedling gets exposed to sunlight following a switch from the etiolated (skotomorphogenesis) to the de-etiolated (photomorphogenesis) stage, involving a series of molecular and physiological changes. Gymnosperms have evolved very differently and adopted diverse strategies as compared to angiosperms; with regards to response to light quality, conifers display a very mild high-irradiance response as compared to angiosperms. Absence of apical hook and synthesis of chlorophyll during skotomorphogenesis are two typical features in gymnosperms which differentiate them from angiosperms (dicots). Information regarding etiolation and de-etiolation processes are well understood in angiosperms, but these mechanisms are less explored in conifer species. It is, therefore, interesting to know how similar these processes are in conifers as compared to angiosperms. We performed a global expression analysis (RNA sequencing) on etiolated and de-etiolated seedlings of two economically important conifer species in Sweden to review the differentially expressed genes associated with the two processes. Based on the results, we propose that high levels of HY5 in conifers under DARK condition coupled with expression of few other genes associated with de-etiolation in angiosperms e.g. SPA, DET1 (lower expression under DARK) and CRY1 (higher expression under DARK), leads to partial expression of photomorphogenic genes in the DARK phenotype in conifers as displayed by absence of apical hook, opening of cotyledons and synthesis of chlorophyll.", "doi": "10.1371/journal.pone.0219272", "pmid": "31276530", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Cryo-EM": "Service", "NGI Stockholm (Genomics Production)": "Service", "Integrated Microscopy Technologies Ume\u00e5": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-19-06007"}, {"db": "pmc", "key": "PMC6611632"}], "notes": [], "created": "2019-12-02T17:20:55.900Z", "modified": "2024-01-16T13:48:44.138Z"}, {"entity": "publication", "iuid": "cce3f4d586ea458d8b32a9957b47abac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cce3f4d586ea458d8b32a9957b47abac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cce3f4d586ea458d8b32a9957b47abac"}}, "title": "Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.", "authors": [{"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Yu", "given": "Changxun", "initials": "C"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Josefsson", "given": "Sarah", "initials": "S"}, {"family": "Lillhonga", "given": "Tom", "initials": "T"}, {"family": "H\u00f6gfors-R\u00f6nnholm", "given": "Eva", "initials": "E"}, {"family": "Sohlenius", "given": "Gustav", "initials": "G"}, {"family": "\u00c5str\u00f6m", "given": "Mats E", "initials": "ME"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2019-07-03", "journal": {"volume": "170", "issn": "1769-7123", "issue": "6-7", "pages": "288-295", "title": "Res. Microbiol.", "issn-l": "0923-2508"}, "abstract": "Due to land uplift after the last ice age, previously stable Baltic Sea sulfidic sediments are becoming dry land. When these sediments are drained, the sulfide minerals are exposed to air and can release large amounts of metals and acid into the environment. This can cause severe ecological damage such as fish kills in rivers feeding the northern Baltic Sea. In this study, five sites were investigated for the occurrence of acid sulfate soils and their geochemistry and microbiology was identified. The pH and soil chemistry identified three of the areas as having classical acid sulfate soil characteristics and culture independent identification of 16S rRNA genes identified populations related to acidophilic bacteria capable of catalyzing sulfidic mineral dissolution, including species likely adapted to low temperature. These results were compared to an acid sulfate soil area that had been flooded for ten years and showed that the previously oxidized sulfidic materials had an increased pH compared to the unremediated oxidized layers. In addition, the microbiology of the flooded soil had changed such that alkalinity producing ferric and sulfate reducing reactions had likely occurred. This suggested that flooding of acid sulfate soils mitigates their environmental impact.", "doi": "10.1016/j.resmic.2019.06.002", "pmid": "31279086", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0923-2508(19)30059-2"}], "notes": [], "created": "2019-12-02T17:19:33.064Z", "modified": "2024-01-16T13:48:44.145Z"}, {"entity": "publication", "iuid": "c98820e9a3eb455caf589dd9177081a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c98820e9a3eb455caf589dd9177081a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c98820e9a3eb455caf589dd9177081a9"}}, "title": "Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection.", "authors": [{"family": "Kalyandurg", "given": "Pruthvi B", "initials": "PB"}, {"family": "Tahmasebi", "given": "Aminallah", "initials": "A"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Lezzhov", "given": "Alexander A", "initials": "AA"}, {"family": "Solovyev", "given": "Andrey G", "initials": "AG"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Savenkov", "given": "Eugene I", "initials": "EI"}], "type": "journal article", "published": "2019-07-01", "journal": {"volume": "535", "issn": "1096-0341", "issue": null, "pages": "111-121", "title": "Virology", "issn-l": "0042-6822"}, "abstract": "Previously, we investigated the evolution of Potato mop-top virus (PMTV) ORFs. Results indicate that positive selection acts exclusively on an ORF encoding the 8K protein, a weak viral suppressor of RNA silencing (VSR). However, how the extraordinary variability contributes to 8K-mediated RNA silencing suppression remains unknown. Here, we characterized the RNA silencing suppression activity of the 8K protein from seven diverse isolates. We show that 8K encoded by isolate P1 exhibits stronger RNA silencing suppression activity than the 8K protein from six other isolates. Mutational analyses revealed that Ser-50 is critical for these differences. By comparing small RNA profiles we found a lower abundance of siRNAs with U residue at the 5'-terminus after expression of the P1 8K compared to expression of 8K from isolate P125, an isolate with weak VSR activity. These results provide new clues as to the role of positive selection in shaping activities of VSRs.", "doi": "10.1016/j.virol.2019.06.018", "pmid": "31299487", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0042-6822(19)30172-2"}], "notes": [], "created": "2020-01-08T16:47:39.169Z", "modified": "2020-01-21T13:56:16.337Z"}, {"entity": "publication", "iuid": "2bb28fbed6f74d3793e4549ac633ce0f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bb28fbed6f74d3793e4549ac633ce0f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bb28fbed6f74d3793e4549ac633ce0f"}}, "title": "Transcriptome analysis of shade avoidance and shade tolerance in conifers.", "authors": [{"family": "Ranade", "given": "Sonali Sachin", "initials": "SS"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Garc\u00eda-Gil", "given": "Mar\u00eda Rosario", "initials": "MR"}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "250", "issn": "1432-2048", "issue": "1", "pages": "299-318", "title": "Planta", "issn-l": "0032-0935"}, "abstract": "Gymnosperms respond differently to light intensity and R:FR; although some aspects of shade response appear conserved, yet underlying mechanisms seem to be diverse in gymnosperms as compared to angiosperms. Shade avoidance syndrome (SAS) is well-characterized in the shade intolerant model species Arabidopsis thaliana whereas much less is known about shade tolerance response (STR), yet regulation of SAS and STR with reference to conifers remains poorly understood. We conducted a comparative study of two conifer species with contrasting responses to shade, Scots pine (shade-intolerant) and Norway spruce (shade-tolerant), with the aim to understand mechanisms behind SAS and STR in conifers. Pine and spruce seedlings were grown under controlled light and shade conditions, and hypocotyl and seedling elongation following different light treatments were determined in both species as indicators of shade responses. Red to far-red light ratio (R:FR) was shown to trigger the shade response in Norway spruce. In Scots pine, we observed an interaction between R:FR and light intensity. RNA sequencing (RNA-Seq) data revealed that SAS and STR responses included changes in expression of genes involved primarily in hormone signalling and pigment biosynthesis. From the RNA-Seq analysis, we propose that although some aspects of shade response appear to be conserved in angiosperms and gymnosperms, yet the underlying mechanisms may be different in gymnosperms that warrants further research.", "doi": "10.1007/s00425-019-03160-z", "pmid": "31028482", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00425-019-03160-z"}], "notes": [], "created": "2019-12-02T17:21:15.825Z", "modified": "2024-01-16T13:48:44.152Z"}, {"entity": "publication", "iuid": "84b19b61f97c4602a643b805bcca2c89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/84b19b61f97c4602a643b805bcca2c89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/84b19b61f97c4602a643b805bcca2c89"}}, "title": "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation.", "authors": [{"family": "Charitou", "given": "Theodosia", "initials": "T"}, {"family": "Srihari", "given": "Sriganesh", "initials": "S"}, {"family": "Lynn", "given": "Miriam A", "initials": "MA"}, {"family": "Jarboui", "given": "Mohamed-Ali", "initials": "MA"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Moldovan", "given": "Max", "initials": "M"}, {"family": "Shirasawa", "given": "Senji", "initials": "S"}, {"family": "Tsunoda", "given": "Toshiyuki", "initials": "T"}, {"family": "Ueffing", "given": "Marius", "initials": "M"}, {"family": "Xie", "given": "Jianling", "initials": "J"}, {"family": "Xin", "given": "Jin", "initials": "J"}, {"family": "Wang", "given": "Xuemin", "initials": "X"}, {"family": "Proud", "given": "Christopher G", "initials": "CG"}, {"family": "Boldt", "given": "Karsten", "initials": "K"}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C"}, {"family": "Kolch", "given": "Walter", "initials": "W"}, {"family": "Lynn", "given": "David J", "initials": "DJ"}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "121", "issn": "1532-1827", "issue": "1", "pages": "37-50", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "Activating mutations in KRAS frequently occur in colorectal cancer (CRC) patients, leading to resistance to EGFR-targeted therapies.\n\nTo better understand the cellular reprogramming which occurs in mutant KRAS cells, we have undertaken a systems-level analysis of four CRC cell lines which express either wild type (wt) KRAS or the oncogenic KRASG13D allele (mtKRAS).\n\nRNAseq revealed that genes involved in ribosome biogenesis, mRNA translation and metabolism were significantly upregulated in mtKRAS cells. Consistent with the transcriptional data, protein synthesis and cell proliferation were significantly higher in the mtKRAS cells. Targeted metabolomics analysis also confirmed the metabolic reprogramming in mtKRAS cells. Interestingly, mtKRAS cells were highly transcriptionally responsive to EGFR activation by TGF\u03b1 stimulation, which was associated with an unexpected downregulation of genes involved in a range of anabolic processes. While TGF\u03b1 treatment strongly activated protein synthesis in wtKRAS cells, protein synthesis was not activated above basal levels in the TGF\u03b1-treated mtKRAS cells. This was likely due to the defective activation of the mTORC1 and other pathways by TGF\u03b1 in mtKRAS cells, which was associated with impaired activation of PKB signalling and a transient induction of AMPK signalling.\n\nWe have found that mtKRAS cells are substantially rewired at the transcriptional, translational and metabolic levels and that this rewiring may reveal new vulnerabilities in oncogenic KRAS CRC cells that could be exploited in future.", "doi": "10.1038/s41416-019-0477-7", "pmid": "31133691", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6738113"}, {"db": "pii", "key": "10.1038/s41416-019-0477-7"}], "notes": [], "created": "2019-12-02T17:19:34.820Z", "modified": "2023-06-19T13:19:23.479Z"}, {"entity": "publication", "iuid": "2f31dc4b786148ef820364041203eb44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f31dc4b786148ef820364041203eb44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f31dc4b786148ef820364041203eb44"}}, "title": "Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality", "authors": [{"family": "Lam", "given": "Matti", "initials": "M"}, {"family": "Moslem", "given": "Mohsen", "initials": "M"}, {"family": "Bryois", "given": "Julien", "initials": "J"}, {"family": "Pronk", "given": "Robin J", "initials": "RJ"}, {"family": "Uhlin", "given": "Elias", "initials": "E"}, {"family": "Ellstr\u00f6m", "given": "Ivar Dehnisch", "initials": "ID"}, {"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Olive", "given": "Jessica", "initials": "J"}, {"family": "Morse", "given": "Rebecca", "initials": "R"}, {"family": "R\u00f6nnholm", "given": "Harriet", "initials": "H"}, {"family": "Louhivuori", "given": "Lauri", "initials": "L"}, {"family": "Korol", "given": "Sergiy V", "initials": "SV"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P"}, {"family": "Anderlid", "given": "Britt Marie", "initials": "BM"}, {"family": "Kele", "given": "Malin", "initials": "M"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Falk", "given": "Anna", "initials": "A"}], "type": "journal-article", "published": "2019-07-00", "journal": {"volume": "383", "issn": "0014-4827", "issue": "1", "pages": "111469", "title": "Experimental Cell Research", "issn-l": "0014-4827"}, "abstract": "We generated human iPS derived neural stem cells and differentiated cells from healthy control individuals and an individual with autism spectrum disorder carrying bi-allelic NRXN1-alpha deletion. We investigated the expression of NRXN1-alpha during neural induction and neural differentiation and observed a pivotal role for NRXN1-alpha during early neural induction and neuronal differentiation. Single cell RNA-seq pinpointed neural stem cells carrying NRXN1-alpha deletion shifting towards radial glia-like cell identity and revealed higher proportion of differentiated astroglia. Furthermore, neuronal cells carrying NRXN1-alpha deletion were identified as immature by single cell RNA-seq analysis, displayed significant depression in calcium signaling activity and presented impaired maturation action potential profile in neurons investigated with electrophysiology. Our observations propose NRXN1-alpha plays an important role for the efficient establishment of neural stem cells, in neuronal differentiation and in maturation of functional excitatory neuronal cells.", "doi": "10.1016/j.yexcr.2019.06.014", "pmid": "31302032", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-08-15T11:49:19.360Z", "modified": "2024-01-16T13:48:44.167Z"}, {"entity": "publication", "iuid": "b8f10d21ddb24a76b7d29cacc49d5ecc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8f10d21ddb24a76b7d29cacc49d5ecc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8f10d21ddb24a76b7d29cacc49d5ecc"}}, "title": "Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.", "authors": [{"family": "Olsson Lindvall", "given": "Martina", "initials": "M"}, {"family": "Hansson", "given": "Lena", "initials": "L"}, {"family": "Klasson", "given": "Sofia", "initials": "S"}, {"family": "Davila Lopez", "given": "Marcela", "initials": "M"}, {"family": "Jern", "given": "Christina", "initials": "C"}, {"family": "Stanne", "given": "Tara M", "initials": "TM"}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "119", "issn": "0340-6245", "issue": "7", "pages": "1072-1083", "title": "Thromb. Haemost.", "issn-l": null}, "abstract": "Elucidating the genetic basis underlying hepatic hemostatic gene expression variability may contribute to unraveling genetic factors contributing to thrombotic or bleeding disorders. We aimed to identify novel cis-regulatory variants involved in regulating hemostatic genes by analyzing allele-specific expression (ASE) in human liver samples.\r\n\r\nBiopsies of human liver tissue and blood were collected from adults undergoing liver surgery at the Sahlgrenska University Hospital ( n = 20). Genomic deoxyribonucleic acid (gDNA) and total ribonucleic acid (RNA) were isolated. A targeted approach was used to enrich and sequence 35 hemostatic genes for single nucleotide polymorphism (SNP) analysis (gDNAseq) and construct individualized genomes for transcript alignment. The allelic ratio of transcripts from targeted RNAseq was determined via ASE analysis. Public expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) data were used to assess novelty and importance of the ASE SNPs (and proxies, r2 \u2265 0.8) for relevant traits/diseases.\r\n\r\nSixty percent of the genes studied showed allelic imbalance across 53 SNPs. Of these, 7 SNPs were previously validated in liver eQTL studies. For 32 with eQTLs in other cell/tissue types, this is the first time genotype-specific expression is demonstrated in liver, and for 14 ASE SNPs, this is the first ever reported genotype-expression association. A total of 29 ASE SNPs were previously associated with the respective plasma protein levels and 17 ASE SNPs to other relevant GWAS traits including venous thromboembolism, coronary artery disease, and stroke.\r\n\r\nOur study provides a comprehensive ASE analysis of hemostatic genes and insights into the regulation of hemostatic genes in human liver.", "doi": "10.1055/s-0039-1687879", "pmid": "31035302", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-02T17:19:35.607Z", "modified": "2024-01-16T13:48:44.174Z"}, {"entity": "publication", "iuid": "bbc87b120ad546f4837264befb18c27b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbc87b120ad546f4837264befb18c27b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbc87b120ad546f4837264befb18c27b"}}, "title": "Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.", "authors": [{"family": "Ferrante", "given": "Maria Immacolata", "initials": "MI"}, {"family": "Entrambasaguas", "given": "Laura", "initials": "L"}, {"family": "Johansson", "given": "Mathias", "initials": "M"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Montresor", "given": "Marina", "initials": "M"}, {"family": "Godhe", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-06-28", "journal": {"volume": "10", "issn": "2073-4425", "issue": "7", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Sexual reproduction plays a fundamental role in diatom life cycles. It contributes to increasing genetic diversity through meiotic recombination and also represents the phase where large-sized cells are produced to counteract the cell size reduction process that characterizes these microalgae. With the aim to identify genes linked to the sexual phase of the centric planktonic diatom Skeletonemamarinoi, we carried out an RNA-seq experiment comparing the expression level of transcripts in sexualized cells with that of large cells not competent for sex. A set of genes involved in meiosis were found upregulated. Despite the fact that flagellate gametes were observed in the sample, we did not detect the expression of genes involved in the synthesis of flagella that were upregulated during sexual reproduction in another centric diatom. A comparison with the set of genes changing during the first phases of sexual reproduction of the pennate diatom Pseudo-nitzschiamultistriata revealed the existence of commonalities, including the strong upregulation of genes with an unknown function that we named Sex Induced Genes (SIG). Our results further broadened the panel of genes that can be used as a marker for sexual reproduction of diatoms, crucial for the interpretation of metatranscriptomic datasets.", "doi": "10.3390/genes10070494", "pmid": "31261777", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes10070494"}, {"db": "pmc", "key": "PMC6678668"}], "notes": [], "created": "2019-12-02T17:20:01.524Z", "modified": "2024-01-16T13:48:44.208Z"}, {"entity": "publication", "iuid": "b8108f9c9adc4678ad72535ebfff1c49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8108f9c9adc4678ad72535ebfff1c49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8108f9c9adc4678ad72535ebfff1c49"}}, "title": "Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.", "authors": [{"family": "Garriss", "given": "Genevi\u00e8ve", "initials": "G"}, {"family": "Nannapaneni", "given": "Priyanka", "initials": "P"}, {"family": "Sim\u00f5es", "given": "Alexandra S", "initials": "AS"}, {"family": "Browall", "given": "Sarah", "initials": "S"}, {"family": "Subramanian", "given": "Karthik", "initials": "K"}, {"family": "S\u00e1-Le\u00e3o", "given": "Raquel", "initials": "R"}, {"family": "Goossens", "given": "Herman", "initials": "H"}, {"family": "de Lencastre", "given": "Herminia", "initials": "H"}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2019-06-25", "journal": {"volume": "10", "issn": "2150-7511", "issue": "3", "title": "MBio", "issn-l": null}, "abstract": "Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation.IMPORTANCES. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae.", "doi": "10.1128/mBio.01286-19", "pmid": "31239383", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mBio.01286-19"}, {"db": "pmc", "key": "PMC6593409"}], "notes": [], "created": "2019-12-02T16:52:29.187Z", "modified": "2024-01-16T13:48:44.221Z"}, {"entity": "publication", "iuid": "db27016298734206894290f8e3052b5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db27016298734206894290f8e3052b5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db27016298734206894290f8e3052b5e"}}, "title": "Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.", "authors": [{"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Johannsen", "given": "Gunnar", "initials": "G"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2019-06-21", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "issn-l": "2235-2988", "volume": "9", "issue": null, "pages": "216"}, "abstract": "Periodontitis is a microbial-induced chronic inflammatory disease, which may not only result in tooth loss, but can also contribute to the development of various systemic diseases. The transition from healthy to diseased periodontium depends on microbial dysbiosis and impaired host immune response. Although periodontitis is a common disease as well as associated with various systemic inflammatory conditions, the taxonomic profiling of the salivary microbiota in periodontitis and its association with host immune and inflammatory mediators has not been reported. Therefore, the aim of this study was to identify key pathogens and their potential interaction with the host's inflammatory mediators in saliva samples for periodontitis risk assessment. The microbial 16S rRNA gene sequencing and the levels of inflammatory mediators were performed in saliva samples from patients with chronic periodontitis and periodontally healthy control subjects. The salivary microbial community composition differed significantly between patients with chronic periodontitis and healthy controls. Our analyses identified a number of microbes, including bacteria assigned to Eubacterium saphenum, Tannerella forsythia, Filifactor alocis, Streptococcus mitis/parasanguinis, Parvimonas micra, Prevotella sp., Phocaeicola sp., and Fretibacterium sp. as more abundant in periodontitis, compared to healthy controls. In samples from healthy individuals, we identified Campylobacter concisus, and Veillonella sp. as more abundant. Integrative analysis of the microbiota and inflammatory mediators/cytokines revealed associations that included positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6R\u03b1, sTNF-R1, and gp130/sIL-6R\u03b2. In addition, a negative correlation was identified between IL-10 and Filifactor alocis. Our results reveal distinct and disease-specific patterns of salivary microbial composition between patients with periodontitis and healthy controls, as well as significant correlations between microbiota and host-mediated inflammatory cytokines. The positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6R\u03b1, sTNF-R1, and gp130/sIL-6R\u03b2 might have the future potential to serve as a combined bacteria-host salivary biomarker panel for diagnosis of the chronic infectious disease periodontitis. However, further studies are required to determine the capacity of these microbes and inflammatory mediators as a salivary biomarker panel for periodontitis.", "doi": "10.3389/fcimb.2019.00216", "pmid": "31281801", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6598052"}], "notes": [], "created": "2019-12-02T16:52:27.072Z", "modified": "2024-01-16T13:48:44.230Z"}, {"entity": "publication", "iuid": "59b8dae6dc8d41c6885ed37cf0f856a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b8dae6dc8d41c6885ed37cf0f856a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b8dae6dc8d41c6885ed37cf0f856a3"}}, "title": "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.", "authors": [{"family": "Smythe", "given": "Ashleigh B", "initials": "AB"}, {"family": "Holovachov", "given": "Oleksandr", "initials": "O"}, {"family": "Kocot", "given": "Kevin M", "initials": "KM"}], "type": "journal article", "published": "2019-06-13", "journal": {"volume": "19", "issn": "1471-2148", "issue": "1", "pages": "121", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum.\n\nWe supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with a high proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA.\n\nExpanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment.", "doi": "10.1186/s12862-019-1444-x", "pmid": "31195978", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-019-1444-x"}, {"db": "pmc", "key": "PMC6567515"}], "notes": [], "created": "2019-12-02T17:20:53.416Z", "modified": "2020-01-21T13:56:15.752Z"}, {"entity": "publication", "iuid": "1798d24fb91f49cabfed216c26dca811", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1798d24fb91f49cabfed216c26dca811.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1798d24fb91f49cabfed216c26dca811"}}, "title": "Modeling Motor Neuron Resilience in ALS Using Stem Cells.", "authors": [{"family": "Allodi", "given": "Ilary", "initials": "I"}, {"family": "Nijssen", "given": "Jik", "initials": "J"}, {"family": "Benitez", "given": "Julio Aguila", "initials": "JA"}, {"family": "Schweingruber", "given": "Christoph", "initials": "C"}, {"family": "Fuchs", "given": "Andrea", "initials": "A"}, {"family": "Bonvicini", "given": "Gillian", "initials": "G"}, {"family": "Cao", "given": "Ming", "initials": "M"}, {"family": "Kiehn", "given": "Ole", "initials": "O"}, {"family": "Hedlund", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2019-06-11", "journal": {"volume": "12", "issn": "2213-6711", "issue": "6", "pages": "1329-1341", "title": "Stem Cell Reports", "issn-l": "2213-6711"}, "abstract": "Oculomotor neurons, which regulate eye movement, are resilient to degeneration in the lethal motor neuron disease amyotrophic lateral sclerosis (ALS). It would be highly advantageous if motor neuron resilience could be modeled in vitro. Toward this goal, we generated a high proportion of oculomotor neurons from mouse embryonic stem cells through temporal overexpression of PHOX2A in neuronal progenitors. We demonstrate, using electrophysiology, immunocytochemistry, and RNA sequencing, that in vitro-generated neurons are bona fide oculomotor neurons based on their cellular properties and similarity to their in vivo counterpart in rodent and man. We also show that in vitro-generated oculomotor neurons display a robust activation of survival-promoting Akt signaling and are more resilient to the ALS-like toxicity of kainic acid than spinal motor neurons. Thus, we can generate bona fide oculomotor neurons in vitro that display a resilience similar to that seen in vivo.", "doi": "10.1016/j.stemcr.2019.04.009", "pmid": "31080111", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S2213-6711(19)30131-6"}, {"db": "pmc", "key": "PMC6565614"}], "notes": [], "created": "2020-01-08T16:47:16.912Z", "modified": "2020-01-21T13:56:16.293Z"}, {"entity": "publication", "iuid": "5772fc9a0bde4a55bcf300028482da2e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5772fc9a0bde4a55bcf300028482da2e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5772fc9a0bde4a55bcf300028482da2e"}}, "title": "Spatiotemporal structure of cell fate decisions in murine neural crest", "authors": [{"family": "Soldatov", "given": "Ruslan", "initials": "R", "orcid": "0000-0002-5670-5881", "researcher": {"href": "https://publications.scilifelab.se/researcher/3800b61f5f7042e89514b439e9532a97.json"}}, {"family": "Kaucka", "given": "Marketa", "initials": "M", "orcid": "0000-0002-8781-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/933187e42ddc4ab6a29c46d5cca411e6.json"}}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME", "orcid": "0000-0002-0563-7399", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e0722d8c5484a13bb37c3a3b084ff8c.json"}}, {"family": "Petersen", "given": "Julian", "initials": "J", "orcid": "0000-0002-7444-0610", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d20bbfd5a540a58aac82ada8d80b0d.json"}}, {"family": "Chontorotzea", "given": "Tatiana", "initials": "T", "orcid": "0000-0002-6134-1365", "researcher": {"href": "https://publications.scilifelab.se/researcher/7426e1056a94430bb9ab69191e623fd2.json"}}, {"family": "Englmaier", "given": "Lukas", "initials": "L", "orcid": "0000-0002-0082-2616", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba3d0eb3f634ccda4e6562c37bd77f2.json"}}, {"family": "Akkuratova", "given": "Natalia", "initials": "N", "orcid": "0000-0001-6733-8119", "researcher": {"href": "https://publications.scilifelab.se/researcher/68fc565dc99b4e8eb61d39dcef0f3a48.json"}}, {"family": "Yang", "given": "Yunshi", "initials": "Y", "orcid": "0000-0003-0396-5257", "researcher": {"href": "https://publications.scilifelab.se/researcher/4663511b58bd4c0f9c69da8445c7974b.json"}}, {"family": "H\u00e4ring", "given": "Martin", "initials": "M", "orcid": "0000-0003-4949-0533", "researcher": {"href": "https://publications.scilifelab.se/researcher/eafb570acc6d40159228d08f9dcc985f.json"}}, {"family": "Dyachuk", "given": "Viacheslav", "initials": "V", "orcid": "0000-0001-8100-7367", "researcher": {"href": "https://publications.scilifelab.se/researcher/a32abc6aafed40e382beb35f873ae91c.json"}}, {"family": "Bock", "given": "Christoph", "initials": "C", "orcid": "0000-0001-6091-3088", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab95ee1c8284fa7bf2e5a2ee987c835.json"}}, {"family": "Farlik", "given": "Matthias", "initials": "M", "orcid": "0000-0003-0698-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/906ad9a447b64e028f9cf41fbeaea108.json"}}, {"family": "Piacentino", "given": "Michael L", "initials": "ML", "orcid": "0000-0003-1773-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75e58e24dbcf4b8ba91ce39db1491c69.json"}}, {"family": "Boismoreau", "given": "Franck", "initials": "F"}, {"family": "Hilscher", "given": "Markus M", "initials": "MM", "orcid": "0000-0001-7782-0830", "researcher": {"href": "https://publications.scilifelab.se/researcher/1de5317c53f34bc89dabfddb0be44983.json"}}, {"family": "Yokota", "given": "Chika", "initials": "C"}, {"family": "Qian", "given": "Xiaoyan", "initials": "X", "orcid": "0000-0001-7509-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/835743f43787492498e3c610184cf9a3.json"}}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Bronner", "given": "Marianne E", "initials": "ME", "orcid": "0000-0003-4274-1862", "researcher": {"href": "https://publications.scilifelab.se/researcher/56516b93bfb047aeab63c9d2fee21d4a.json"}}, {"family": "Croci", "given": "Laura", "initials": "L", "orcid": "0000-0002-7826-428X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e08f8646894441297506e2a3eb5fb57.json"}}, {"family": "Hsiao", "given": "Wen Yu", "initials": "WY"}, {"family": "Guertin", "given": "David A", "initials": "DA"}, {"family": "Brunet", "given": "Jean Francois", "initials": "JF", "orcid": "0000-0002-1985-6103", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e7516ee3e5a47ed9b6163b10d5baf9a.json"}}, {"family": "Consalez", "given": "Gian Giacomo", "initials": "GG", "orcid": "0000-0003-4594-6273", "researcher": {"href": "https://publications.scilifelab.se/researcher/1eabaebce3194d9c93e65ce4123f4254.json"}}, {"family": "Ernfors", "given": "Patrik", "initials": "P", "orcid": "0000-0002-1140-3986", "researcher": {"href": "https://publications.scilifelab.se/researcher/c31df7b8976c496c9d3e3199a91f9d22.json"}}, {"family": "Fried", "given": "Kaj", "initials": "K", "orcid": "0000-0002-9997-7078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46eaae026524ee6b9b589f12846b458.json"}}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}, {"family": "Adameyko", "given": "Igor", "initials": "I", "orcid": "0000-0001-5471-0356", "researcher": {"href": "https://publications.scilifelab.se/researcher/346f484a56cb4ad5b866b194ccd44e4f.json"}}], "type": "journal-article", "published": "2019-06-07", "journal": {"volume": "364", "issn": "0036-8075", "issue": "6444", "pages": "eaas9536", "title": "Science", "issn-l": null}, "abstract": "Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single-cell analysis, we show that mouse trunk neural crest cells become biased toward neuronal lineages when they delaminate from the neural tube, whereas cranial neural crest cells acquire ectomesenchyme potential dependent on activation of the transcription factor Twist1. The choices that neural crest cells make to become sensory, glial, autonomic, or mesenchymal cells can be formalized as a series of sequential binary decisions. Each branch of the decision tree involves initial coactivation of bipotential properties followed by gradual shifts toward commitment. Competing fate programs are coactivated before cells acquire fate-specific phenotypic traits. Determination of a specific fate is achieved by increased synchronization of relevant programs and concurrent repression of competing fate programs.", "doi": "10.1126/science.aas9536", "pmid": "31171666", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "In Situ Sequencing": "Collaborative"}, "xrefs": [{"db": "pii", "key": "364/6444/eaas9536"}], "notes": [], "created": "2019-06-12T08:11:45.162Z", "modified": "2025-10-17T13:02:18.356Z"}, {"entity": "publication", "iuid": "d171962fdb334ddb8594478ee9618c44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d171962fdb334ddb8594478ee9618c44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d171962fdb334ddb8594478ee9618c44"}}, "title": "Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Rastas", "given": "Pasi", "initials": "P"}, {"family": "Hornett", "given": "Emily A", "initials": "EA"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Clark", "given": "Nathan", "initials": "N"}, {"family": "Morehouse", "given": "Nathan", "initials": "N"}, {"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M"}, {"family": "Cols", "given": "Jofre Carnicer", "initials": "JC"}, {"family": "Dircksen", "given": "Heinrich", "initials": "H"}, {"family": "Meslin", "given": "Camille", "initials": "C"}, {"family": "Keehnen", "given": "Naomi", "initials": "N"}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Sikkink", "given": "Kristin", "initials": "K"}, {"family": "Vives", "given": "Maria", "initials": "M"}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Woronik", "given": "Alyssa", "initials": "A"}, {"family": "Boggs", "given": "Carol L", "initials": "CL"}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "5", "issn": "2375-2548", "issue": "6", "pages": "eaau3648", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly ( Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.", "doi": "10.1126/sciadv.aau3648", "pmid": "31206013", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "aau3648"}, {"db": "pmc", "key": "PMC6561736"}], "notes": [], "created": "2019-12-02T16:53:05.154Z", "modified": "2020-01-21T13:56:15.532Z"}, {"entity": "publication", "iuid": "ecdd0ea759dd48d5938553600833739d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ecdd0ea759dd48d5938553600833739d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ecdd0ea759dd48d5938553600833739d"}}, "title": "Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells", "authors": [{"family": "Tibbitt", "given": "Christopher Andrew", "initials": "CA"}, {"family": "Stark", "given": "Julian Mario", "initials": "JM"}, {"family": "Martens", "given": "Liesbet", "initials": "L"}, {"family": "Ma", "given": "Junjie", "initials": "J"}, {"family": "Mold", "given": "Jeff Eron", "initials": "JE"}, {"family": "Deswarte", "given": "Kim", "initials": "K"}, {"family": "Oliynyk", "given": "Ganna", "initials": "G"}, {"family": "Feng", "given": "Xiaogang", "initials": "X"}, {"family": "Lambrecht", "given": "Bart Norbert", "initials": "BN"}, {"family": "De Bleser", "given": "Pieter", "initials": "P"}, {"family": "Nyl\u00e9n", "given": "Susanne", "initials": "S"}, {"family": "Hammad", "given": "Hamida", "initials": "H"}, {"family": "Arsenian Henriksson", "given": "Marie", "initials": "M"}, {"family": "Saeys", "given": "Yvan", "initials": "Y"}, {"family": "Coquet", "given": "Jonathan Marie", "initials": "JM"}], "type": "journal-article", "published": "2019-06-00", "journal": {"volume": "51", "issn": "1097-4180", "issue": "1", "pages": "169-184.e5", "title": "Immunity", "issn-l": "1074-7613"}, "abstract": "Naive CD4 + T cells differentiate into functionally diverse T helper (Th) cell subsets. Th2 cells play a pathogenic role in asthma, yet a clear picture of their transcriptional profile is lacking. We performed single-cell RNA sequencing (scRNA-seq) of T helper cells from lymph node, lung, and airways in the house dust mite (HDM) model of allergic airway disease. scRNA-seq resolved transcriptional profiles of naive CD4+ T, Th1, Th2, regulatory T (Treg) cells, and a CD4+ T cell population responsive to type I interferons. Th2 cells in the airways were enriched for transcription of many genes, including Cd200r1, Il6, Plac8, and Igfbp7, and their mRNA profile was supported by analysis of chromatin accessibility and flow cytometry. Pathways associated with lipid metabolism were enriched in Th2 cells, and experiments with inhibitors of key metabolic pathways supported roles for glucose and lipid metabolism. These findings provide insight into the differentiation of pathogenic Th2 cells in the context of allergy.", "doi": "10.1016/j.immuni.2019.05.014", "pmid": "31231035", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2019-07-01T07:43:34.091Z", "modified": "2020-10-08T16:40:27.576Z"}, {"entity": "publication", "iuid": "59b109067ae843b8bb09daec1e8b2e5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b109067ae843b8bb09daec1e8b2e5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b109067ae843b8bb09daec1e8b2e5a"}}, "title": "Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.", "authors": [{"family": "Maffezzini", "given": "Camilla", "initials": "C"}, {"family": "Laine", "given": "Isabelle", "initials": "I"}, {"family": "Dallabona", "given": "Cristina", "initials": "C"}, {"family": "Clemente", "given": "Paula", "initials": "P"}, {"family": "Calvo-Garrido", "given": "Javier", "initials": "J"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Naess", "given": "Karin", "initials": "K"}, {"family": "Barbaro", "given": "Michela", "initials": "M"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Donnini", "given": "Claudia", "initials": "C"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}, {"family": "Wedell", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "7", "issn": "2324-9269", "issue": "6", "pages": "e654", "title": "Mol Genet Genomic Med", "issn-l": "2324-9269"}, "abstract": "Mutations in mitochondrial aminoacyl tRNA synthetases form a subgroup of mitochondrial disorders often only perturbing brain function by affecting mitochondrial translation. Here we report two siblings with mitochondrial disease, due to compound heterozygous mutations in the mitochondrial tryptophanyl-tRNA synthetase (WARS2) gene, presenting with severe neurological symptoms but normal mitochondrial function in skeletal muscle biopsies and cultured skin fibroblasts.\n\nWhole exome sequencing on genomic DNA samples from both subjects and their parents identified two compound heterozygous variants c.833T>G (p.Val278Gly) and c.938A>T (p.Lys313Met) in the WARS2 gene as potential disease-causing variants. We generated patient-derived neuroepithelial stem cells and modeled the disease in yeast and Drosophila melanogaster to confirm pathogenicity.\n\nBiochemical analysis of patient-derived neuroepithelial stem cells revealed a mild combined complex I and IV defect, while modeling the disease in yeast demonstrated that the reported aminoacylation defect severely affects respiration and viability. Furthermore, silencing of wild type WARS2 in Drosophila melanogaster showed that a partial defect in aminoacylation is enough to cause lethality.\n\nOur results establish the identified WARS2 variants as disease-causing and highlight the benefit of including human neuronal models, when investigating mutations specifically affecting the nervous system.", "doi": "10.1002/mgg3.654", "pmid": "30920170", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6565557"}], "notes": [], "created": "2019-11-25T10:51:56.375Z", "modified": "2020-01-21T13:56:16.268Z"}, {"entity": "publication", "iuid": "e1e30adcf1ba4b84a710f35638d4bf59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1e30adcf1ba4b84a710f35638d4bf59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1e30adcf1ba4b84a710f35638d4bf59"}}, "title": "Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.", "authors": [{"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Markljung", "given": "Ellen", "initials": "E"}, {"family": "Baranowska K\u00f6rberg", "given": "Izabella", "initials": "I"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Cao", "given": "Jia", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Holmdahl", "given": "Gundela", "initials": "G"}, {"family": "Barker", "given": "Gillian", "initials": "G"}, {"family": "Anderberg", "given": "Magnus", "initials": "M"}, {"family": "Vukojevi\u0107", "given": "Vladana", "initials": "V"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "7", "issn": "2324-9269", "issue": "6", "pages": "e666", "title": "Mol Genet Genomic Med", "issn-l": "2324-9269"}, "abstract": "The bladder exstrophy-epispadias complex (BEEC) is a congenital malformation of the bladder and urethra. The underlying causes of this malformation are still largely unknown; however, aside from environment, genetics is thought to play an essential role. The recurrent 22q11.2 microduplication is the most persistently detected genetic aberration found in BEEC cases.\n\nWe performed array comparative genomic hybridization (array-CGH) analysis of 76 Swedish BEEC patients. Statistical analysis was performed on current dataset pooled with previously published data on the 22q11.2 microduplication in BEEC patients. We performed massive parallel sequencing (MPS) of the 22q11.2 region in 20 BEEC patients without the 22q11.2 microduplication followed by functional studies.\n\nWe identified three additional cases with the 22q11.2 microduplication. Pooling data from this study with previously published reports showed a statistically significant enrichment of the 22q11.2 microduplication in BEEC patients (2.61% in cases vs. 0.08% in controls; OR = 32.6; p = 8.7 \u00d7 10 -4 ). MPS of the 22q11.2 region in 20 BEEC patients without the 22q11.2 microduplication identified a novel variant in LZTR1 (p.Ser698Phe) in one patient. Functional evaluation of the LZTR1 p.Ser698Phe variant in live NIH 3T3 cells showed that the concentration and cytoplasmic mobility differ between the Lztr1wt and Lztr1mut , indicating a potential functional effect of the LZTR1mut .\n\nOur study further emphasizes the involvement of the 22q11.2 region in BEEC development and highlights LZTR1 as a candidate gene underlying the urogenital malformation.", "doi": "10.1002/mgg3.666", "pmid": "31044557", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6565582"}], "notes": [], "created": "2019-12-02T16:50:51.425Z", "modified": "2024-01-16T13:48:44.280Z"}, {"entity": "publication", "iuid": "74d4aa31e7774b5d81c9f6b39c75f31c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74d4aa31e7774b5d81c9f6b39c75f31c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74d4aa31e7774b5d81c9f6b39c75f31c"}}, "title": "Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.", "authors": [{"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Damlien", "given": "Hege", "initials": "H"}, {"family": "Manninen", "given": "Mikael A", "initials": "MA", "orcid": "0000-0002-8906-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce8d3c355c374e8794526fdfeb1c87e8.json"}}, {"family": "Nordqvist", "given": "Bengt", "initials": "B"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2019-05-15", "journal": {"volume": "2", "issn": "2399-3642", "issue": null, "pages": "185", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.", "doi": "10.1038/s42003-019-0399-1", "pmid": "31123709", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "399"}, {"db": "pmc", "key": "PMC6520363"}, {"db": "Dryad", "key": "10.5061/dryad.j3k19p9"}], "notes": [], "created": "2019-12-02T17:20:27.160Z", "modified": "2024-01-16T13:48:44.340Z"}, {"entity": "publication", "iuid": "a60e7870d37e4fc7b2d4daa9b9f62a4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a60e7870d37e4fc7b2d4daa9b9f62a4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a60e7870d37e4fc7b2d4daa9b9f62a4d"}}, "title": "Adult Neural Progenitor Cells Transplanted into Spinal Cord Injury Differentiate into Oligodendrocytes, Enhance Myelination, and Contribute to Recovery.", "authors": [{"family": "Sankavaram", "given": "Sreenivasa Raghavan", "initials": "SR"}, {"family": "Hakim", "given": "Ramil", "initials": "R"}, {"family": "Covacu", "given": "Ruxandra", "initials": "R"}, {"family": "Frostell", "given": "Arvid", "initials": "A"}, {"family": "Neumann", "given": "Susanne", "initials": "S"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}, {"family": "Brundin", "given": "Lou", "initials": "L"}], "type": "journal article", "published": "2019-05-14", "journal": {"volume": "12", "issn": "2213-6711", "issue": "5", "pages": "950-966", "title": "Stem Cell Reports", "issn-l": "2213-6711"}, "abstract": "Long-term survival and integration of neural progenitor cells (NPCs) transplanted following spinal cord injury (SCI) have been observed. However, questions concerning the differentiation choice, the mechanism of action, and the contribution of NPCs to functional recovery remains unanswered. Therefore, we investigated the differentiation of NPCs, global transcriptomal changes in transplanted NPCs, the effect of NPCs on neuroinflammation, and the causality between NPC transplantation and functional recovery. We found that NPCs transplanted following SCI differentiate mainly into oligodendrocytes and enhance myelination, upregulate genes related to synaptic signaling and mitochondrial activity, and downregulate genes related to cytokine production and immune system response. NPCs suppress the expression of pro-inflammatory cytokines/chemokines; moreover, NPC ablation confirm that NPCs were responsible for enhanced recovery in hindlimb locomotor function. Understanding the reaction of transplanted NPCs is important for exploiting their full potential. Existence of causality implies that NPCs are useful in the treatment of SCI.", "doi": "10.1016/j.stemcr.2019.03.013", "pmid": "31031190", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S2213-6711(19)30098-0"}, {"db": "pmc", "key": "PMC6524946"}], "notes": [], "created": "2020-01-08T16:47:15.594Z", "modified": "2020-01-21T13:56:16.277Z"}, {"entity": "publication", "iuid": "9177255872b8466f8a249a93d1f5f2fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9177255872b8466f8a249a93d1f5f2fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9177255872b8466f8a249a93d1f5f2fd"}}, "title": "Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.", "authors": [{"family": "Eriksson", "given": "Kaja", "initials": "K"}, {"family": "Fei", "given": "Guozhong", "initials": "G"}, {"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Benchimol", "given": "Daniel", "initials": "D"}, {"family": "Lee", "given": "Linkiat", "initials": "L"}, {"family": "Hu", "given": "Yue O O", "initials": "YOO"}, {"family": "Kats", "given": "Anna", "initials": "A"}, {"family": "Saevarsdottir", "given": "Saedis", "initials": "S"}, {"family": "Catrina", "given": "Anca Irinel", "initials": "AI"}, {"family": "Klinge", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Lundberg", "given": "Karin", "initials": "K"}, {"family": "Jansson", "given": "Leif", "initials": "L"}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2019-05-08", "journal": {"volume": "8", "issn": "2077-0383", "issue": "5", "title": "J Clin Med", "issn-l": "2077-0383"}, "abstract": "This study aimed to investigate the periodontal health of patients with established rheumatoid arthritis (RA) in relation to oral microbiota, systemic and oral inflammatory mediators, and RA disease activity. Forty patients underwent full-mouth dental/periodontal and rheumatological examination, including collection of blood, saliva, gingival crevicular fluid (GCF) and subgingival plaque. Composition of plaque and saliva microbiota were analysed using 16S rRNA sequencing and levels of inflammatory mediators by multiplex-immunoassay. The majority of the patients (75%) had moderate or severe periodontitis and the rest had no/mild periodontitis. Anti-citrullinated protein antibody (ACPA) positivity was significantly more frequent in the moderate/severe periodontitis (86%) compared to the no/mild group (50%). No significance between groups was observed for RA disease duration or activity, or type of medication. Levels of sCD30/TNFRSF8, IFN-\u03b12, IL-19, IL-26, MMP-1, gp130/sIL-6R\u00df, and sTNF-R1 were significantly higher in serum or GCF, and April/TNFSF13 was significantly higher in serum and saliva samples in moderate/severe periodontitis. The microbial composition in plaque also differed significantly between the two groups. In conclusion, the majority of RA patients had moderate/severe periodontitis and that this severe form of the disease was significantly associated with ACPA positivity, an altered subgingival microbial profile, and increased levels of systemic and oral inflammatory mediators.", "doi": "10.3390/jcm8050630", "pmid": "31072030", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "jcm8050630"}, {"db": "pmc", "key": "PMC6572048"}], "notes": [], "created": "2019-12-02T16:52:27.808Z", "modified": "2024-01-16T13:48:44.354Z"}, {"entity": "publication", "iuid": "cadae02ceb7f4210bcf3917a66f37b41", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cadae02ceb7f4210bcf3917a66f37b41.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cadae02ceb7f4210bcf3917a66f37b41"}}, "title": "Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "Tomas Axel", "initials": "TA"}], "type": "journal article", "published": "2019-05-02", "journal": {"volume": "14", "issn": "1932-6203", "issue": "5", "pages": "e0216294", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Barnacle settlement involves sensing of a variety of exogenous cues. A pair of antennules is the main sensory organ that the cyprid larva uses to explore the surface. Antennules are equipped with a number of setae that have both chemo- and mechanosensing function. The current study explores the repertoire of sensory receptors in Balanus improvisus cyprid antennules with the goal to better understand sensory systems involved in the settling behavior of this species. We carried out transcriptome sequencing of dissected B. improvisus cyprid antennules. The generated transcriptome assembly was used to search for sensory receptors using HMM models. Among potential chemosensory genes, we identified the ionotropic receptors IR25a, IR8a and IR93a, and several divergent IR candidates to be expressed in the cyprid antennules. We found one gustatory-like receptor but no odorant receptors, chemosensory or odorant-binding proteins. Apart from chemosensory receptors, we also identified 13 potential mechanosensory genes represented by several transient receptor potential channels (TRP) subfamilies. Furthermore, we analyzed changes in expression profiles of IRs and TRPs during the B. improvisus settling process. Several of the sensory genes were differentially expressed during the course of larval settlement. This study gives expanded knowledge about the sensory systems present in barnacles, a taxonomic group for which only limited information about receptors is currently available. It furthermore serves as a starting point for more in depth studies of how sensory signaling affects settling behavior in barnacles with implications for preventing biofouling.", "doi": "10.1371/journal.pone.0216294", "pmid": "31048879", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-32972"}, {"db": "pmc", "key": "PMC6497305"}], "notes": [], "created": "2019-12-02T16:50:53.507Z", "modified": "2024-01-16T13:48:44.367Z"}, {"entity": "publication", "iuid": "b9b342441fc24f6b9cd0aa485a815d2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b9b342441fc24f6b9cd0aa485a815d2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b9b342441fc24f6b9cd0aa485a815d2c"}}, "title": "Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.", "authors": [{"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Armstrong", "given": "Ellie E", "initials": "EE"}, {"family": "Nylander", "given": "Johan", "initials": "J"}, {"family": "Thomas", "given": "Gregg W C", "initials": "GWC"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Benz", "given": "Brett W", "initials": "BW"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "8", "issn": "2047-217X", "issue": "5", "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for \"startle response\" and \"olfactory receptor activity\" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.", "doi": "10.1093/gigascience/giz003", "pmid": "30689847", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5300102"}, {"db": "pmc", "key": "PMC6497032"}], "notes": [], "created": "2019-12-02T17:19:31.826Z", "modified": "2024-01-16T13:48:44.395Z"}, {"entity": "publication", "iuid": "b1f4d18f745842fda29e557e90de70ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1f4d18f745842fda29e557e90de70ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1f4d18f745842fda29e557e90de70ed"}}, "title": "Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.", "authors": [{"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA", "orcid": "0000-0002-0408-3515", "researcher": {"href": "https://publications.scilifelab.se/researcher/e007c24aef2344d582f2e3d318b3f7cd.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "S\u00f6derberg", "given": "Jonas", "initials": "J"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2019-05-01", "journal": {"volume": "14", "issn": "1932-6203", "issue": "5", "pages": "e0215077", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.", "doi": "10.1371/journal.pone.0215077", "pmid": "31042716", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-18-32895"}, {"db": "pmc", "key": "PMC6493715"}], "notes": [], "created": "2019-11-24T12:41:36.969Z", "modified": "2021-07-07T15:19:08.434Z"}, {"entity": "publication", "iuid": "5cb8eb65fea748b69bd38d1f1bc5e7a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5cb8eb65fea748b69bd38d1f1bc5e7a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5cb8eb65fea748b69bd38d1f1bc5e7a3"}}, "title": "Gene expression profile of extraocular muscles following resection strabismus surgery.", "authors": [{"family": "Rodr\u00edguez", "given": "Maria Angels", "initials": "MA"}, {"family": "Sandgren Hochhard", "given": "Karin", "initials": "K"}, {"family": "Vicente", "given": "Andr\u00e9", "initials": "A"}, {"family": "Liu", "given": "Jing-Xia", "initials": "JX"}, {"family": "Pedrosa Domell\u00f6f", "given": "Fatima", "initials": "F"}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "182", "issn": "1096-0007", "issue": null, "pages": "182-193", "title": "Exp. Eye Res.", "issn-l": "0014-4835"}, "abstract": "This paper aims to identify key biological processes triggered by resection surgery in the extraocular muscles (EOMs) of a rabbit model of strabismus surgery by studying changes in gene expression. Resection surgery was performed in the superior rectus of 16 rabbits and a group of non-operated rabbits served as control. Muscle samples were collected from groups of four animals 1, 2, 4 and 6 weeks after surgery and processed for RNA-sequencing and immunohistochemistry. We identified a total of 164; 136; 64 and 12 differentially expressed genes 1, 2, 4 and 6 weeks after surgery. Gene Ontology enrichment analysis revealed that differentially expressed genes were involved in biological pathways related to metabolism, response to stimulus mainly related with regulation of immune response, cell cycle and extracellular matrix. A complementary pathway analysis and network analysis performed with Ingenuity Pathway Analysis tool corroborated and completed these findings. Collagen I, fibronectin and versican, evaluated by immunofluorescence, showed that changes at the gene expression level resulted in variation at the protein level. Tenascin-C staining in resected muscles demonstrated the formation of new tendon and myotendinous junctions. These data provide new insights about the biological response of the EOMs to resection surgery and may form the basis for future strategies to improve the outcome of strabismus surgery.", "doi": "10.1016/j.exer.2019.03.022", "pmid": "30953624", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4835(19)30027-2"}], "notes": [], "created": "2020-01-07T13:20:46.691Z", "modified": "2021-07-02T10:55:41.968Z"}, {"entity": "publication", "iuid": "1138e1f8b82c448587d58bae89ae15a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1138e1f8b82c448587d58bae89ae15a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1138e1f8b82c448587d58bae89ae15a5"}}, "title": "Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.", "authors": [{"family": "Xu", "given": "Luohao", "initials": "L"}, {"family": "Auer", "given": "Gabriel", "initials": "G"}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Deng", "given": "Yuan", "initials": "Y"}, {"family": "Feng", "given": "Shaohong", "initials": "S"}, {"family": "Zhang", "given": "Guojie", "initials": "G", "orcid": "0000-0001-6860-1521", "researcher": {"href": "https://publications.scilifelab.se/researcher/62f3c7981a1c43909817e72519232ff8.json"}}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "Christidis", "given": "Les", "initials": "L"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Irestedt", "given": "Martin", "initials": "M", "orcid": "0000-0003-1680-6861", "researcher": {"href": "https://publications.scilifelab.se/researcher/f390f09c31994a01a88d8e0d82c01ce6.json"}}, {"family": "Zhou", "given": "Qi", "initials": "Q", "orcid": "0000-0002-7419-2047", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69266aa587d4126a23aa91c5bedfff8.json"}}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "3", "issn": "2397-334X", "issue": "5", "pages": "834-844", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.", "doi": "10.1038/s41559-019-0850-1", "pmid": "30936435", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-019-0850-1"}], "notes": [], "created": "2019-12-02T17:20:28.490Z", "modified": "2024-01-16T13:48:44.423Z"}, {"entity": "publication", "iuid": "7915130bcb4c4d22a9517ae48ec1c487", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7915130bcb4c4d22a9517ae48ec1c487.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7915130bcb4c4d22a9517ae48ec1c487"}}, "title": "An Atlas of Vagal Sensory Neurons and Their Molecular Specialization", "authors": [{"family": "Kupari", "given": "Jussi", "initials": "J"}, {"family": "H\u00e4ring", "given": "Martin", "initials": "M"}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}], "type": "journal-article", "published": "2019-05-00", "journal": {"title": "Cell Rep", "issn": "2211-1247", "issn-l": null, "volume": "27", "issue": "8", "pages": "2508-2523.e4"}, "abstract": "Sensory functions of the vagus nerve are critical for conscious perceptions and for monitoring visceral functions in the cardio-pulmonary and gastrointestinal systems. Here, we present a comprehensive identification, classification, and validation of the neuron types in the neural crest (jugular) and placode (nodose) derived vagal ganglia by single-cell RNA sequencing (scRNA-seq) transcriptomic analysis. Our results reveal major differences between neurons derived from different embryonic origins. Jugular neurons exhibit fundamental similarities to the somatosensory spinal neurons, including major types, such as C-low threshold mechanoreceptors (C-LTMRs), A-LTMRs, A\u03b4-nociceptors, and cold-, and mechano-heat C-nociceptors. In contrast, the nodose ganglion contains 18 distinct types dedicated to surveying the physiological state of the internal body. Our results reveal a vast diversity of vagal neuron types, including many previously unanticipated types, as well as proposed types that are consistent with chemoreceptors, nutrient detectors, baroreceptors, and stretch and volume mechanoreceptors of the respiratory, gastrointestinal, and cardiovascular systems.", "doi": "10.1016/j.celrep.2019.04.096", "pmid": "31116992", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-05-28T12:36:42.513Z", "modified": "2024-01-16T13:48:44.430Z"}, {"entity": "publication", "iuid": "823dc730a9e840b98708400b86b3f7d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/823dc730a9e840b98708400b86b3f7d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/823dc730a9e840b98708400b86b3f7d1"}}, "title": "Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient", "authors": [{"family": "Helgadottir", "given": "Hafdis T", "initials": "HT"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Wall\u00e9n Arzt", "given": "Emelie", "initials": "E"}, {"family": "Lindstr\u00f6m", "given": "Anna Karin", "initials": "AK"}, {"family": "Graff", "given": "Caroline", "initials": "C"}, {"family": "Eriksson", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2019-04-24", "journal": {"volume": "28", "issn": "0964-6906", "issue": "16", "pages": "2675-2685", "title": "Hum Mol Genet", "issn-l": "0964-6906"}, "abstract": "Alzheimer's disease (AD) is the most common neurodegenerative disease worldwide. Familial cases suggest genetic components; however, monogenetic causes are few, and the vast majority of incidences have unknown cause. Sequencing efforts have focused on germline mutations, but improved technology has opened up for studies on somatic mutations in affected brain tissue samples. Here we use ultra-deep sequencing on brain and blood from early-onset AD (EOAD) and late-onset AD (LOAD) patients and non-AD individuals (n = 16). In total, 2.86 Mb of genomic regions, previously associated with AD, were targeted included 28 genes and upstream and downstream regulatory regions. Tailored downstream bioinformatics filtering identified 11 somatic single nucleotide variants in the temporal cortex in AD patients and none in the controls. One variant was validated to be present at 0.4% allele frequency in temporal cortex of a LOAD patient. This variant was predicted to affect transcription factor binding sites upstream of the CD55 gene, contributing to AD pathogenesis by affecting the complement system. Our results suggest that future studies targeting larger portions of the genome for somatic mutation analysis are important to obtain an increased understanding for the molecular basis of both EOAD and LOAD.", "doi": "10.1093/hmg/ddz085", "pmid": "31216356", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2019-08-05T12:46:47.639Z", "modified": "2024-01-16T13:48:44.438Z"}, {"entity": "publication", "iuid": "c95059ab85f54855b9c9f2c9f8679d42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c95059ab85f54855b9c9f2c9f8679d42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c95059ab85f54855b9c9f2c9f8679d42"}}, "title": "PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.", "authors": [{"family": "Falc\u00e3o", "given": "Ana Mendanha", "initials": "AM"}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Scaglione", "given": "Antonella", "initials": "A"}, {"family": "Rinwa", "given": "Puneet", "initials": "P"}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Liang", "given": "Jialiang", "initials": "J"}, {"family": "Larsen", "given": "Sara C", "initials": "SC"}, {"family": "Heskol", "given": "Abeer", "initials": "A"}, {"family": "Frawley", "given": "Rebecca", "initials": "R"}, {"family": "Klingener", "given": "Michael", "initials": "M"}, {"family": "Varas-Godoy", "given": "Manuel", "initials": "M"}, {"family": "Raposo", "given": "Alexandre A S F", "initials": "AASF"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}, {"family": "Castro", "given": "Diogo S", "initials": "DS"}, {"family": "Nielsen", "given": "Michael L", "initials": "ML"}, {"family": "Casaccia", "given": "Patrizia", "initials": "P"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal article", "published": "2019-04-23", "journal": {"volume": "27", "issn": "2211-1247", "issue": "4", "pages": "1090-1102.e10", "title": "Cell Rep", "issn-l": null}, "abstract": "Citrullination, the deimination of peptidylarginine residues into peptidylcitrulline, has been implicated in the etiology of several diseases. In multiple sclerosis, citrullination is thought to be a major driver of pathology through hypercitrullination and destabilization of myelin. As such, inhibition of citrullination has been suggested as a therapeutic strategy for MS. Here, in contrast, we show that citrullination by peptidylarginine deiminase 2 (PAD2) contributes to normal oligodendrocyte differentiation, myelination, and motor function. We identify several targets for PAD2, including myelin and chromatin-related proteins, implicating PAD2 in epigenomic regulation. Accordingly, we observe that PAD2 inhibition and its knockdown affect chromatin accessibility and prevent the upregulation of oligodendrocyte differentiation genes. Moreover, mice lacking PAD2 display motor dysfunction and a decreased number of myelinated axons in the corpus callosum. We conclude that citrullination contributes to proper oligodendrocyte lineage progression and myelination.", "doi": "10.1016/j.celrep.2019.03.108", "pmid": "31018126", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(19)30455-3"}, {"db": "pmc", "key": "PMC6486480"}], "notes": [], "created": "2019-12-02T17:20:29.567Z", "modified": "2024-01-16T13:48:44.447Z"}, {"entity": "publication", "iuid": "f3999ad8c5444765b9b286d1e989c482", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3999ad8c5444765b9b286d1e989c482.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3999ad8c5444765b9b286d1e989c482"}}, "title": "The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement", "authors": [{"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}], "type": "journal-article", "published": "2019-04-21", "journal": {"volume": "35", "issn": "0892-7014", "issue": "4", "pages": "416-428", "title": "Biofouling", "issn-l": null}, "abstract": "A key question in barnacle biology is the nature of cues that induce gregarious settlement. One of the characterised cues is the waterborne settlement pheromone (WSP). This study aimed to identify WSP homologues in Balanus improvisus and to investigate their expression during settlement. Six WSP homologues were identified, all containing an N-terminal signal peptide, a conserved core region, and a variable C-terminus comprising several -GR- and -HDDH- motifs. The B. improvisus WSP homologues were expressed in all settlement stages but showed different expression patterns. The homologue most similar to the B. amphitrite WSP was the most abundant and was constantly expressed during settlement. In contrast, several of the other WSP homologues showed the greatest expression in the juvenile stage. The presence of several WSP homologues suggests the existence of a pheromone mix, where con-specificity might be determined by a combination of sequence characteristics and the concentration of the individual components.", "doi": "10.1080/08927014.2019.1602123", "pmid": "31142149", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-11-25T14:28:40.486Z", "modified": "2024-01-16T13:48:44.455Z"}, {"entity": "publication", "iuid": "34431505d38f4f6eb101f11d50a4f4f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34431505d38f4f6eb101f11d50a4f4f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34431505d38f4f6eb101f11d50a4f4f1"}}, "title": "The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J"}, {"family": "Frankl-Vilches", "given": "Carolina", "initials": "C"}, {"family": "da Silva Dos Santos", "given": "Michelly", "initials": "M"}, {"family": "de Oliveira", "given": "Edivaldo H C", "initials": "EHC"}, {"family": "Gahr", "given": "Manfred", "initials": "M"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2019-04-13", "journal": {"volume": "10", "issn": "2073-4425", "issue": "4", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch ( Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.", "doi": "10.3390/genes10040301", "pmid": "31013951", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "genes10040301"}, {"db": "pmc", "key": "PMC6523648"}], "notes": [], "created": "2019-12-02T17:20:49.877Z", "modified": "2024-01-16T13:48:44.479Z"}, {"entity": "publication", "iuid": "ea3c5fb6a9354e7e9c03e02d99b380de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea3c5fb6a9354e7e9c03e02d99b380de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea3c5fb6a9354e7e9c03e02d99b380de"}}, "title": "SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.", "authors": [{"family": "Calvo-Garrido", "given": "Javier", "initials": "J"}, {"family": "Maffezzini", "given": "Camilla", "initials": "C"}, {"family": "Schober", "given": "Florian A", "initials": "FA"}, {"family": "Clemente", "given": "Paula", "initials": "P"}, {"family": "Uhlin", "given": "Elias", "initials": "E"}, {"family": "Kele", "given": "Malin", "initials": "M"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Bruhn", "given": "Helene", "initials": "H"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2019-04-09", "journal": {"volume": "12", "issn": "2213-6711", "issue": "4", "pages": "696-711", "title": "Stem Cell Reports", "issn-l": "2213-6711"}, "abstract": "Neurodegenerative disorders are an increasingly common and irreversible burden on society, often affecting the aging population, but their etiology and disease mechanisms are poorly understood. Studying monogenic neurodegenerative diseases with known genetic cause provides an opportunity to understand cellular mechanisms also affected in more complex disorders. We recently reported that loss-of-function mutations in the autophagy adaptor protein SQSTM1/p62 lead to a slowly progressive neurodegenerative disease presenting in childhood. To further elucidate the neuronal involvement, we studied the cellular consequences of loss of p62 in a neuroepithelial stem cell (NESC) model and differentiated neurons derived from reprogrammed p62 patient cells or by CRISPR/Cas9-directed gene editing in NESCs. Transcriptomic and proteomic analyses suggest that p62 is essential for neuronal differentiation by controlling the metabolic shift from aerobic glycolysis to oxidative phosphorylation required for neuronal maturation. This shift is blocked by the failure to sufficiently downregulate lactate dehydrogenase expression due to the loss of p62, possibly through impaired Hif-1\u03b1 downregulation and increased sensitivity to oxidative stress. The findings imply an important role for p62 in neuronal energy metabolism and particularly in the regulation of the shift between glycolysis and oxidative phosphorylation required for normal neurodifferentiation.", "doi": "10.1016/j.stemcr.2019.01.023", "pmid": "30827875", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S2213-6711(19)30025-6"}, {"db": "pmc", "key": "PMC6449840"}], "notes": [], "created": "2019-11-25T15:59:40.691Z", "modified": "2024-01-16T13:48:44.488Z"}, {"entity": "publication", "iuid": "6ab4121934ba49068e285057df24bd62", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ab4121934ba49068e285057df24bd62.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ab4121934ba49068e285057df24bd62"}}, "title": "SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.", "authors": [{"family": "Hu", "given": "Francis Jingxin", "initials": "FJ"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2019-04-08", "journal": {"volume": "47", "issn": "1362-4962", "issue": "6", "pages": "e34", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Mutagenesis libraries are essential for combinatorial protein engineering. Despite improvements in gene synthesis and directed mutagenesis, current methodologies still have limitations regarding the synthesis of complete antibody single-chain variable fragment (scFv) genes and simultaneous diversification of all six CDRs. Here, we describe the generation of mutagenesis libraries for antibody affinity maturation using a cell-free solid-phase technique for annealing of single-strand mutagenic oligonucleotides. The procedure consists of PCR-based incorporation of uracil into a wild-type template, bead-based capture, elution of single-strand DNA, and in vitro uracil excision enzyme based degradation of the template DNA. Our approach enabled rapid (8 hours) mutagenesis and automated cloning of 50 position-specific alanine mutants for mapping of a scFv antibody paratope. We further exemplify our method by generating affinity maturation libraries with diversity introduced in critical, nonessential, or all CDR positions randomly. Assessment with Illumina deep sequencing showed less than 1% wild-type in two libraries and the ability to diversify all CDR positions simultaneously. Selections of the libraries with bacterial display and deep sequencing evaluation of the selection output showed that diversity introduced in non-essential positions allowed for a more effective enrichment of improved binders compared to the other two diversification strategies.", "doi": "10.1093/nar/gkz050", "pmid": "30715449", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5304719"}, {"db": "pmc", "key": "PMC6451119"}], "notes": [], "created": "2019-12-02T16:50:56.362Z", "modified": "2024-01-16T13:48:44.498Z"}, {"entity": "publication", "iuid": "f272f13d61ce44f89297c9f2144a3ad9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f272f13d61ce44f89297c9f2144a3ad9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f272f13d61ce44f89297c9f2144a3ad9"}}, "title": "Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.", "authors": [{"family": "Maniatis", "given": "Silas", "initials": "S", "orcid": "0000-0002-0888-1477", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cd9acba967c4d84b3c3c4c97c1301be.json"}}, {"family": "\u00c4ij\u00f6", "given": "Tarmo", "initials": "T", "orcid": "0000-0002-3008-4634", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb8806f1f3464220b432068f535f8fa1.json"}}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Braine", "given": "Catherine", "initials": "C", "orcid": "0000-0001-5798-2453", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc00fabb439340b5a18c62d9ef6cadb4.json"}}, {"family": "Kang", "given": "Kristy", "initials": "K", "orcid": "0000-0002-1862-1046", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c848653e7a247558269b1eb67a476f8.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A", "orcid": "0000-0001-7005-3050", "researcher": {"href": "https://publications.scilifelab.se/researcher/2692ce2f0780409fac3e8954de712a48.json"}}, {"family": "Fagegaltier", "given": "Delphine", "initials": "D", "orcid": "0000-0001-9154-6786", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f44d5ba12fe42d8b09195c30652a6d0.json"}}, {"family": "Andrusivov\u00e1", "given": "\u017daneta", "initials": "\u017d"}, {"family": "Saarenp\u00e4\u00e4", "given": "Sami", "initials": "S", "orcid": "0000-0003-4731-6857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6979cdfc0b4e4285f9d810c39bb7b7.json"}}, {"family": "Saiz-Castro", "given": "Gonzalo", "initials": "G"}, {"family": "Cuevas", "given": "Miguel", "initials": "M", "orcid": "0000-0003-4469-7180", "researcher": {"href": "https://publications.scilifelab.se/researcher/6da4a1a648f14028b2cf45f10de4ff15.json"}}, {"family": "Watters", "given": "Aaron", "initials": "A", "orcid": "0000-0001-6464-804X", "researcher": {"href": "https://publications.scilifelab.se/researcher/694fa52263974617ad59152256eb8c88.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Bonneau", "given": "Richard", "initials": "R", "orcid": "0000-0003-4354-7906", "researcher": {"href": "https://publications.scilifelab.se/researcher/e94e098adc3e4514ae8b1521fa8c4b1d.json"}}, {"family": "Phatnani", "given": "Hemali", "initials": "H", "orcid": "0000-0002-6571-3891", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e45957f8a4a4545a384403b225450a5.json"}}], "type": "journal article", "published": "2019-04-05", "journal": {"volume": "364", "issn": "1095-9203", "issue": "6435", "pages": "89-93", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Paralysis occurring in amyotrophic lateral sclerosis (ALS) results from denervation of skeletal muscle as a consequence of motor neuron degeneration. Interactions between motor neurons and glia contribute to motor neuron loss, but the spatiotemporal ordering of molecular events that drive these processes in intact spinal tissue remains poorly understood. Here, we use spatial transcriptomics to obtain gene expression measurements of mouse spinal cords over the course of disease, as well as of postmortem tissue from ALS patients, to characterize the underlying molecular mechanisms in ALS. We identify pathway dynamics, distinguish regional differences between microglia and astrocyte populations at early time points, and discern perturbations in several transcriptional pathways shared between murine models of ALS and human postmortem spinal cords.", "doi": "10.1126/science.aav9776", "pmid": "30948552", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "364/6435/89"}], "notes": [], "created": "2019-12-02T16:50:32.552Z", "modified": "2021-07-08T13:15:15.716Z"}, {"entity": "publication", "iuid": "be25c56a70af4398864750e03ececdc5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be25c56a70af4398864750e03ececdc5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be25c56a70af4398864750e03ececdc5"}}, "title": "Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.", "authors": [{"family": "Pekkinen", "given": "Minna", "initials": "M"}, {"family": "Terhal", "given": "Paulien A", "initials": "PA"}, {"family": "Botto", "given": "Lorenzo D", "initials": "LD"}, {"family": "Henning", "given": "Petra", "initials": "P"}, {"family": "M\u00e4kitie", "given": "Riikka E", "initials": "RE"}, {"family": "Roschger", "given": "Paul", "initials": "P"}, {"family": "Jain", "given": "Amrita", "initials": "A"}, {"family": "Kol", "given": "Matthijs", "initials": "M"}, {"family": "Kjellberg", "given": "Matti A", "initials": "MA"}, {"family": "Paschalis", "given": "Eleftherios P", "initials": "EP"}, {"family": "van Gassen", "given": "Koen", "initials": "K"}, {"family": "Murray", "given": "Mary", "initials": "M"}, {"family": "Bayrak-Toydemir", "given": "Pinar", "initials": "P"}, {"family": "Magnusson", "given": "Maria K", "initials": "MK"}, {"family": "Jans", "given": "Judith", "initials": "J"}, {"family": "Kausar", "given": "Mehran", "initials": "M"}, {"family": "Carey", "given": "John C", "initials": "JC"}, {"family": "Somerharju", "given": "Pentti", "initials": "P"}, {"family": "Lerner", "given": "Ulf H", "initials": "UH"}, {"family": "Olkkonen", "given": "Vesa M", "initials": "VM"}, {"family": "Klaushofer", "given": "Klaus", "initials": "K"}, {"family": "Holthuis", "given": "Joost Cm", "initials": "JC"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}], "type": "journal article", "published": "2019-04-04", "journal": {"volume": "4", "issn": "2379-3708", "issue": "7", "title": "JCI Insight", "issn-l": "2379-3708"}, "abstract": "Mechanisms leading to osteoporosis are incompletely understood. Genetic disorders with skeletal fragility provide insight into metabolic pathways contributing to bone strength. We evaluated 6 families with rare skeletal phenotypes and osteoporosis by next-generation sequencing. In all the families, we identified a heterozygous variant in SGMS2, a gene prominently expressed in cortical bone and encoding the plasma membrane-resident sphingomyelin synthase SMS2. Four unrelated families shared the same nonsense variant, c.148C>T (p.Arg50*), whereas the other families had a missense variant, c.185T>G (p.Ile62Ser) or c.191T>G (p.Met64Arg). Subjects with p.Arg50* presented with childhood-onset osteoporosis with or without cranial sclerosis. Patients with p.Ile62Ser or p.Met64Arg had a more severe presentation, with neonatal fractures, severe short stature, and spondylometaphyseal dysplasia. Several subjects had experienced peripheral facial nerve palsy or other neurological manifestations. Bone biopsies showed markedly altered bone material characteristics, including defective bone mineralization. Osteoclast formation and function in vitro was normal. While the p.Arg50* mutation yielded a catalytically inactive enzyme, p.Ile62Ser and p.Met64Arg each enhanced the rate of de novo sphingomyelin production by blocking export of a functional enzyme from the endoplasmic reticulum. SGMS2 pathogenic variants underlie a spectrum of skeletal conditions, ranging from isolated osteoporosis to complex skeletal dysplasia, suggesting a critical role for plasma membrane-bound sphingomyelin metabolism in skeletal homeostasis.", "doi": "10.1172/jci.insight.126180", "pmid": "30779713", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "126180"}, {"db": "pmc", "key": "PMC6483641"}], "notes": [], "created": "2019-12-02T17:20:27.836Z", "modified": "2024-01-16T13:48:44.530Z"}, {"entity": "publication", "iuid": "779091cd62cc4a6c9e742911d1a1d949", "links": {"self": {"href": "https://publications.scilifelab.se/publication/779091cd62cc4a6c9e742911d1a1d949.json"}, "display": {"href": "https://publications.scilifelab.se/publication/779091cd62cc4a6c9e742911d1a1d949"}}, "title": "A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.", "authors": [{"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Sybers", "given": "David", "initials": "D"}, {"family": "Maklad", "given": "Hassan Ramadan", "initials": "HR"}, {"family": "Lemmens", "given": "Liesbeth", "initials": "L"}, {"family": "Lewyllie", "given": "Charlotte", "initials": "C"}, {"family": "Zhou", "given": "Xiaoxiao", "initials": "X"}, {"family": "Schult", "given": "Frank", "initials": "F"}, {"family": "Br\u00e4sen", "given": "Christopher", "initials": "C"}, {"family": "Siebers", "given": "Bettina", "initials": "B"}, {"family": "Valeg\u00e5rd", "given": "Karin", "initials": "K"}, {"family": "Lind\u00e5s", "given": "Ann-Christin", "initials": "AC"}, {"family": "Peeters", "given": "Eveline", "initials": "E"}], "type": "journal article", "published": "2019-04-04", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1542", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes. By contrast, although certain archaea appear to metabolize fatty acids, the regulation of the underlying pathways in these organisms remains unclear. Here, we show that a TetR-family transcriptional regulator (FadR Sa) is involved in regulation of fatty acid metabolism in the crenarchaeon Sulfolobus acidocaldarius. Functional and structural analyses show that FadRSa binds to DNA at semi-palindromic recognition sites in two distinct stoichiometric binding modes depending on the operator sequence. Genome-wide transcriptomic and chromatin immunoprecipitation analyses demonstrate that the protein binds to only four genomic sites, acting as a repressor of a 30-kb gene cluster comprising 23 open reading frames encoding lipases and \u03b2-oxidation enzymes. Fatty acyl-CoA molecules cause dissociation of FadRSa binding by inducing conformational changes in the protein. Our results indicate that, despite its similarity in overall structure to bacterial TetR-family FadR regulators, FadRSa displays a different acyl-CoA binding mode and a distinct regulatory mechanism.", "doi": "10.1038/s41467-019-09479-1", "pmid": "30948713", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09479-1"}, {"db": "pmc", "key": "PMC6449355"}], "notes": [], "created": "2019-12-02T17:20:02.213Z", "modified": "2020-01-21T13:56:15.630Z"}, {"entity": "publication", "iuid": "9e7445ddca39474ea6088a1685804c21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e7445ddca39474ea6088a1685804c21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e7445ddca39474ea6088a1685804c21"}}, "title": "Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.", "authors": [{"family": "Hakim", "given": "Ramil", "initials": "R"}, {"family": "Covacu", "given": "Ruxandra", "initials": "R"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Frostell", "given": "Arvid", "initials": "A"}, {"family": "Sankavaram", "given": "Sreenivasa Raghavan", "initials": "SR"}, {"family": "Brundin", "given": "Lou", "initials": "L"}, {"family": "Svensson", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2019-04-03", "journal": {"volume": "10", "issn": "1757-6512", "issue": "1", "pages": "115", "title": "Stem Cell Res Ther", "issn-l": "1757-6512"}, "abstract": "Mesenchymal stem cells (MSCs) and their cellular response to various stimuli have been characterized in great detail in culture conditions. In contrast, the cellular response of MSCs in an in vivo setting is still uncharted territory. In this study, we investigated the cellular response of MSCs following transplantation into spinal cord injury (SCI).\n\nMouse bone marrow-derived MSCs were transplanted 24 h following severe contusion SCI in mice. As controls, MSCs transplanted to the uninjured spinal cord and non-transplanted MSCs were used. At 7 days post transplantation, the MSCs were isolated from the SCI, and their global transcriptional changes, survival, differentiation, proliferation, apoptosis, and phenotypes were investigated using RNA sequencing, immunohistochemistry, and flow cytometry.\n\nMSCs transplanted into SCI downregulated genes related to cell-cycle regulation/progression, DNA metabolic/biosynthetic process, and DNA repair and upregulated genes related to immune system response, cytokine production/response, response to stress/stimuli, signal transduction and signaling pathways, apoptosis, and phagocytosis/endocytosis. MSCs maintained their surface expression of Sca1 and CD29 but upregulated expression of CD45 following transplantation. Transplanted MSCs maintained their surface expression of MHC-I but upregulated surface expression of MHC-II. Transplanted MSCs survived and proliferated to a low extent, did not express Caspase-3, and did not differentiate into neurons or astrocytes.\n\nMSCs transplanted into SCI upregulate expression of CD45 and MHC-II and expression of genes related to cytokine production, phagocytosis/endocytosis, and immune cells/response and thereby adopt immune cell-like characteristics within the recipient.", "doi": "10.1186/s13287-019-1218-9", "pmid": "30944028", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13287-019-1218-9"}, {"db": "pmc", "key": "PMC6448247"}], "notes": [], "created": "2019-12-02T17:20:55.116Z", "modified": "2024-01-16T13:48:44.557Z"}, {"entity": "publication", "iuid": "513e971d1f3a44ef9d29c3679be9e61a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/513e971d1f3a44ef9d29c3679be9e61a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/513e971d1f3a44ef9d29c3679be9e61a"}}, "title": "Novel fibronectin mutations and expansion of the phenotype in spondylometaphyseal dysplasia with \"corner fractures\".", "authors": [{"family": "Costantini", "given": "Alice", "initials": "A"}, {"family": "Valta", "given": "Helena", "initials": "H"}, {"family": "Baratang", "given": "Nissan Vida", "initials": "NV"}, {"family": "Yap", "given": "Patrick", "initials": "P"}, {"family": "Bertola", "given": "D\u00e9bora R", "initials": "DR"}, {"family": "Yamamoto", "given": "Guilherme L", "initials": "GL"}, {"family": "Kim", "given": "Chong A", "initials": "CA"}, {"family": "Chen", "given": "Jiani", "initials": "J"}, {"family": "Wierenga", "given": "Klaas J", "initials": "KJ"}, {"family": "Fanning", "given": "Elizabeth A", "initials": "EA"}, {"family": "Escobar", "given": "Luis", "initials": "L"}, {"family": "McWalter", "given": "Kirsty", "initials": "K"}, {"family": "McLaughlin", "given": "Heather", "initials": "H"}, {"family": "Willaert", "given": "Rebecca", "initials": "R"}, {"family": "Begtrup", "given": "Amber", "initials": "A"}, {"family": "Alm", "given": "Jessica J", "initials": "JJ"}, {"family": "Reinhardt", "given": "Dieter P", "initials": "DP"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Campeau", "given": "Philippe M", "initials": "PM"}], "type": "case reports", "published": "2019-04-00", "journal": {"title": "Bone", "issn": "1873-2763", "volume": "121", "pages": "163-171", "issn-l": null}, "abstract": "Heterozygous pathogenic variants in the FN1 gene, encoding fibronectin (FN), have recently been shown to be associated with a skeletal disorder in some individuals affected by spondylometaphyseal dysplasia with \"corner fractures\" (SMD-CF). The most striking feature characterizing SMD-CF is irregularly shaped metaphyses giving the appearance of \"corner fractures\". An array of secondary features, including developmental coxa vara, ovoid vertebral bodies and severe scoliosis, may also be present. FN is an important extracellular matrix component for bone and cartilage development. Here we report five patients affected by this subtype of SMD-CF caused by five novel FN1 missense mutations: p.Cys123Tyr, p.Cys169Tyr, p.Cys213Tyr, p.Cys231Trp and p.Cys258Tyr. All individuals shared a substitution of a cysteine residue, disrupting disulfide bonds in the FN type-I assembly domains located in the N-terminal assembly region. The abnormal metaphyseal ossification and \"corner fracture\" appearances were the most remarkable clinical feature in these patients. In addition, generalized skeletal fragility with low-trauma bilateral femoral fractures was identified in one patient. Interestingly, the distal femoral changes in this patient healed with skeletal maturation. Our report expands the phenotypic and genetic spectrum of the FN1-related SMD-CF and emphasizes the importance of FN in bone formation and possibly also in the maintenance of bone strength.", "doi": "10.1016/j.bone.2018.12.020", "pmid": "30599297", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S8756-3282(18)30470-8"}], "notes": [], "created": "2021-12-06T13:45:23.318Z", "modified": "2021-12-06T13:45:23.353Z"}, {"entity": "publication", "iuid": "c48c5cd0ff6043e6b6daa85a3ba0a668", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c48c5cd0ff6043e6b6daa85a3ba0a668.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c48c5cd0ff6043e6b6daa85a3ba0a668"}}, "title": "Gain-of-function mutation of microRNA-140 in human skeletal dysplasia.", "authors": [{"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Suzuki", "given": "Hiroshi I", "initials": "HI"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Mirzamohammadi", "given": "Fatemeh", "initials": "F"}, {"family": "Borochowitz", "given": "Zvi U", "initials": "ZU"}, {"family": "Ayturk", "given": "Ugur M", "initials": "UM"}, {"family": "Tzur", "given": "Shay", "initials": "S"}, {"family": "Horemuzova", "given": "Eva", "initials": "E"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Weis", "given": "Mary Ann", "initials": "MA"}, {"family": "Grigelionis", "given": "Gintautas", "initials": "G"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Marsk", "given": "Elin", "initials": "E"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Eyre", "given": "David R", "initials": "DR"}, {"family": "Warman", "given": "Matthew L", "initials": "ML"}, {"family": "Nishimura", "given": "Gen", "initials": "G"}, {"family": "Sharp", "given": "Phillip A", "initials": "PA"}, {"family": "Kobayashi", "given": "Tatsuya", "initials": "T"}], "type": "journal article", "published": "2019-04-00", "journal": {"volume": "25", "issn": "1546-170X", "issue": "4", "pages": "583-590", "title": "Nat. Med.", "issn-l": "1078-8956"}, "abstract": "MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Heterozygous loss-of-function point mutations of miRNA genes are associated with several human congenital disorders 1-5, but neomorphic (gain-of-new-function) mutations in miRNAs due to nucleotide substitutions have not been reported. Here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated MIR140 gene encoding microRNA-140 (miR-140) in a novel autosomal dominant human skeletal dysplasia. Mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of miR-140-null mice6. This mutant miRNA gene yields abundant mutant miR-140-5p expression without miRNA-processing defects. In chondrocytes, the mutation causes widespread derepression of wild-type miR-140-5p targets and repression of mutant miR-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. Furthermore, the mutant miR-140-5p seed competes with the conserved RNA-binding protein Ybx1 for overlapping binding sites. This finding may explain the potent target repression and robust in vivo effect by this mutant miRNA even in the absence of evolutionary selection of miRNA-target RNA interactions, which contributes to the strong regulatory effects of conserved miRNAs7,8. Our study presents the first case of a pathogenic gain-of-function miRNA mutation and provides molecular insight into neomorphic actions of emerging and/or mutant miRNAs.", "doi": "10.1038/s41591-019-0353-2", "pmid": "30804514", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-019-0353-2"}, {"db": "pmc", "key": "PMC6622181"}, {"db": "mid", "key": "NIHMS1518562"}], "notes": [], "created": "2019-11-23T23:29:57.941Z", "modified": "2020-01-21T13:56:15.491Z"}, {"entity": "publication", "iuid": "bd2759fb45af4bd9a9e69a0e7f2e9d24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd2759fb45af4bd9a9e69a0e7f2e9d24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd2759fb45af4bd9a9e69a0e7f2e9d24"}}, "title": "A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis", "authors": [{"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Sj\u00f6str\u00f6m", "given": "Olle", "initials": "O"}, {"family": "Nylander", "given": "Carin", "initials": "C"}, {"family": "Osterman", "given": "Pia", "initials": "P"}, {"family": "Sj\u00f6gren", "given": "Rickard", "initials": "R"}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Cederquist", "given": "Kristina", "initials": "K"}, {"family": "Chabes", "given": "Andrei", "initials": "A"}, {"family": "Trygg", "given": "Johan", "initials": "J"}, {"family": "Melin", "given": "Beatrice S", "initials": "BS"}, {"family": "Johansson", "given": "Erik", "initials": "E"}], "type": "journal-article", "published": "2019-03-27", "journal": {"volume": "14", "issn": "1932-6203", "issue": "3", "pages": "e0213350", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Whole-genome sequencing is a promising approach for human autosomal dominant disease studies. However, the vast number of genetic variants observed by this method constitutes a challenge when trying to identify the causal variants. This is often handled by restricting disease studies to the most damaging variants, e.g. those found in coding regions, and overlooking the remaining genetic variation. Such a biased approach explains in part why the genetic causes of many families with dominantly inherited diseases, in spite of being included in whole-genome sequencing studies, are left unsolved today. Here we explore the use of a geographically matched control population to minimize the number of candidate disease-causing variants without excluding variants based on assumptions on genomic position or functional predictions. To exemplify the benefit of the geographically matched control population we apply a typical disease variant filtering strategy in a family with an autosomal dominant form of colorectal cancer. With the use of the geographically matched control population we end up with 26 candidate variants genome wide. This is in contrast to the tens of thousands of candidates left when only making use of available public variant datasets. The effect of the local control population is dual, it (1) reduces the total number of candidate variants shared between affected individuals, and more importantly (2) increases the rate by which the number of candidate variants are reduced as additional affected family members are included in the filtering strategy. We demonstrate that the application of a geographically matched control population effectively limits the number of candidate disease-causing variants and may provide the means by which variants suitable for functional studies are identified genome wide.", "doi": "10.1371/journal.pone.0213350", "pmid": "30917156", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-04-04T19:12:26.169Z", "modified": "2024-01-16T13:48:44.593Z"}, {"entity": "publication", "iuid": "2c5232dce8a649afb39a17f5f5337037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c5232dce8a649afb39a17f5f5337037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c5232dce8a649afb39a17f5f5337037"}}, "title": "Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of \u00c7atalh\u00f6y\u00fck People and Their Genetic Affinities.", "authors": [{"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Dabert", "given": "Miros\u0142awa", "initials": "M"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Marciniak", "given": "Arkadiusz", "initials": "A"}], "type": "journal article", "published": "2019-03-11", "journal": {"volume": "10", "issn": "2073-4425", "issue": "3", "title": "Genes", "issn-l": "2073-4425"}, "abstract": "\u00c7atalh\u00f6y\u00fck is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of \u00c7atalh\u00f6y\u00fck buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including \u00c7atalh\u00f6y\u00fck, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.", "doi": "10.3390/genes10030207", "pmid": "30862131", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "genes10030207"}, {"db": "pmc", "key": "PMC6471721"}], "notes": [], "created": "2019-12-02T17:21:16.505Z", "modified": "2020-01-21T13:56:15.784Z"}, {"entity": "publication", "iuid": "1d328e64e34640b0a95fec849508c102", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d328e64e34640b0a95fec849508c102.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d328e64e34640b0a95fec849508c102"}}, "title": "Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.", "authors": [{"family": "Cheng", "given": "Shangli", "initials": "S"}, {"family": "Pei", "given": "Yu", "initials": "Y"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Peng", "given": "Guangdun", "initials": "G"}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Tam", "given": "Patrick P L", "initials": "PPL"}, {"family": "Jing", "given": "Naihe", "initials": "N"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}], "type": "journal article", "published": "2019-03-05", "journal": {"volume": "26", "issn": "2211-1247", "issue": "10", "pages": "2593-2607.e3", "title": "Cell Rep", "issn-l": null}, "abstract": "Following implantation, the epiblast (EPI) cells transit from the naive to primed pluripotency, accompanied by dynamic changes in X chromosome activity in females. To investigate the molecular attributes of this process, we performed single-cell RNA-seq analysis of 1,724 cells of E5.25, E5.5, E6.25, and E6.5 mouse embryos. We identified three cellular states in the EPI cells that capture the transition along the pluripotency continuum and the acquisition of primitive streak propensity. The transition of three EPI states was driven by inductive signaling activity emanating from the visceral endoderm (VE). In the EPI of female embryos, X chromosome reactivation (XCR) was initiated prior to the completion of imprinted X chromosome inactivation (XCI), and the ensuing random XCI was highly asynchronous. Moreover, imprinted paternal XCI proceeded faster in the VE than the extraembryonic ectoderm. Our study has provided a detailed molecular roadmap of the emergent lineage commitment before gastrulation and characterized X chromosome dynamics during early mouse development.", "doi": "10.1016/j.celrep.2019.02.031", "pmid": "30840884", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(19)30202-5"}], "notes": [], "created": "2019-12-02T17:20:51.306Z", "modified": "2024-01-16T13:48:44.631Z"}, {"entity": "publication", "iuid": "527b93a1737346c4810dd8d61f246859", "links": {"self": {"href": "https://publications.scilifelab.se/publication/527b93a1737346c4810dd8d61f246859.json"}, "display": {"href": "https://publications.scilifelab.se/publication/527b93a1737346c4810dd8d61f246859"}}, "title": "Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.", "authors": [{"family": "Kuruvilla", "given": "Jacob", "initials": "J"}, {"family": "Bayat", "given": "Narges", "initials": "N"}, {"family": "Cristobal", "given": "Susana", "initials": "S"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "19", "issn": "1615-9861", "issue": "5", "pages": "e1800228", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "The large interactive surfaces of nanoparticles (NPs) increase the opportunities to develop NPs for vascular targeting. Proteomic analysis of endothelial cells exposed to NPs reveals the cellular response and turns the focus into the impairment of the endothelial permeability. Here, quantitative proteomics and transcriptome sequencing are combined to evaluate the effects of exposure to sub-lethal concentrations of TiO 2 -USNPs and TiO2 -NPs on human dermal microvascular endothelial cells. Endothelial cells react to preserve the semi-permeable properties that are essential for vascular tissue fluid homeostasis, vascular development, and angiogenesis. The main impact of the exposure was alteration of functional complexes involved in cell adhesion, vesicular transport, and cytoskeletal structure. Those are the core cellular structures that are linked to the permeability and the integrity of the endothelial tissue. Moreover, the extracellular proteins uptake along wih the NPs into the endothelial cells escape the lysosomal degradation pathway. These findings improve the understanding of the interaction of NPs with endothelial cell. The effects of the studied NPs modulating cell-cell adhesion and vesicular transport can help to evaluate the distribution of NPs via intravenous administration.", "doi": "10.1002/pmic.201800228", "pmid": "30632670", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-02T16:53:03.662Z", "modified": "2020-01-21T13:56:15.520Z"}, {"entity": "publication", "iuid": "119e2b2c180c420caed1f5ea104e8518", "links": {"self": {"href": "https://publications.scilifelab.se/publication/119e2b2c180c420caed1f5ea104e8518.json"}, "display": {"href": "https://publications.scilifelab.se/publication/119e2b2c180c420caed1f5ea104e8518"}}, "title": "A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.", "authors": [{"family": "Newton", "given": "Phillip T", "initials": "PT"}, {"family": "Li", "given": "Lei", "initials": "L"}, {"family": "Zhou", "given": "Baoyi", "initials": "B"}, {"family": "Schweingruber", "given": "Christoph", "initials": "C"}, {"family": "Hovorakova", "given": "Maria", "initials": "M"}, {"family": "Xie", "given": "Meng", "initials": "M"}, {"family": "Sun", "given": "Xiaoyan", "initials": "X"}, {"family": "Sandhow", "given": "Lakshmi", "initials": "L"}, {"family": "Artemov", "given": "Artem V", "initials": "AV"}, {"family": "Ivashkin", "given": "Evgeny", "initials": "E"}, {"family": "Suter", "given": "Simon", "initials": "S"}, {"family": "Dyachuk", "given": "Vyacheslav", "initials": "V"}, {"family": "El Shahawy", "given": "Maha", "initials": "M"}, {"family": "Gritli-Linde", "given": "Amel", "initials": "A"}, {"family": "Bouderlique", "given": "Thibault", "initials": "T"}, {"family": "Petersen", "given": "Julian", "initials": "J"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Enikolopov", "given": "Grigori", "initials": "G"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Kasper", "given": "Maria", "initials": "M"}, {"family": "Hedlund", "given": "Eva", "initials": "E"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}, {"family": "S\u00e4vendahl", "given": "Lars", "initials": "L"}, {"family": "Chagin", "given": "Andrei S", "initials": "AS"}], "type": "journal article", "published": "2019-03-00", "journal": {"volume": "567", "issn": "1476-4687", "issue": "7747", "pages": "234-238", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Longitudinal bone growth in children is sustained by growth plates, narrow discs of cartilage that provide a continuous supply of chondrocytes for endochondral ossification1. However, it remains unknown how this supply is maintained throughout childhood growth. Chondroprogenitors in the resting zone are thought to be gradually consumed as they supply cells for longitudinal growth1,2, but this model has never been proved. Here, using clonal genetic tracing with multicolour reporters and functional perturbations, we demonstrate that longitudinal growth during the fetal and neonatal periods involves depletion of chondroprogenitors, whereas later in life, coinciding with the formation of the secondary ossification centre, chondroprogenitors acquire the capacity for self-renewal, resulting in the formation of large, stable monoclonal columns of chondrocytes. Simultaneously, chondroprogenitors begin to express stem cell markers and undergo symmetric cell division. Regulation of the pool of self-renewing progenitors involves the hedgehog and mammalian target of rapamycin complex 1 (mTORC1) signalling pathways. Our findings indicate that a stem cell niche develops postnatally in the epiphyseal growth plate, which provides a continuous supply of chondrocytes over a prolonged period.", "doi": "10.1038/s41586-019-0989-6", "pmid": "30814736", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-019-0989-6"}], "notes": [], "created": "2019-12-02T16:50:34.317Z", "modified": "2021-07-08T13:26:08.086Z"}, {"entity": "publication", "iuid": "f7cf107063f3409a88a49fd4035438eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f7cf107063f3409a88a49fd4035438eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f7cf107063f3409a88a49fd4035438eb"}}, "title": "Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.", "authors": [{"family": "Das", "given": "Sarbashis", "initials": "S", "orcid": "0000-0001-8799-691X", "researcher": {"href": "https://publications.scilifelab.se/researcher/978ddc1e4d8f46499f60b1d343934063.json"}}, {"family": "Frisk", "given": "Christoffer", "initials": "C"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Walentinsson", "given": "Anna", "initials": "A"}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Hage", "given": "Camilla", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Maret", "given": "Eva", "initials": "E"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}], "type": "journal article", "published": "2019-02-28", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "3179", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Heart failure affects 2-3% of adult Western population. Prevalence of heart failure with preserved left ventricular (LV) ejection fraction (HFpEF) increases. Studies suggest HFpEF patients to have altered myocardial structure and functional changes such as incomplete relaxation and increased cardiac stiffness. We hypothesised that patients undergoing elective coronary bypass surgery (CABG) with HFpEF characteristics would show distinctive gene expression compared to patients with normal LV physiology. Myocardial biopsies for mRNA expression analysis were obtained from sixteen patients with LV ejection fraction \u226545%. Five out of 16 patients (31%) had echocardiographic characteristics and increased NTproBNP levels indicative of HFpEF and this group was used as HFpEF proxy, while 11 patients had Normal LV physiology. Utilising principal component analysis, the gene expression data clustered into two groups, corresponding to HFpEF proxy and Normal physiology, and 743 differentially expressed genes were identified. The associated top biological functions were cardiac muscle contraction, oxidative phosphorylation, cellular remodelling and matrix organisation. Our results also indicate that upstream regulatory events, including inhibition of transcription factors STAT4, SRF and TP53, and activation of transcription repressors HEY2 and KDM5A, could provide explanatory mechanisms to observed gene expression differences and ultimately cardiac dysfunction in the HFpEF proxy group.", "doi": "10.1038/s41598-019-39445-2", "pmid": "30816197", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-39445-2"}, {"db": "pmc", "key": "PMC6395693"}], "notes": [], "created": "2019-12-02T16:50:33.258Z", "modified": "2024-01-16T13:48:44.655Z"}, {"entity": "publication", "iuid": "0a8dcfa3c3464289b8dc2cb2afd99897", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a8dcfa3c3464289b8dc2cb2afd99897.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a8dcfa3c3464289b8dc2cb2afd99897"}}, "title": "Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract.", "authors": [{"family": "Sahara", "given": "Makoto", "initials": "M"}, {"family": "Santoro", "given": "Federica", "initials": "F"}, {"family": "Sohlm\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Zhou", "given": "Chikai", "initials": "C"}, {"family": "Witman", "given": "Nevin", "initials": "N"}, {"family": "Leung", "given": "Chuen Yan", "initials": "CY"}, {"family": "Mononen", "given": "Mimmi", "initials": "M"}, {"family": "Bylund", "given": "Kristine", "initials": "K"}, {"family": "Gruber", "given": "Peter", "initials": "P"}, {"family": "Chien", "given": "Kenneth R", "initials": "KR"}], "type": "journal article", "published": "2019-02-25", "journal": {"volume": "48", "issn": "1878-1551", "issue": "4", "pages": "475-490.e7", "title": "Dev. Cell", "issn-l": "1534-5807"}, "abstract": "The morphogenetic process of mammalian cardiac development is complex and highly regulated spatiotemporally by multipotent cardiac stem/progenitor cells (CPCs). Mouse studies have been informative for understanding mammalian cardiogenesis; however, similar insights have been poorly established in humans. Here, we report comprehensive gene expression profiles of human cardiac derivatives from multipotent CPCs to intermediates and mature cardiac cells by population and single-cell RNA-seq using human embryonic stem cell-derived and embryonic/fetal heart-derived cardiac cells micro-dissected from specific heart compartments. Importantly, we discover a uniquely human subset of cono-ventricular region-specific CPCs, marked by LGR5. At 4 to 5 weeks of fetal age, the LGR5 + population appears to emerge specifically in the proximal outflow tract of human embryonic hearts and thereafter promotes cardiac development and alignment through expansion of the ISL1+TNNT2+ intermediates. The current study contributes to a deeper understanding of human cardiogenesis, which may uncover the putative origins of certain human congenital cardiac malformations.", "doi": "10.1016/j.devcel.2019.01.005", "pmid": "30713072", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S1534-5807(19)30005-X"}], "notes": [], "created": "2020-01-08T16:49:49.261Z", "modified": "2020-01-21T13:56:16.596Z"}, {"entity": "publication", "iuid": "b80d77eea7d44b3da4c34cce978d12ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b80d77eea7d44b3da4c34cce978d12ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b80d77eea7d44b3da4c34cce978d12ea"}}, "title": "A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.", "authors": [{"family": "Wang", "given": "Dongxue", "initials": "D", "orcid": "0000-0002-4402-0690", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e916e3dc0e146eca88aff76d9af2dd7.json"}}, {"family": "Eraslan", "given": "Basak", "initials": "B"}, {"family": "Wieland", "given": "Thomas", "initials": "T"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hopf", "given": "Thomas", "initials": "T"}, {"family": "Zolg", "given": "Daniel Paul", "initials": "DP"}, {"family": "Zecha", "given": "Jana", "initials": "J"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Li", "given": "Li-Hua", "initials": "LH"}, {"family": "Meng", "given": "Chen", "initials": "C"}, {"family": "Frejno", "given": "Martin", "initials": "M", "orcid": "0000-0002-6651-1773", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5acc7237f9b4987bb4f819f8a3e8bb8.json"}}, {"family": "Schmidt", "given": "Tobias", "initials": "T"}, {"family": "Schnatbaum", "given": "Karsten", "initials": "K"}, {"family": "Wilhelm", "given": "Mathias", "initials": "M"}, {"family": "Ponten", "given": "Frederik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gagneur", "given": "Julien", "initials": "J", "orcid": "0000-0002-8924-8365", "researcher": {"href": "https://publications.scilifelab.se/researcher/84dcbe1ca0ed4f18ad1e928862e873f5.json"}}, {"family": "Hahne", "given": "Hannes", "initials": "H", "orcid": "0000-0003-3601-0051", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a519deb0cc49019c31e57aa45c7ad3.json"}}, {"family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "researcher": {"href": "https://publications.scilifelab.se/researcher/33488ede76b34566903fea22c400aa3e.json"}}], "type": "journal article", "published": "2019-02-18", "journal": {"volume": "15", "issn": "1744-4292", "issue": "2", "pages": "e8503", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Genome-, transcriptome- and proteome-wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein-level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue-specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.", "doi": "10.15252/msb.20188503", "pmid": "30777892", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6379049"}], "notes": [], "created": "2020-01-08T16:47:13.410Z", "modified": "2021-07-08T13:44:33.541Z"}, {"entity": "publication", "iuid": "c47497e000f947118fd126486d3cb30a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c47497e000f947118fd126486d3cb30a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c47497e000f947118fd126486d3cb30a"}}, "title": "Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).", "authors": [{"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D"}, {"family": "Salcedo", "given": "Adriana", "initials": "A"}, {"family": "Eriksson", "given": "Mimmi C", "initials": "MC"}, {"family": "Duan", "given": "Tianlin", "initials": "T"}, {"family": "Tawari", "given": "Nilesh", "initials": "N"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Guerrina", "given": "Maria", "initials": "M"}, {"family": "Kreiner", "given": "Julia M", "initials": "JM"}, {"family": "Kent", "given": "Tyler V", "initials": "TV"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "Stinchcombe", "given": "John R", "initials": "JR"}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "Wright", "given": "Stephen I", "initials": "SI"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "15", "issn": "1553-7404", "issue": "2", "pages": "e1007949", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (CbpCg) and the other one from the selfing and genetically depauperate Capsella orientalis (CbpCo). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (Ne), signatures of positive and negative selection, and gene expression patterns. In all three regions, Ne of the two subgenomes decreased gradually over time and the CbpCo subgenome accumulated more deleterious changes than CbpCg. There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the CbpCg subgenome in Europe and the Middle East, and on the CbpCo subgenome in Asia. In contrast, differences in expression were limited with the CbpCg subgenome slightly more expressed than CbpCo in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions.", "doi": "10.1371/journal.pgen.1007949", "pmid": "30768594", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-01932"}, {"db": "pmc", "key": "PMC6395008"}], "notes": [], "created": "2019-12-02T16:52:32.088Z", "modified": "2024-01-16T13:48:44.756Z"}, {"entity": "publication", "iuid": "f754205bb071486683b1bde1528c6303", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f754205bb071486683b1bde1528c6303.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f754205bb071486683b1bde1528c6303"}}, "title": "Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F", "orcid": "0000-0002-0243-0018", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e630602a0a449e899701c781ee59fb6.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1a6b6936aa442384c5aef0eff0715a.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"volume": "15", "issn": "1553-7404", "issue": "2", "pages": "e1007858", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Complex chromosomal rearrangements (CCRs) are rearrangements involving more than two chromosomes or more than two breakpoints. Whole genome sequencing (WGS) allows for outstanding high resolution characterization on the nucleotide level in unique sequences of such rearrangements, but problems remain for mapping breakpoints in repetitive regions of the genome, which are known to be prone to rearrangements. Hence, multiple complementary WGS experiments are sometimes needed to solve the structures of CCRs. We have studied three individuals with CCRs: Case 1 and Case 2 presented with de novo karyotypically balanced, complex interchromosomal rearrangements (46,XX,t(2;8;15)(q35;q24.1;q22) and 46,XY,t(1;10;5)(q32;p12;q31)), and Case 3 presented with a de novo, extremely complex intrachromosomal rearrangement on chromosome 1. Molecular cytogenetic investigation revealed cryptic deletions in the breakpoints of chromosome 2 and 8 in Case 1, and on chromosome 10 in Case 2, explaining their clinical symptoms. In Case 3, 26 breakpoints were identified using WGS, disrupting five known disease genes. All rearrangements were subsequently analyzed using optical maps, linked-read WGS, and short-read WGS. In conclusion, we present a case series of three unique de novo CCRs where we by combining the results from the different technologies fully solved the structure of each rearrangement. The power in combining short-read WGS with long-molecule sequencing or optical mapping in these unique de novo CCRs in a clinical setting is demonstrated.", "doi": "10.1371/journal.pgen.1007858", "pmid": "30735495", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-00854"}, {"db": "pmc", "key": "PMC6368290"}], "notes": [], "created": "2019-11-25T10:49:59.013Z", "modified": "2024-01-16T13:48:44.771Z"}, {"entity": "publication", "iuid": "15f3d03dd9644d2a8669f366fe8f2b5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15f3d03dd9644d2a8669f366fe8f2b5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15f3d03dd9644d2a8669f366fe8f2b5d"}}, "title": "The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.", "authors": [{"family": "Lindefeldt", "given": "Marie", "initials": "M"}, {"family": "Eng", "given": "Alexander", "initials": "A"}, {"family": "Darban", "given": "Hamid", "initials": "H"}, {"family": "Bjerkner", "given": "Annelie", "initials": "A"}, {"family": "Zetterstr\u00f6m", "given": "Cecilia K", "initials": "CK"}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Borenstein", "given": "Elhanan", "initials": "E"}, {"family": "Dahlin", "given": "Maria", "initials": "M"}, {"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S"}], "type": "journal article", "published": "2019-01-23", "journal": {"volume": "5", "issn": "2055-5008", "issue": null, "pages": "5", "title": "NPJ Biofilms Microbiomes", "issn-l": "2055-5008"}, "abstract": "The gut microbiota has been linked to various neurological disorders via the gut-brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer's, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after 3 months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing, both taxonomic and functional profiles were established. Here we report that alpha diversity is not changed significantly during the diet, but differences in both taxonomic and functional composition are detected. Relative abundance of bifidobacteria as well as E. rectale and Dialister is significantly diminished during the intervention. An increase in relative abundance of E. coli is observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicates that bifidobacteria and Escherichia are important contributors to the observed functional shifts. As relative abundance of health-promoting, fiber-consuming bacteria becomes less abundant during KD, we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD.", "doi": "10.1038/s41522-018-0073-2", "pmid": "30701077", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "73"}, {"db": "pmc", "key": "PMC6344533"}], "notes": [], "created": "2019-12-02T16:50:29.494Z", "modified": "2020-01-21T13:56:15.296Z"}, {"entity": "publication", "iuid": "d1c8e072e8cd4de2b8a48cd0ecf0b1e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1c8e072e8cd4de2b8a48cd0ecf0b1e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1c8e072e8cd4de2b8a48cd0ecf0b1e8"}}, "title": "Altered human oligodendrocyte heterogeneity in multiple sclerosis", "authors": [{"family": "J\u00e4kel", "given": "Sarah", "initials": "S"}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Falc\u00e3o", "given": "Ana Mendanha", "initials": "AM"}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Lee", "given": "Ka Wai", "initials": "KW"}, {"family": "Knuesel", "given": "Irene", "initials": "I"}, {"family": "Malhotra", "given": "Dheeraj", "initials": "D"}, {"family": "ffrench-Constant", "given": "Charles", "initials": "C"}, {"family": "Williams", "given": "Anna", "initials": "A"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal-article", "published": "2019-01-23", "journal": {"volume": null, "issn": "1476-4687", "issue": null, "pages": null, "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Oligodendrocyte pathology is increasingly implicated in neurodegenerative diseases as oligodendrocytes both myelinate and provide metabolic support to axons. In multiple sclerosis (MS), demyelination in the central nervous system thus leads to neurodegeneration, but the severity of MS between patients is very variable. Disability does not correlate well with the extent of demyelination 1, which suggests that other factors contribute to this variability. One such factor may be oligodendrocyte heterogeneity. Not all oligodendrocytes are the same-those from the mouse spinal cord inherently produce longer myelin sheaths than those from the cortex2, and single-cell analysis of the mouse central nervous system identified further differences3,4. However, the extent of human oligodendrocyte heterogeneity and its possible contribution to MS pathology remain unknown. Here we performed single-nucleus RNA sequencing from white matter areas of post-mortem human brain from patients with MS and from unaffected controls. We identified subclusters of oligodendroglia in control human white matter, some with similarities to mouse, and defined new markers for these cell states. Notably, some subclusters were underrepresented in MS tissue, whereas others were more prevalent. These differences in mature oligodendrocyte subclusters may indicate different functional states of oligodendrocytes in MS lesions. We found similar changes in normal-appearing white matter, showing that MS is a more diffuse disease than its focal demyelination suggests. Our findings of an altered oligodendroglial heterogeneity in MS may be important for understanding disease progression and developing therapeutic approaches.", "doi": "10.1038/s41586-019-0903-2", "pmid": "30747918", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-25T07:49:40.444Z", "modified": "2024-01-16T13:48:44.821Z"}, {"entity": "publication", "iuid": "cae9c2df7b7d47efacb17c8207b6c573", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cae9c2df7b7d47efacb17c8207b6c573.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cae9c2df7b7d47efacb17c8207b6c573"}}, "title": "Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.", "authors": [{"family": "Karkman", "given": "Antti", "initials": "A"}, {"family": "P\u00e4rn\u00e4nen", "given": "Katariina", "initials": "K"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2019-01-08", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "80", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Discharge of treated sewage leads to release of antibiotic resistant bacteria, resistance genes and antibiotic residues to the environment. However, it is unclear whether increased abundance of antibiotic resistance genes in sewage and sewage-impacted environments is due to on-site selection pressure by residual antibiotics, or is simply a result of fecal contamination with resistant bacteria. Here we analyze relative resistance gene abundance and accompanying extent of fecal pollution in publicly available metagenomic data, using crAssphage sequences as a marker of human fecal contamination (crAssphage is a bacteriophage that is exceptionally abundant in, and specific to, human feces). We find that the presence of resistance genes can largely be explained by fecal pollution, with no clear signs of selection in the environment, with the exception of environments polluted by very high levels of antibiotics from manufacturing, where selection is evident. Our results demonstrate the necessity to take into account fecal pollution levels to avoid making erroneous assumptions regarding environmental selection of antibiotic resistance.", "doi": "10.1038/s41467-018-07992-3", "pmid": "30622259", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07992-3"}, {"db": "pmc", "key": "PMC6325112"}], "notes": [], "created": "2020-01-08T16:47:12.638Z", "modified": "2020-01-21T13:56:16.251Z"}, {"entity": "publication", "iuid": "1f920fd4f19a40ecb0f0ef5a1e7959f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f920fd4f19a40ecb0f0ef5a1e7959f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f920fd4f19a40ecb0f0ef5a1e7959f6"}}, "title": "Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Guschanski", "given": "Katerina", "initials": "K"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2019-01-07", "journal": {"volume": "29", "issn": "1879-0445", "issue": "1", "title": "Curr. Biol.", "pages": "165-170.e6", "issn-l": "0960-9822"}, "abstract": "Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.", "doi": "10.1016/j.cub.2018.11.055", "pmid": "30595519", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(18)31554-9"}], "notes": [], "created": "2019-01-07T15:14:46.864Z", "modified": "2021-07-07T20:31:10.716Z"}, {"entity": "publication", "iuid": "b01e6c59687e4c1cb8baf5fa63fdc47f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b01e6c59687e4c1cb8baf5fa63fdc47f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b01e6c59687e4c1cb8baf5fa63fdc47f"}}, "title": "Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes).", "authors": [{"family": "Cai", "given": "Tianlong", "initials": "T"}, {"family": "Cibois", "given": "Alice", "initials": "A"}, {"family": "Alstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Moyle", "given": "Robert G", "initials": "RG"}, {"family": "Kennedy", "given": "Jonathan D", "initials": "JD"}, {"family": "Shao", "given": "Shimiao", "initials": "S"}, {"family": "Zhang", "given": "Ruiying", "initials": "R"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Gelang", "given": "Magnus", "initials": "M"}, {"family": "Qu", "given": "Yanhua", "initials": "Y"}, {"family": "Lei", "given": "Fumin", "initials": "F"}, {"family": "Fjelds\u00e5", "given": "Jon", "initials": "J"}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Mol. Phylogenet. Evol.", "issn": "1095-9513", "volume": "130", "pages": "346-356", "issn-l": "1055-7903"}, "abstract": "The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a \"scrap basket\" in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18-20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.", "doi": "10.1016/j.ympev.2018.10.010", "pmid": "30321696", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(18)30278-1"}], "notes": [], "created": "2021-12-06T13:45:22.081Z", "modified": "2021-12-06T13:45:22.095Z"}, {"entity": "publication", "iuid": "17a8c61af04d40a19d6176e1cda30cef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17a8c61af04d40a19d6176e1cda30cef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17a8c61af04d40a19d6176e1cda30cef"}}, "title": "PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia.", "authors": [{"family": "Chase", "given": "Andrew", "initials": "A"}, {"family": "Pellagatti", "given": "Andrea", "initials": "A"}, {"family": "Singh", "given": "Shalini", "initials": "S"}, {"family": "Score", "given": "Joannah", "initials": "J"}, {"family": "Tapper", "given": "William J", "initials": "WJ"}, {"family": "Lin", "given": "Feng", "initials": "F"}, {"family": "Hoade", "given": "Yvette", "initials": "Y"}, {"family": "Bryant", "given": "Catherine", "initials": "C"}, {"family": "Trim", "given": "Nicola", "initials": "N"}, {"family": "Yip", "given": "Bon Ham", "initials": "BH"}, {"family": "Zoi", "given": "Katerina", "initials": "K"}, {"family": "Rasi", "given": "Chiara", "initials": "C"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Boultwood", "given": "Jacqueline", "initials": "J"}, {"family": "Cross", "given": "Nicholas C P", "initials": "NCP"}], "type": "journal article", "published": "2018-12-20", "journal": {"volume": null, "issn": "1476-5551", "issue": null, "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "Acquired uniparental disomy (aUPD, also known as copy-neutral loss of heterozygosity) is a common feature of cancer cells and characterized by extended tracts of somatically-acquired homozygosity without any concurrent loss or gain of genetic material. The presumed genetic targets of many regions of aUPD remain unknown. Here we describe the association of chromosome 22 aUPD with mutations that delete the C-terminus of PRR14L in patients with chronic myelomonocytic leukemia (CMML), related myeloid neoplasms and age-related clonal hematopoiesis (ARCH). Myeloid panel analysis identified a median of three additional mutated genes (range 1-6) in cases with a myeloid neoplasm (n\u2009=\u20098), but no additional mutations in cases with ARCH (n\u2009=\u20092) suggesting that mutated PRR14L alone may be sufficient to drive clonality. PRR14L has very limited homology to other proteins and its function is unknown. ShRNA knockdown of PRR14L in human CD34+ cells followed by in vitro growth and differentiation assays showed an increase in monocytes and decrease in neutrophils, decrease in neutrophils, consistent with a CMML-like phenotype. RNA-Seq and cellular localization studies suggest a role for PRR14L in cell division. PRR14L is thus a novel, biallelically mutated gene and potential founding abnormality in myeloid neoplasms.", "doi": "10.1038/s41375-018-0340-5", "pmid": "30573780", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41375-018-0340-5"}], "notes": [], "created": "2019-01-07T15:14:46.197Z", "modified": "2020-01-21T13:56:13.505Z"}, {"entity": "publication", "iuid": "9363446f0fb74636b399f76c2a069f9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9363446f0fb74636b399f76c2a069f9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9363446f0fb74636b399f76c2a069f9b"}}, "title": "Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR.", "authors": [{"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Bang", "given": "Benedicte", "initials": "B"}, {"family": "\u00d6fverholm", "given": "Ingegerd Ivanov", "initials": "II"}, {"family": "Tran", "given": "Anh-Nhi", "initials": "AN"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "letter", "published": "2018-12-05", "journal": {"volume": null, "issn": "1530-8561", "issue": null, "title": "Clin. Chem.", "issn-l": "0009-9147"}, "abstract": null, "doi": "10.1373/clinchem.2018.293548", "pmid": "30518665", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "clinchem.2018.293548"}], "notes": [], "created": "2019-01-07T15:13:37.066Z", "modified": "2020-01-21T13:56:13.448Z"}, {"entity": "publication", "iuid": "baf65350323c4815a96754f0ca0369af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/baf65350323c4815a96754f0ca0369af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/baf65350323c4815a96754f0ca0369af"}}, "title": "A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.", "authors": [{"family": "Ni", "given": "Gaofeng", "initials": "G"}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Palma", "given": "Daniela", "initials": "D"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2018-12-05", "journal": {"volume": "9", "issn": "1664-302X", "issue": null, "pages": "2945", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe-mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the \r\n            Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.", "doi": "10.3389/fmicb.2018.02945", "pmid": "30568637", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6289977"}], "notes": [], "created": "2019-01-07T15:14:47.522Z", "modified": "2020-01-21T13:56:14.774Z"}, {"entity": "publication", "iuid": "bf80a77c714149e6afd1d0a41d15178d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf80a77c714149e6afd1d0a41d15178d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf80a77c714149e6afd1d0a41d15178d"}}, "title": "Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.", "authors": [{"family": "Bartoschek", "given": "Michael", "initials": "M", "orcid": "0000-0002-1567-795X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4b53427bada4ea58971be691444ea45.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N"}, {"family": "Bocci", "given": "Matteo", "initials": "M", "orcid": "0000-0002-8774-0006", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff52ba58701141f88766777a3d7ef21e.json"}}, {"family": "L\u00f6vrot", "given": "John", "initials": "J", "orcid": "0000-0002-9339-8059", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c71f7e4aa948d99d8dfbb9bf9e5d2e.json"}}, {"family": "Larsson", "given": "Christer", "initials": "C"}, {"family": "Sommarin", "given": "Mikael", "initials": "M"}, {"family": "Madsen", "given": "Chris D", "initials": "CD", "orcid": "0000-0001-6838-2103", "researcher": {"href": "https://publications.scilifelab.se/researcher/466f82bcf9364350a22cd7d3be0833e4.json"}}, {"family": "Lindgren", "given": "David", "initials": "D"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "Karlsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Pietras", "given": "Kristian", "initials": "K", "orcid": "0000-0001-6738-4705", "researcher": {"href": "https://publications.scilifelab.se/researcher/5be0a3ec07654822a91df964eab1d6e4.json"}}], "type": "journal article", "published": "2018-12-04", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "5150", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium. Gene profiles for each CAF subtype correlate to distinctive functional programs and hold independent prognostic capability in clinical cohorts by association to metastatic disease. In conclusion, the improved resolution of the widely defined CAF population opens the possibility for biomarker-driven development of drugs for precision targeting of CAFs.", "doi": "10.1038/s41467-018-07582-3", "pmid": "30514914", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-07582-3"}, {"db": "pmc", "key": "PMC6279758"}], "notes": [], "created": "2018-12-04T14:20:27.020Z", "modified": "2024-01-16T13:48:44.935Z"}, {"entity": "publication", "iuid": "951a8407b6a64bb09952eda7af1c4b26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/951a8407b6a64bb09952eda7af1c4b26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/951a8407b6a64bb09952eda7af1c4b26"}}, "title": "The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.", "authors": [{"family": "Synnott", "given": "Naoise C", "initials": "NC"}, {"family": "Madden", "given": "Stephen F", "initials": "SF"}, {"family": "Bykov", "given": "Vladimir J N", "initials": "VJN"}, {"family": "Crown", "given": "John", "initials": "J"}, {"family": "Wiman", "given": "Klas G", "initials": "KG"}, {"family": "Duffy", "given": "Michael J", "initials": "MJ"}], "type": "journal article", "published": "2018-12-00", "journal": {"volume": "11", "issn": "1936-5233", "issue": "6", "pages": "1343-1349", "title": "Transl Oncol", "issn-l": null}, "abstract": "TP53 is the most frequently mutated gene in human cancer and thus an attractive target for novel cancer therapy. Several compounds that can reactive mutant p53 protein have been identified. APR-246 is currently being tested in a phase II clinical trial in high-grade serous ovarian cancer. We have used RNA-seq analysis to study the effects of APR-246 on gene expression in human breast cancer cell lines. Although the effect of APR-246 on gene expression was largely cell line dependent, six genes were upregulated across all three cell lines studied, i.e., TRIM16, SLC7A11, TXNRD1, SRXN1, LOC344887, and SLC7A11-AS1. We did not detect upregulation of canonical p53 target genes such as CDKN1A (p21), 14-3-3\u03c3, BBC3 (PUMA), and PMAIP1 (NOXA) by RNA-seq, but these genes were induced according to analysis by qPCR. Gene ontology analysis showed that APR-246 induced changes in pathways such as response to oxidative stress, gene expression, cell proliferation, response to nitrosative stress, and the glutathione biosynthesis process. Our results are consistent with the dual action of APR-246, i.e., reactivation of mutant p53 and modulation of redox activity. SLC7A11, TRIM16, TXNRD1, and SRXN1 are potential new pharmacodynamic biomarkers for assessing the response to APR-246 in both preclinical and clinical studies.", "doi": "10.1016/j.tranon.2018.08.009", "pmid": "30196236", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1936-5233(18)30358-9"}, {"db": "pmc", "key": "PMC6132178"}], "notes": [], "created": "2018-10-31T19:45:57.122Z", "modified": "2024-01-16T13:48:44.965Z"}, {"entity": "publication", "iuid": "791d6a9d1a0548cc8e8c542c88a7269c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/791d6a9d1a0548cc8e8c542c88a7269c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/791d6a9d1a0548cc8e8c542c88a7269c"}}, "title": "Somatic mutagenesis in satellite cells associates with human skeletal muscle aging", "authors": [{"family": "Franco", "given": "Irene", "initials": "I"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Olsson", "given": "Karl", "initials": "K"}, {"family": "Vrta\u010dnik", "given": "Peter", "initials": "P"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Helgadottir", "given": "Hafdis T", "initials": "HT"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Rev\u00eachon", "given": "Gwladys", "initials": "G"}, {"family": "Bosia", "given": "Carla", "initials": "C"}, {"family": "Pagnani", "given": "Andrea", "initials": "A"}, {"family": "Provero", "given": "Paolo", "initials": "P"}, {"family": "Gustafsson", "given": "Thomas", "initials": "T"}, {"family": "Fischer", "given": "Helene", "initials": "H"}, {"family": "Eriksson", "given": "Maria", "initials": "M"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Human aging is associated with a decline in skeletal muscle (SkM) function and a reduction in the number and activity of satellite cells (SCs), the resident stem cells. To study the connection between SC aging and muscle impairment, we analyze the whole genome of single SC clones of the leg muscle vastus lateralis from healthy individuals of different ages (21-78 years). We find an accumulation rate of 13 somatic mutations per genome per year, consistent with proliferation of SCs in the healthy adult muscle. SkM-expressed genes are protected from mutations, but aging results in an increase in mutations in exons and promoters, targeting genes involved in SC activity and muscle function. In agreement with SC mutations affecting the whole tissue, we detect a missense mutation in a SC propagating to the muscle. Our results suggest somatic mutagenesis in SCs as a driving force in the age-related decline of SkM function.", "doi": "10.1038/s41467-018-03244-6", "pmid": "29476074", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-02-26T14:11:01.492Z", "modified": "2024-01-16T13:48:44.998Z"}, {"entity": "publication", "iuid": "ae28c25c11f74bc182125086f0dec5ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae28c25c11f74bc182125086f0dec5ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae28c25c11f74bc182125086f0dec5ca"}}, "title": "RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Di Bucchianico", "given": "Sebastiano", "initials": "S"}, {"family": "Lindvall", "given": "Jessica", "initials": "J", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": null, "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Despite a considerable focus on the adverse effects of silver nanoparticles (AgNPs) in recent years, studies on the potential long-term effects of AgNPs are scarce. The aim of this study was to explore the effects of AgNPs following repeated low-dose, long-term exposure of human bronchial epithelial cells. To this end, the human BEAS-2B cell line was exposed to 1\u2009\u00b5g/mL AgNPs (10\u2009nm) for 6 weeks followed by RNA-sequencing (RNA-Seq) as well as genome-wide DNA methylation analysis. The transcriptomics analysis showed that a substantial number of genes (1717) were differentially expressed following AgNP exposure whereas only marginal effects on DNA methylation were observed. Downstream analysis of the transcriptomics data identified several affected pathways including the 'fibrosis' and 'epithelial-mesenchymal transition' (EMT) pathway. Subsequently, functional validation studies were performed using AgNPs of two different sizes (10\u2009nm and 75\u2009nm). Both NPs increased collagen deposition, indicative of fibrosis, and induced EMT, as evidenced by an increased invasion index, anchorage independent cell growth, as well as cadherin switching. In conclusion, using a combination of RNA-Seq and functional assays, our study revealed that repeated low-dose, long-term exposure of human BEAS-2B cells to AgNPs is pro-fibrotic, induces EMT and cell transformation.", "doi": "10.1038/s41598-018-25085-5", "pmid": "29703973", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "ArrayExpress", "description": "RNA-Seq of BEAS-2B cells treated with low doses of Ag nanoparticles for 6 weeks", "key": "E-MTAB-6321"}, {"db": "ArrayExpress", "description": "DNA methylation profiling of BEAS-2B cells exposed to low doses of Ag nanoparticles for 6 weeks", "key": "E-MTAB-6331"}], "notes": [], "created": "2018-05-03T10:11:16.742Z", "modified": "2021-07-05T12:48:15.926Z"}, {"entity": "publication", "iuid": "f431ae3d2b964a4daf0a073938e8b951", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f431ae3d2b964a4daf0a073938e8b951.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f431ae3d2b964a4daf0a073938e8b951"}}, "title": "Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability.", "authors": [{"family": "Kvarnung", "given": "Malin", "initials": "M", "orcid": "0000-0003-0193-0165", "researcher": {"href": "https://publications.scilifelab.se/researcher/77c2ad2b3e1442f5937aded8e129994a.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Holmberg", "given": "Eva", "initials": "E"}, {"family": "Burstedt", "given": "Magnus", "initials": "M"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lundberg", "given": "Elisabeth S", "initials": "ES"}], "type": "journal article", "published": "2018-12-00", "journal": {"volume": "94", "issn": "1399-0004", "issue": "6", "title": "Clin. Genet.", "pages": "528-537", "issn-l": "0009-9163"}, "abstract": "We have investigated 20 consanguineous families with multiple children affected by rare disorders. Detailed clinical examinations, exome sequencing of affected as well as unaffected family members and further validation of likely pathogenic variants were performed. In 16/20 families, we identified pathogenic variants in autosomal recessive disease genes (ALMS1, PIGT, FLVCR2, TFG, CYP7B1, ALG14, EXOSC3, MEGF10, ASAH1, WDR62, ASPM, PNPO, ERCC5, KIAA1109, RIPK4, MAN1B1). A number of these genes have only rarely been reported previously and our findings thus confirm them as disease genes, further delineate the associated phenotypes and expand the mutation spectrum with reports of novel variants. We highlight the findings in two affected siblings with splice altering variants in ALG14 and propose a new clinical entity, which includes severe intellectual disability, epilepsy, behavioral problems and mild dysmorphic features, caused by biallelic variants in ALG14.", "doi": "10.1111/cge.13448", "pmid": "30221345", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T19:44:56.743Z", "modified": "2024-01-16T13:48:45.052Z"}, {"entity": "publication", "iuid": "fd7be1158fed4b8099143c1223dfa9c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd7be1158fed4b8099143c1223dfa9c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd7be1158fed4b8099143c1223dfa9c6"}}, "title": "Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Karlsson", "given": "Christofer M G", "initials": "CMG"}, {"family": "Divne", "given": "Anna Maria", "initials": "AM"}, {"family": "Bergin", "given": "Claudia", "initials": "C"}, {"family": "Homa", "given": "Felix", "initials": "F"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJG"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "6", "issn": "2049-2618", "issue": "1", "pages": null, "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.\n\nWe compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.\n\nThe strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.", "doi": "10.1186/s40168-018-0550-0", "pmid": "30266101", "labels": {"Microbial Single Cell Genomics": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Baltic Sea Surface Water Metagenome", "key": "PRJNA273799"}, {"db": "SRA", "description": "Baltic Sea Surface Water Metagenome", "key": "SRP058493"}], "notes": [], "created": "2018-10-19T15:07:15.693Z", "modified": "2024-01-16T13:48:45.059Z"}, {"entity": "publication", "iuid": "2cbe3cb13de242308430d8bb2440ff5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cbe3cb13de242308430d8bb2440ff5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cbe3cb13de242308430d8bb2440ff5b"}}, "title": "A major locus controls local adaptation and adaptive life history variation in a perennial plant", "authors": [{"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Ding", "given": "Jihua", "initials": "J"}, {"family": "Tan", "given": "Biyue", "initials": "B"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Michelson", "given": "Ingrid H", "initials": "IH"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "19", "issn": "1474-760X", "issue": "1", "pages": null, "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits often show strong local adaptation along environmental gradients but, despite their importance, the genetic architecture of these traits remains poorly understood.\n\nWe integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations.\n\nOur results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.", "doi": "10.1186/s13059-018-1444-y", "pmid": "29866176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": "Populus tremula Raw sequence reads", "key": "PRJNA297202"}], "notes": [], "created": "2018-06-04T13:44:31.229Z", "modified": "2024-01-16T13:48:45.155Z"}, {"entity": "publication", "iuid": "d2a5def06c4c4e11b87c62b594c4363a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2a5def06c4c4e11b87c62b594c4363a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2a5def06c4c4e11b87c62b594c4363a"}}, "title": "A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons", "authors": [{"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Toskas", "given": "Konstantinos", "initials": "K"}, {"family": "Rraklli", "given": "Vilma", "initials": "V"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Holmberg", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2018-12-00", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": null, "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors. Furthermore, we utilize the map generated by our analysis to show that the transcriptional response of midbrain dopaminergic neurons following 6-OHDA or methamphetamine injection is characterized by increased expression of genes with promoters dually marked by H3K4me3/H3K27me3. Our study provides an in vivo genome-wide analysis of permissive/repressive histone modifications coupled to gene expression in these rare neuronal subtypes.", "doi": "10.1038/s41467-018-03538-9", "pmid": "29581424", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "GEO", "description": "RNA-seq, ChIP-seq and TRAP-seq data", "key": "GSE107656"}], "notes": [], "created": "2018-04-25T12:52:16.083Z", "modified": "2024-01-16T13:48:45.162Z"}, {"entity": "publication", "iuid": "3afc5479350a4c2f97b2a399131784f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3afc5479350a4c2f97b2a399131784f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3afc5479350a4c2f97b2a399131784f1"}}, "title": "Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers.", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2018-11-27", "journal": {"volume": "9", "issn": "1664-302X", "issue": null, "pages": "2880", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "The continental deep biosphere is suggested to contain a substantial fraction of the earth's total biomass and microorganisms inhabiting this environment likely have a substantial impact on biogeochemical cycles. However, the deep microbial community is still largely unknown and can be influenced by parameters such as temperature, pressure, water residence times, and chemistry of the waters. In this study, 21 boreholes representing a range of deep continental groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory were subjected to high-throughput 16S rRNA gene sequencing to characterize how the different water types influence the microbial communities. Geochemical parameters showed the stability of the waters and allowed their classification into three groups. These were (i) waters influenced by infiltration from the Baltic Sea with a \"modern marine (MM)\" signature, (ii) a \"thoroughly mixed (TM)\" water containing groundwaters of several origins, and (iii) deep \"old saline (OS)\" waters. Decreasing microbial cell numbers positively correlated with depth. In addition, there was a stronger positive correlation between increased cell numbers and dissolved organic carbon for the MM compared to the OS waters. This supported that the MM waters depend on organic carbon infiltration from the Baltic Sea while the ancient saline waters were fed by \"geogases\" such as carbon dioxide and hydrogen. The 16S rRNA gene relative abundance of the studied groundwaters revealed different microbial community compositions. Interestingly, the TM water showed the highest dissimilarity compared to the other two water types, potentially due to the several contrasting water types contributing to this groundwater. The main identified microbial phyla in the groundwaters were Gammaproteobacteria, unclassified sequences, Campylobacterota (formerly Epsilonproteobacteria), Patescibacteria, Deltaproteobacteria, and Alphaproteobacteria. Many of these taxa are suggested to mediate ferric iron and nitrate reduction, especially in the MM waters. This indicated that nitrate reduction may be a neglected but important process in the deep continental biosphere. In addition to the high number of unclassified sequences, almost 50% of the identified phyla were archaeal or bacterial candidate phyla. The percentage of unknown and candidate phyla increased with depth, pointing to the importance and necessity of further studies to characterize deep biosphere microbial populations.", "doi": "10.3389/fmicb.2018.02880", "pmid": "30538690", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6277548"}], "notes": [], "created": "2019-01-07T15:14:48.233Z", "modified": "2020-01-21T13:56:13.527Z"}, {"entity": "publication", "iuid": "cc30831e3cc647858c35e963f1214907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc30831e3cc647858c35e963f1214907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc30831e3cc647858c35e963f1214907"}}, "title": "Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "Holmfeldt", "given": "Karin", "initials": "K"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal-article", "published": "2018-11-20", "journal": {"volume": "9", "issn": "2150-7511", "issue": "6", "pages": null, "title": "MBio", "issn-l": null}, "abstract": "The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, \n                in situ fixed RNA transcripts from two deep continental groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20\u2009years, defined as \"modern marine,\" and an \"old saline\" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available.IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.", "doi": "10.1128/mbio.01792-18", "pmid": "30459191", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-12-05T08:23:11.449Z", "modified": "2024-01-16T13:48:45.178Z"}, {"entity": "publication", "iuid": "b7e5974c4859449e9ce3e3deaec20c1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7e5974c4859449e9ce3e3deaec20c1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7e5974c4859449e9ce3e3deaec20c1e"}}, "title": "Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters.", "authors": [{"family": "Pedersen", "given": "Jeppe N", "initials": "JN"}, {"family": "Bombar", "given": "Deniz", "initials": "D"}, {"family": "Paerl", "given": "Ryan W", "initials": "RW"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}], "type": "journal article", "published": "2018-11-16", "journal": {"volume": "9", "issn": "1664-302X", "issue": null, "pages": "2759", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Putative heterotrophic bacteria carrying out N\r\n            2-fixation, so-called non-cyanobacterial diazotrophs (NCDs), are widely distributed in marine waters, but details of how the O2-inhibited N2-fixation process is promoted in the oxic water column remains ambiguous. Here we carried out two experiments with water from a eutrophic temperate fjord to examine whether low-oxygen microenvironments within particulate organic matter could be loci suitable for N2-fixation. First, water enriched with natural particles or sediment showed higher N2-fixation rates than bulk water, and nitrogenase genes (nifH) revealed that specific diazotrophs were affiliated with the particulate matter. Second, pristine artificial surfaces were rapidly colonized by diverse bacteria, while putative diazotrophs emerged relatively late (after 80 h) during the colonization, and phylotypes related to Pseudomonas and to anaerobic bacteria became dominant with time. Our study pinpoints natural particles as sites of N2-fixation, and indicates that resuspension of sediment material can elevate pelagic N2-fixation. Moreover, we show that diverse natural diazotrophs can colonize artificial surfaces, but colonization by \"pioneer\" bacterioplankton that more rapidly associate with surfaces appears to be a prerequisite. Whereas our experimental study supports the idea of pelagic particles as sites of N2-fixation by heterotrophic bacteria, future in situ studies are needed in order to establish identity, activity and ecology of particle associated NCDs as a function of individual particle characteristics.", "doi": "10.3389/fmicb.2018.02759", "pmid": "30505296", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6250843"}], "notes": [], "created": "2019-01-07T15:14:45.387Z", "modified": "2020-01-21T13:56:14.783Z"}, {"entity": "publication", "iuid": "1c854d000cef41898abc281c3f96c4e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c854d000cef41898abc281c3f96c4e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c854d000cef41898abc281c3f96c4e3"}}, "title": "Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.", "authors": [{"family": "De Wit", "given": "Pierre", "initials": "P"}, {"family": "Yamada", "given": "Keith", "initials": "K"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2018-11-14", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "16824", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the first-ever transcriptome assembly for this species, and found 3,233 differentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to differentially expressed genes, the most notable being \"alkaloid metabolic process\". Within this category, we found eight differentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the differentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxification. This is a first step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.", "doi": "10.1038/s41598-018-34937-z", "pmid": "30429500", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-34937-z"}, {"db": "pmc", "key": "PMC6235865"}], "notes": [], "created": "2019-01-04T14:04:11.901Z", "modified": "2020-01-21T13:56:13.568Z"}, {"entity": "publication", "iuid": "35234fdfb5a84f84b1abdd29c159662c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35234fdfb5a84f84b1abdd29c159662c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35234fdfb5a84f84b1abdd29c159662c"}}, "title": "Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).", "authors": [{"family": "Salgado", "given": "Marco G", "initials": "MG"}, {"family": "van Velzen", "given": "Robin", "initials": "R"}, {"family": "Nguyen", "given": "Thanh Van", "initials": "TV"}, {"family": "Battenberg", "given": "Kai", "initials": "K"}, {"family": "Berry", "given": "Alison M", "initials": "AM"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}], "type": "journal article", "published": "2018-11-14", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": "1629", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of \r\n            Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.", "doi": "10.3389/fpls.2018.01629", "pmid": "30487804", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6246699"}], "notes": [], "created": "2019-01-04T14:04:17.164Z", "modified": "2020-01-21T13:56:14.792Z"}, {"entity": "publication", "iuid": "600002c1545f47b7b6cdf6d664511eb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/600002c1545f47b7b6cdf6d664511eb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/600002c1545f47b7b6cdf6d664511eb1"}}, "title": "Parallel plumage colour evolution and introgressive hybridization in wheatears.", "authors": [{"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Warmuth", "given": "Vera", "initials": "V"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Aliabadian", "given": "Mansour", "initials": "M"}, {"family": "F\u00f6rschler", "given": "Marc", "initials": "M"}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Burri", "given": "Reto", "initials": "R"}], "type": "journal article", "published": "2018-11-12", "journal": {"volume": null, "issn": "1420-9101", "issue": null, "title": "J. Evol. Biol.", "issn-l": "1010-061X"}, "abstract": "Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa - pied wheatear (O.\u00a0pleschanka), Cyprus wheatear (O.\u00a0cypriaca), and western and eastern subspecies of black-eared wheatear (O.\u00a0h.\u00a0hispanica and O.\u00a0h.\u00a0melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20\u00a0000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.", "doi": "10.1111/jeb.13401", "pmid": "30421480", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-04T14:04:11.141Z", "modified": "2020-01-21T13:56:13.455Z"}, {"entity": "publication", "iuid": "6cadcf95a314477a877cde31dd341c89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cadcf95a314477a877cde31dd341c89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cadcf95a314477a877cde31dd341c89"}}, "title": "Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis", "authors": [{"family": "Falc\u00e3o", "given": "Ana Mendanha", "initials": "AM"}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Marques", "given": "Sueli", "initials": "S"}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "J\u00e4kel", "given": "Sarah", "initials": "S"}, {"family": "Agirre", "given": "Eneritz", "initials": "E"}, {"family": "Samudyata", "given": "", "initials": ""}, {"family": "Floriddia", "given": "Elisa M", "initials": "EM"}, {"family": "Vanichkina", "given": "Darya P", "initials": "DP"}, {"family": "ffrench-Constant", "given": "Charles", "initials": "C"}, {"family": "Williams", "given": "Anna", "initials": "A"}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal-article", "published": "2018-11-12", "journal": {"volume": null, "issn": "1078-8956", "issue": null, "pages": null, "title": "Nat Med", "issn-l": "1078-8956"}, "abstract": "Multiple sclerosis (MS) is characterized by an immune system attack targeting myelin, which is produced by oligodendrocytes (OLs). We performed single-cell transcriptomic analysis of OL lineage cells from the spinal cord of mice induced with experimental autoimmune encephalomyelitis (EAE), which mimics several aspects of MS. We found unique OLs and OL precursor cells (OPCs) in EAE and uncovered several genes specifically alternatively spliced in these cells. Surprisingly, EAE-specific OL lineage populations expressed genes involved in antigen processing and presentation via major histocompatibility complex class I and II (MHC-I and -II), and in immunoprotection, suggesting alternative functions of these cells in a disease context. Importantly, we found that disease-specific oligodendroglia are also present in human MS brains and that a substantial number of genes known to be susceptibility genes for MS, so far mainly associated with immune cells, are expressed in the OL lineage cells. Finally, we demonstrate that OPCs can phagocytose and that MHC-II-expressing OPCs can activate memory and effector CD4-positive T cells. Our results suggest that OLs and OPCs are not passive targets but instead active immunomodulators in MS. The disease-specific OL lineage cells, for which we identify several biomarkers, may represent novel direct targets for immunomodulatory therapeutic approaches in MS.", "doi": "10.1038/s41591-018-0236-y", "pmid": "30420755", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "GEO", "description": "RNA-seq data", "key": "GSE113973"}], "notes": [], "created": "2018-11-15T15:59:21.309Z", "modified": "2024-01-16T13:48:45.209Z"}, {"entity": "publication", "iuid": "51df1c5fe3f94631a980b3a69ab8490c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51df1c5fe3f94631a980b3a69ab8490c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51df1c5fe3f94631a980b3a69ab8490c"}}, "title": "Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.", "authors": [{"family": "Nazaryan-Petersen", "given": "Lusine", "initials": "L"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfdfac2208ce4d1a877fa4957e2f4ea4.json"}}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Ottosson", "given": "Jesper", "initials": "J"}, {"family": "Gacic", "given": "Jelena", "initials": "J", "orcid": "0000-0002-1431-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2a1747f125144b48815d5793ac1bc13.json"}}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O", "orcid": "0000-0002-4547-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce0614bdc717455b9af64a05ab4aa4aa.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Hjortsh\u00f8j", "given": "Tina Duelund", "initials": "TD"}, {"family": "Jespersgaard", "given": "Cathrine", "initials": "C"}, {"family": "Houssari", "given": "Rayan", "initials": "R"}, {"family": "Pignata", "given": "Laura", "initials": "L"}, {"family": "Bak", "given": "Mads", "initials": "M"}, {"family": "Tommerup", "given": "Niels", "initials": "N", "orcid": "0000-0003-2304-0112", "researcher": {"href": "https://publications.scilifelab.se/researcher/d163b474ab954465b310cc47ac7403eb.json"}}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES", "orcid": "0000-0001-5692-725X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c7a2e475443ef9fdbbd7b46c9991e.json"}}, {"family": "T\u00fcmer", "given": "Zeynep", "initials": "Z"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "14", "issn": "1553-7404", "issue": "11", "pages": "e1007780", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both \"simple\" and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements.", "doi": "10.1371/journal.pgen.1007780", "pmid": "30419018", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-18-01290"}, {"db": "pmc", "key": "PMC6258378"}], "notes": [], "created": "2019-01-04T14:04:10.399Z", "modified": "2021-07-07T15:19:21.415Z"}, {"entity": "publication", "iuid": "f061f70eb9734def938dd0213c971296", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f061f70eb9734def938dd0213c971296.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f061f70eb9734def938dd0213c971296"}}, "title": "Notch signaling promotes a HIF2\u03b1-driven hypoxic response in multiple tumor cell types.", "authors": [{"family": "Mutvei", "given": "Anders P", "initials": "AP"}, {"family": "Landor", "given": "Sebastian K-J", "initials": "SK"}, {"family": "Fox", "given": "Rhys", "initials": "R"}, {"family": "Braune", "given": "Eike-Benjamin", "initials": "EB"}, {"family": "Tsoi", "given": "Yat Long", "initials": "YL"}, {"family": "Phoon", "given": "Yee Peng", "initials": "YP"}, {"family": "Sahlgren", "given": "Cecilia", "initials": "C"}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Jin", "given": "Shaobo", "initials": "S"}, {"family": "Lendahl", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "37", "issn": "1476-5594", "issue": "46", "title": "Oncogene", "pages": "6083-6095", "issn-l": "0950-9232"}, "abstract": "Hyperactivation of Notch signaling and the cellular hypoxic response are frequently observed in cancers, with increasing reports of connections to tumor initiation and progression. The two signaling mechanisms are known to intersect, but while it is well established that hypoxia regulates Notch signaling, less is known about whether Notch can regulate the cellular hypoxic response. We now report that Notch signaling specifically controls expression of HIF2\u03b1, a key mediator of the cellular hypoxic response. Transcriptional upregulation of HIF2\u03b1 by Notch under normoxic conditions leads to elevated HIF2\u03b1 protein levels in primary breast cancer cells as well as in human breast cancer, medulloblastoma, and renal cell carcinoma cell lines. The elevated level of HIF2\u03b1 protein was in certain tumor cell types accompanied by downregulation of HIF1\u03b1 protein levels, indicating that high Notch signaling may drive a HIF1\u03b1-to-HIF2\u03b1 switch. At the transcriptome level, the presence of HIF2\u03b1 was required for approximately 21% of all Notch-induced genes: among the 1062 genes that were upregulated by Notch in medulloblastoma cells during normoxia, upregulation was abrogated in 227 genes when HIF2\u03b1 expression was knocked down by HIF2\u03b1 siRNA. In conclusion, our data show that Notch signaling affects the hypoxic response via regulation of HIF2\u03b1, which may be important for future cancer therapies.", "doi": "10.1038/s41388-018-0400-3", "pmid": "29993038", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6237764"}, {"db": "pii", "key": "10.1038/s41388-018-0400-3"}], "notes": [], "created": "2018-10-31T19:48:30.853Z", "modified": "2024-01-16T13:48:45.231Z"}, {"entity": "publication", "iuid": "ba3bc1c0a7244242b962888f6748f6d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba3bc1c0a7244242b962888f6748f6d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba3bc1c0a7244242b962888f6748f6d2"}}, "title": "Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.", "authors": [{"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Navarro", "given": "Jos\u00e9 Fern\u00e1ndez", "initials": "JF"}, {"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2018-11-00", "journal": {"volume": "13", "issn": "1750-2799", "issue": "11", "pages": "2501-2534", "title": "Nat Protoc", "issn-l": null}, "abstract": "Spatial resolution of gene expression enables gene expression events to be pinpointed to a specific location in biological tissue. Spatially resolved gene expression in tissue sections is traditionally analyzed using immunohistochemistry (IHC) or in situ hybridization (ISH). These technologies are invaluable tools for pathologists and molecular biologists; however, their throughput is limited to the analysis of only a few genes at a time. Recent advances in RNA sequencing (RNA-seq) have made it possible to obtain unbiased high-throughput gene expression data in bulk. Spatial Transcriptomics combines the benefits of traditional spatially resolved technologies with the massive throughput of RNA-seq. Here, we present a protocol describing how to apply the Spatial Transcriptomics technology to mammalian tissue. This protocol combines histological staining and spatially resolved RNA-seq data from intact tissue sections. Once suitable tissue-specific conditions have been established, library construction and sequencing can be completed in ~5-6 d. Data processing takes a few hours, with the exact timing dependent on the sequencing depth. Our method requires no special instruments and can be performed in any laboratory with access to a cryostat, microscope and next-generation sequencing.", "doi": "10.1038/s41596-018-0045-2", "pmid": "30353172", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41596-018-0045-2"}], "notes": [], "created": "2019-01-04T14:04:14.055Z", "modified": "2023-06-19T13:17:45.566Z"}, {"entity": "publication", "iuid": "8bbce7fb2cee400fba35ba3b383f90ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bbce7fb2cee400fba35ba3b383f90ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bbce7fb2cee400fba35ba3b383f90ab"}}, "title": "SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.", "authors": [{"family": "Xu", "given": "Jiejia", "initials": "J"}, {"family": "Gruber", "given": "Peter J", "initials": "PJ"}, {"family": "Chien", "given": "Kenneth R", "initials": "KR"}], "type": "journal article", "published": "2018-10-30", "journal": {"volume": null, "issn": "1549-4918", "issue": null, "title": "Stem Cells", "issn-l": "1066-5099"}, "abstract": "Understanding stage-specific molecular mechanisms of human cardiomyocyte (CM) progenitor formation and subsequent differentiation are critical to identify pathways that might lead to congenital cardiovascular defects and malformations. In particular, gene mutations in the transforming growth factor (TGF)\u03b2 superfamily signaling pathways can cause human congenital heart defects, and murine loss of function studies of a central component in this pathway, Smad4, leads to early embryonic lethality. To define the role of SMAD4 at the earliest stages of human cardiogenesis, we generated SMAD4 mutant human embryonic stem cells (hESCs). Herein, we show that the loss of SMAD4 has no effect on hESC self-renewal, or neuroectoderm formation, but is essential for the formation of cardiac mesoderm, with a subsequent complete loss of CM formation during human ES cell cardiogenesis. Via transcriptional profiling, we show that SMAD4 mutant cell lines fail to generate cardiac mesodermal precursors, clarifying a role of NODAL/SMAD4 signaling in cardiac mesodermal precursor formation via enhancing the expression of primitive streak genes. Since SMAD4 relative pathways have been linked to congenital malformations, it will become of interest to determine whether these may due, in part, to defective cell fate decision during cardiac mesodermal precursor formation. Stem Cells 2018.", "doi": "10.1002/stem.2943", "pmid": "30376214", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-07T15:13:41.689Z", "modified": "2020-01-21T13:56:13.493Z"}, {"entity": "publication", "iuid": "7b9a4b3254e04ef1aa2d5b21da472e47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b9a4b3254e04ef1aa2d5b21da472e47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b9a4b3254e04ef1aa2d5b21da472e47"}}, "title": "Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen", "authors": [{"family": "Lin", "given": "Yao Cheng", "initials": "YC"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Zuccolo", "given": "Andrea", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "de la Torre", "given": "Amanda", "initials": "A"}, {"family": "Cossu", "given": "Rosa M", "initials": "RM"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Leitch", "given": "Ilia J", "initials": "IJ"}, {"family": "Pellicer", "given": "Jaume", "initials": "J"}, {"family": "Park", "given": "Eung Jun", "initials": "EJ"}, {"family": "Van Montagu", "given": "Marc", "initials": "M"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal-article", "published": "2018-10-29", "journal": {"volume": null, "issn": "0027-8424", "issue": null, "pages": "201801437", "title": "Proc Natl Acad Sci USA", "issn-l": "0027-8424"}, "abstract": null, "doi": "10.1073/pnas.1801437115", "pmid": "30373829", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "European Nucleotide Archive", "description": "GENOME AND POPULATION SEQUENCING OF ASPEN ADVANCES POPULUS AS A MODEL SYSTEM FOR PLANT RESEARCH", "key": "PRJEB23585"}, {"db": "PlantGenie.org", "description": "ftp://plantgenie.org/Publications/Lin2018/pnas201801437/", "key": "pnas201801437"}], "notes": [], "created": "2018-10-31T12:03:08.142Z", "modified": "2024-01-16T13:48:45.277Z"}, {"entity": "publication", "iuid": "9794a8977d51497392f9ef4fda1d2517", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9794a8977d51497392f9ef4fda1d2517.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9794a8977d51497392f9ef4fda1d2517"}}, "title": "Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.", "authors": [{"family": "Tanaka", "given": "Nobuyuki", "initials": "N"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Reddy", "given": "Aparna", "initials": "A"}, {"family": "Nishimura", "given": "Kaneyasu", "initials": "K"}, {"family": "Niwa", "given": "Naoya", "initials": "N"}, {"family": "Hongo", "given": "Hiroshi", "initials": "H"}, {"family": "Ogihara", "given": "Koichiro", "initials": "K"}, {"family": "Kosaka", "given": "Takeo", "initials": "T"}, {"family": "Mizuno", "given": "Ryuichi", "initials": "R"}, {"family": "Kikuchi", "given": "Eiji", "initials": "E"}, {"family": "Mikami", "given": "Shuji", "initials": "S"}, {"family": "Miyakawa", "given": "Ayako", "initials": "A"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Oya", "given": "Mototsugu", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2018-10-26", "journal": {"volume": null, "issn": "2045-7634", "issue": null, "title": "Cancer Med", "issn-l": "2045-7634"}, "abstract": "Cancers acquire resistance to systemic treatment with platinum-based chemotherapy (eg, cisplatin [CDDP]) as a result of a dynamic intratumoral heterogeneity (ITH) and clonal repopulation. However, little is known about the influence of chemotherapy on ITH at the single-cell level. Here, mapping the transcriptome of cancers treated with CDDP by scRNA-seq, we uncovered a novel gene, COX7B, associated with platinum-resistance, and surrogate marker, CD63. Knockdown of COX7B in cancer cells decreased the sensitivity of CDDP whereas overexpression recovered the sensitivity of CDDP. Low COX7B levels correlated with higher mortality rates in patients with various types of cancer and were significantly associated with poor response to chemotherapy in urinary bladder cancer. Tumor samples from patients, who underwent CDDP therapy, showed decreased COX7B protein levels after the treatment. Analyzing scRNA-seq data from platinum-na\u00efve cancer cells demonstrated a low-COX7B subclone that could be sorted out from bulk cancer cells by assaying CD63. This low-COX7B subclone behaved as cells with acquired platinum-resistance when challenged to CDDP. Our results offer a new transcriptome landscape of platinum-resistance that provides valuable insights into chemosensitivity and drug resistance in cancers, and we identify a novel platinum resistance gene, COX7B, and a surrogate marker, CD63.", "doi": "10.1002/cam4.1828", "pmid": "30367559", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T13:32:10.404Z", "modified": "2024-01-16T13:48:45.286Z"}, {"entity": "publication", "iuid": "6c018d7fe577404c9ce7c148a8d5ecd4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c018d7fe577404c9ce7c148a8d5ecd4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c018d7fe577404c9ce7c148a8d5ecd4"}}, "title": "Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.", "authors": [{"family": "J\u00e4rver", "given": "Peter", "initials": "P", "orcid": "0000-0001-9643-5874", "researcher": {"href": "https://publications.scilifelab.se/researcher/7645ffd2a3f7458b805892f41fd1e124.json"}}, {"family": "Dondalska", "given": "Aleksandra", "initials": "A"}, {"family": "Poux", "given": "Candice", "initials": "C"}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Sk\u00f6ld", "given": "Annette E", "initials": "AE"}, {"family": "Dereuddre-Bosquet", "given": "Nathalie", "initials": "N"}, {"family": "Martinon", "given": "Fr\u00e9deric", "initials": "F"}, {"family": "P\u00e5lsson", "given": "Sandra", "initials": "S"}, {"family": "Zaghloul", "given": "Eman", "initials": "E"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Sander", "given": "Birgitta", "initials": "B"}, {"family": "Lennox", "given": "Kim A", "initials": "KA"}, {"family": "Behlke", "given": "Mark A", "initials": "MA"}, {"family": "El-Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "LeGrand", "given": "Roger", "initials": "R"}, {"family": "Spetz", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0003-3964-9512", "researcher": {"href": "https://publications.scilifelab.se/researcher/70270e32d48d486799cc9dd61e36a4f1.json"}}], "type": "journal article", "published": "2018-10-26", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "15841", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Recognition of nucleic acids by endosomal Toll-like receptors (TLR) is essential to combat pathogens, but requires strict control to limit inflammatory responses. The mechanisms governing this tight regulation are unclear. We found that single-stranded oligonucleotides (ssON) inhibit endocytic pathways used by cargo destined for TLR3/4/7 signaling endosomes. Both ssDNA and ssRNA conferred the endocytic inhibition, it was concentration dependent, and required a certain ssON length. The ssON-mediated inhibition modulated signaling downstream of TLRs that localized within the affected endosomal pathway. We further show that injection of ssON dampens dsRNA-mediated inflammatory responses in the skin of non-human primates. These studies reveal a regulatory role for extracellular ssON in the endocytic uptake of TLR ligands and provide a mechanistic explanation of their immunomodulation. The identified ssON-mediated interference of endocytosis (SOMIE) is a regulatory process that temporarily dampens TLR3/4/7 signaling, thereby averting excessive immune responses.", "doi": "10.1038/s41598-018-33960-4", "pmid": "30367171", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-33960-4"}, {"db": "pmc", "key": "PMC6203749"}], "notes": [], "created": "2019-01-04T14:04:14.911Z", "modified": "2021-07-08T11:26:36.978Z"}, {"entity": "publication", "iuid": "b07837ce578f42bea588be846c6153ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b07837ce578f42bea588be846c6153ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b07837ce578f42bea588be846c6153ef"}}, "title": "Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.", "authors": [{"family": "Joost", "given": "Simon", "initials": "S"}, {"family": "Jacob", "given": "Tina", "initials": "T"}, {"family": "Sun", "given": "Xiaoyan", "initials": "X"}, {"family": "Annusver", "given": "Karl", "initials": "K"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Sur", "given": "Inderpreet", "initials": "I"}, {"family": "Kasper", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2018-10-16", "journal": {"volume": "25", "issn": "2211-1247", "issue": "3", "pages": "585-597.e7", "title": "Cell Rep", "issn-l": null}, "abstract": "Epithelial tissues, such as the skin, rely on cellular plasticity of stem cells (SCs) from different niches to restore tissue function after injury. How these molecularly and functionally diverse SC populations respond to injury remains elusive. Here, we genetically labeled Lgr5- or Lgr6-expressing cells from the hair follicle bulge and interfollicular epidermis (IFE), respectively, and monitored their individual transcriptional adaptations during wound healing using single-cell transcriptomics. Both Lgr5 and Lgr6 progeny rapidly induced a genetic wound signature that, for Lgr5 progeny, included the remodeling of receptors to permit interactions with the wound environment, a property that Lgr6 progeny possessed even before wounding. When contributing to re-epithelialization, Lgr5 progeny gradually replaced their bulge identity with an IFE identity, and this process started already before Lgr5 progeny left the bulge. Altogether, this study reveals how different SCs respond and adapt to a new environment, potentially explaining cellular plasticity of many epithelial tissues.", "doi": "10.1016/j.celrep.2018.09.059", "pmid": "30332640", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(18)31504-3"}, {"db": "ArrayExpress", "description": "Single-cell RNA-seq analysis of cutaneous wound healing in mouse", "key": "E-MTAB-6583"}, {"db": "ArrayExpress", "description": "Bulk-cell RNA-seq analysis of early cutaneous wound healing in mouse", "key": "E-MTAB-6686"}], "notes": [], "created": "2018-10-31T13:35:22.994Z", "modified": "2024-01-16T13:48:45.293Z"}, {"entity": "publication", "iuid": "b564a433cc584924b3acf7a917124c4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b564a433cc584924b3acf7a917124c4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b564a433cc584924b3acf7a917124c4e"}}, "title": "Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma", "authors": [{"family": "Thrane", "given": "Kim", "initials": "K", "orcid": "0000-0003-3109-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1bd1b94e1694de9a5c27fd8f331dc86.json"}}, {"family": "Eriksson", "given": "Hanna", "initials": "H"}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal-article", "published": "2018-10-15", "journal": {"volume": "78", "issn": "0008-5472", "issue": "20", "pages": "5970-5979", "title": "Cancer Res", "issn-l": "0008-5472"}, "abstract": "Cutaneous malignant melanoma (melanoma) is characterized by a high mutational load, extensive intertumoral and intratumoral genetic heterogeneity, and complex tumor microenvironment (TME) interactions. Further insights into the mechanisms underlying melanoma are crucial for understanding tumor progression and responses to treatment. Here we adapted the technology of spatial transcriptomics (ST) to melanoma lymph node biopsies and successfully sequenced the transcriptomes of over 2,200 tissue domains. Deconvolution combined with traditional approaches for dimensional reduction of transcriptome-wide data enabled us to both visualize the transcriptional landscape within the tissue and identify gene expression profiles linked to specific histologic entities. Our unsupervised analysis revealed a complex spatial intratumoral composition of melanoma metastases that was not evident through morphologic annotation. Each biopsy showed distinct gene expression profiles and included examples of the coexistence of multiple melanoma signatures within a single tumor region as well as shared profiles for lymphoid tissue characterized according to their spatial location and gene expression profiles. The lymphoid area in close proximity to the tumor region displayed a specific expression pattern, which may reflect the TME, a key component to fully understanding tumor progression. In conclusion, using the ST technology to generate gene expression profiles reveals a detailed landscape of melanoma metastases. This should inspire researchers to integrate spatial information into analyses aiming to identify the factors underlying tumor progression and therapy outcome.Significance: Applying ST technology to gene expression profiling in melanoma lymph node metastases reveals a complex transcriptional landscape in a spatial context, which is essential for understanding the multiple components of tumor progression and therapy outcome. Cancer Res; 78(20); 5970-9. \u00a92018 AACR.", "doi": "10.1158/0008-5472.can-18-0747", "pmid": "30154148", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-18-0747"}], "notes": [], "created": "2018-10-31T19:44:53.867Z", "modified": "2024-01-16T13:48:45.301Z"}, {"entity": "publication", "iuid": "072524b5e6fe4e87a4939a2560b7814d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/072524b5e6fe4e87a4939a2560b7814d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/072524b5e6fe4e87a4939a2560b7814d"}}, "title": "Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.", "authors": [{"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "S\u00f6derberg", "given": "Elin M V", "initials": "EMV"}, {"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "Mateoiu", "given": "Claudia", "initials": "C"}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2018-10-12", "journal": {"volume": "9", "issn": "1949-2553", "issue": "80", "pages": "35162-35180", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Ovarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for early-stage (I and II) ovarian carcinomas (n=96) in relation to clinicopathological characteristics and clinical outcome, thereby identifying novel genetic features of ovarian carcinomas. Furthermore, mutation frequencies of specific genetic variants and/or their gene expression patterns were associated with histotype and overall survival, \n            e.g. SLC28A2 (mucinous ovarian carcinoma histotype), ARCN1 (low expression in 0-2 year survival group), and tumor suppressor MTUS1 (mutation status and overall survival). The long non-coding RNA MALAT1 was identified as a highly promiscuous fusion transcript in ovarian carcinoma. Moreover, gene expression deregulation for 23 genes was associated with tumor aggressiveness. Taken together, the novel biomarkers identified here may improve ovarian carcinoma subclassification and patient stratification according to histotype and overall survival.", "doi": "10.18632/oncotarget.26225", "pmid": "30416686", "labels": {"Systems Biology": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "26225"}, {"db": "pmc", "key": "PMC6205557"}], "notes": [], "created": "2019-01-04T14:04:15.592Z", "modified": "2020-01-21T13:56:17.723Z"}, {"entity": "publication", "iuid": "d794f36d72b34629b910abcbdfae6a78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d794f36d72b34629b910abcbdfae6a78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d794f36d72b34629b910abcbdfae6a78"}}, "title": "Enhanced validation of antibodies for research applications.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Hober", "given": "Andreas", "initials": "A", "orcid": "0000-0001-8947-2562", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a007c2aea2c40ada113ffe87fc3daf0.json"}}, {"family": "Linderb\u00e4ck", "given": "Klas", "initials": "K"}, {"family": "Maddalo", "given": "Gianluca", "initials": "G"}, {"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-5248-8568", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23dc2e614784017b08cb2d8f6b60ded.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2018-10-08", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "4130", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.", "doi": "10.1038/s41467-018-06642-y", "pmid": "30297845", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06642-y"}, {"db": "pmc", "key": "PMC6175901"}], "notes": [], "created": "2018-10-31T19:45:59.871Z", "modified": "2024-01-16T13:48:45.378Z"}, {"entity": "publication", "iuid": "39c6d6654fb7485c9ba727f21f554c4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/39c6d6654fb7485c9ba727f21f554c4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/39c6d6654fb7485c9ba727f21f554c4e"}}, "title": "Partial genomic survival of cave bears in living brown bears.", "authors": [{"family": "Barlow", "given": "Axel", "initials": "A", "orcid": "0000-0002-5532-9458", "researcher": {"href": "https://publications.scilifelab.se/researcher/293d4982ed124c75896e1838bab18b8f.json"}}, {"family": "Cahill", "given": "James A", "initials": "JA", "orcid": "0000-0002-7145-0215", "researcher": {"href": "https://publications.scilifelab.se/researcher/847ec3b224fe4d23947158d8229ba5b1.json"}}, {"family": "Hartmann", "given": "Stefanie", "initials": "S"}, {"family": "Theunert", "given": "Christoph", "initials": "C"}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Fortes", "given": "Gloria G", "initials": "GG"}, {"family": "Paijmans", "given": "Johanna L A", "initials": "JLA"}, {"family": "Rabeder", "given": "Gernot", "initials": "G"}, {"family": "Frischauf", "given": "Christine", "initials": "C"}, {"family": "Grandal-d'Anglade", "given": "Aurora", "initials": "A"}, {"family": "Garc\u00eda-V\u00e1zquez", "given": "Ana", "initials": "A"}, {"family": "Murtskhvaladze", "given": "Marine", "initials": "M"}, {"family": "Saarma", "given": "Urmas", "initials": "U"}, {"family": "Anijalg", "given": "Peeter", "initials": "P"}, {"family": "Skrbin\u0161ek", "given": "Toma\u017e", "initials": "T"}, {"family": "Bertorelle", "given": "Giorgio", "initials": "G"}, {"family": "Gasparian", "given": "Boris", "initials": "B"}, {"family": "Bar-Oz", "given": "Guy", "initials": "G"}, {"family": "Pinhasi", "given": "Ron", "initials": "R"}, {"family": "Slatkin", "given": "Montgomery", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2018-10-00", "journal": {"volume": "2", "issn": "2397-334X", "issue": "10", "pages": "1563-1570", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.", "doi": "10.1038/s41559-018-0654-8", "pmid": "30150744", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-018-0654-8"}, {"db": "pmc", "key": "PMC6590514"}, {"db": "mid", "key": "NIHMS1017233"}], "notes": [], "created": "2018-10-31T19:46:52.580Z", "modified": "2021-07-07T20:31:10.764Z"}, {"entity": "publication", "iuid": "c18fc22d368f4c109f76e74dbc4c0d6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d"}}, "title": "Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Shcherbakov", "given": "Nikolai", "initials": "N", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Shuteleva", "given": "Iia", "initials": "I", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Leonova", "given": "Tatiana", "initials": "T"}, {"family": "Kraeva", "given": "Liudmila", "initials": "L", "orcid": "0000-0002-6524-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/f11ac245436b40a88c66740d94f27353.json"}}, {"family": "Sungatov", "given": "Flarit A", "initials": "FA", "orcid": "0000-0001-5982-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bbdcfb0afa84a899f1dead7ff3c5531.json"}}, {"family": "Sultanova", "given": "Alfija N", "initials": "AN", "orcid": "0000-0002-5409-8344", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc71e882ea64d408cb1d5201aae554a.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Sinika", "given": "Vitaly", "initials": "V", "orcid": "0000-0002-1621-9205", "researcher": {"href": "https://publications.scilifelab.se/researcher/64dffb07a3a342d78eb91d9c02f87f83.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-10-00", "journal": {"volume": "4", "issn": "2375-2548", "issue": "10", "pages": "eaat4457", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.", "doi": "10.1126/sciadv.aat4457", "pmid": "30417088", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "aat4457"}, {"db": "pmc", "key": "PMC6223350"}], "notes": [], "created": "2018-10-22T10:10:13.051Z", "modified": "2024-01-16T13:48:45.440Z"}, {"entity": "publication", "iuid": "156d9c73b1124ae2b3bc792402debf37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/156d9c73b1124ae2b3bc792402debf37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/156d9c73b1124ae2b3bc792402debf37"}}, "title": "Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias.", "authors": [{"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Vaz", "given": "Raquel", "initials": "R"}, {"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Tham", "given": "Emma", "initials": "E"}, {"family": "Horemuzova", "given": "Eva", "initials": "E"}, {"family": "Voss", "given": "Ulrika", "initials": "U"}, {"family": "Nishimura", "given": "Gen", "initials": "G"}, {"family": "Klintberg", "given": "Bo", "initials": "B"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2018-10-00", "journal": {"volume": "39", "issn": "1098-1004", "issue": "10", "pages": "1456-1467", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Skeletal dysplasias are a diverse group of rare Mendelian disorders with clinical and genetic heterogeneity. Here, we used targeted copy number variant (CNV) screening and identified intragenic exonic duplications, formed through Alu-Alu fusion events, in two individuals with skeletal dysplasia and negative exome sequencing results. First, we detected a homozygous tandem duplication of exon 9 and 10 in IFT81 in a boy with Jeune syndrome, or short-rib thoracic dysplasia (SRTD) (MIM# 208500). Western blot analysis did not detect any wild-type IFT81 protein in fibroblasts from the patient with the IFT81 duplication, but only a shorter isoform of IFT81 that was also present in the normal control samples. Complementary zebrafish studies suggested that loss of full-length IFT81 protein but expression of a shorter form of IFT81 protein affects the phenotype while being compatible with life. Second, a de novo tandem duplication of exons 2 to 5 in MATN3 was identified in a girl with multiple epiphyseal dysplasia (MED) type 5 (MIM# 607078). Our data highlights the importance of detection and careful characterization of intragenic duplication CNVs, presenting them as a novel and very rare genetic mechanism in IFT81-related Jeune syndrome and MATN3-related MED.", "doi": "10.1002/humu.23605", "pmid": "30080953", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-29T09:07:40.413Z", "modified": "2024-01-16T13:48:45.450Z"}, {"entity": "publication", "iuid": "cba4114e50d94c988dc4b3e505dbacb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cba4114e50d94c988dc4b3e505dbacb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cba4114e50d94c988dc4b3e505dbacb4"}}, "title": "Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.", "authors": [{"family": "Ni", "given": "Gaofeng", "initials": "G"}, {"family": "Canizales", "given": "Sebastian", "initials": "S"}, {"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Palwai", "given": "Viraja R", "initials": "VR"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Sleutels", "given": "Tom", "initials": "T"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2018-09-28", "journal": {"volume": "9", "issn": "1664-302X", "issue": null, "pages": "2308", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a ", "doi": "10.3389/fmicb.2018.02308", "pmid": "30323799", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6172326"}, {"db": "BioProject", "description": "Psychrophilic microbiome from a bioelectrochemical system", "key": "PRJNA473625"}], "notes": [], "created": "2018-10-31T19:47:10.849Z", "modified": "2024-01-16T13:48:45.457Z"}, {"entity": "publication", "iuid": "2bd3d54ed9c44971aedad700fd890627", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bd3d54ed9c44971aedad700fd890627.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bd3d54ed9c44971aedad700fd890627"}}, "title": "High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.", "authors": [{"family": "Ritter", "given": "Camila D", "initials": "CD"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Roger", "given": "Fabian", "initials": "F"}, {"family": "Tuomisto", "given": "Hanna", "initials": "H"}, {"family": "Barnes", "given": "Christopher", "initials": "C"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal article", "published": "2018-09-25", "journal": {"volume": "6", "issn": "2167-8359", "issue": null, "pages": "e5661", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.\n\nWe used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.\n\nSoil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, v\u00e1rzea, igap\u00f3 and campina) than between substrates (soil and litter).\n\nIn spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world's largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.", "doi": "10.7717/peerj.5661", "pmid": "30280033", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5661"}, {"db": "pmc", "key": "PMC6161700"}], "notes": [], "created": "2018-10-31T19:47:36.212Z", "modified": "2024-01-16T13:48:45.479Z"}, {"entity": "publication", "iuid": "bd9ce56d91f24b62abce9e7413819c9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd9ce56d91f24b62abce9e7413819c9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd9ce56d91f24b62abce9e7413819c9c"}}, "title": "SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.", "authors": [{"family": "Yu", "given": "Simei", "initials": "S"}, {"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Ga\u00f1ez-Zapater", "given": "Antoni", "initials": "A"}, {"family": "Jain", "given": "Shruti", "initials": "S"}, {"family": "Rolicka", "given": "Anna", "initials": "A"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK"}, {"family": "Visa", "given": "Neus", "initials": "N"}], "type": "journal article", "published": "2018-09-19", "journal": {"volume": "46", "issn": "1362-4962", "issue": "16", "pages": "8557-8573", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "SWI/SNF complexes associate with genes and regulate transcription by altering the chromatin at the promoter. It has recently been shown that these complexes play a role in pre-mRNA processing by associating at alternative splice sites. Here, we show that SWI/SNF complexes are involved also in pre-mRNA 3' end maturation by facilitating 3' end cleavage of specific pre-mRNAs. Comparative proteomics show that SWI/SNF ATPases interact physically with subunits of the cleavage and polyadenylation complexes in fly and human cells. In Drosophila melanogaster, the SWI/SNF ATPase Brahma (dBRM) interacts with the CPSF6 subunit of cleavage factor I. We have investigated the function of dBRM in 3' end formation in S2 cells by RNA interference, single-gene analysis and RNA sequencing. Our data show that dBRM facilitates pre-mRNA cleavage in two different ways: by promoting the association of CPSF6 to the cleavage region and by stabilizing positioned nucleosomes downstream of the cleavage site. These findings show that SWI/SNF complexes play a role also in the cleavage of specific pre-mRNAs in animal cells.", "doi": "10.1093/nar/gky438", "pmid": "29860334", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5025902"}, {"db": "pmc", "key": "PMC6144808"}, {"db": "GEO", "description": "The distribution of Brahma in the genome of Drosophila melanogaster S2 cells and the roles of Brahma in transcription and pre-mRNA processing", "key": "GSE95236"}], "notes": [], "created": "2018-10-31T19:47:59.160Z", "modified": "2024-01-16T13:48:45.494Z"}, {"entity": "publication", "iuid": "df0a1aaa78164376888bf09b18a0d205", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df0a1aaa78164376888bf09b18a0d205.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df0a1aaa78164376888bf09b18a0d205"}}, "title": "Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.", "authors": [{"family": "Petitpr\u00e9", "given": "Charles", "initials": "C"}, {"family": "Wu", "given": "Haohao", "initials": "H"}, {"family": "Sharma", "given": "Anil", "initials": "A"}, {"family": "Tokarska", "given": "Anna", "initials": "A"}, {"family": "Fontanet", "given": "Paula", "initials": "P"}, {"family": "Wang", "given": "Yiqiao", "initials": "Y"}, {"family": "Helmbacher", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Yackle", "given": "Kevin", "initials": "K"}, {"family": "Silberberg", "given": "Gilad", "initials": "G"}, {"family": "Hadjab", "given": "Saida", "initials": "S"}, {"family": "Lallemend", "given": "Fran\u00e7ois", "initials": "F"}], "type": "journal article", "published": "2018-09-12", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "3691", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Spiral ganglion (SG) neurons of the cochlea convey all auditory inputs to the brain, yet the cellular and molecular complexity necessary to decode the various acoustic features in the SG has remained unresolved. Using single-cell RNA sequencing, we identify four types of SG neurons, including three novel subclasses of type I neurons and the type II neurons, and provide a comprehensive genetic framework that define their potential synaptic communication patterns. The connectivity patterns of the three subclasses of type I neurons with inner hair cells and their electrophysiological profiles suggest that they represent the intensity-coding properties of auditory afferents. Moreover, neuron type specification is already established at birth, indicating a neuronal diversification process independent of neuronal activity. Thus, this work provides a transcriptional catalog of neuron types in the cochlea, which serves as a valuable resource for dissecting cell-type-specific functions of dedicated afferents in auditory perception and in hearing disorders.", "doi": "10.1038/s41467-018-06033-3", "pmid": "30209249", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06033-3"}, {"db": "pmc", "key": "PMC6135759"}, {"db": "GEO", "description": "Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system", "key": "GSE117055"}], "notes": [], "created": "2018-10-31T13:03:39.950Z", "modified": "2024-01-16T13:48:45.517Z"}, {"entity": "publication", "iuid": "f35cd246d7a84453b1ac19f3d163b109", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f35cd246d7a84453b1ac19f3d163b109.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f35cd246d7a84453b1ac19f3d163b109"}}, "title": "Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C"}, {"family": "Zachrisson", "given": "Torun", "initials": "T"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Sobrado", "given": "Veronica", "initials": "V"}, {"family": "Evans", "given": "Jane", "initials": "J"}, {"family": "Knipper", "given": "Corina", "initials": "C"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-09-10", "journal": {"volume": "28", "issn": "1879-0445", "issue": "17", "pages": "2730-2738.e10", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.", "doi": "10.1016/j.cub.2018.06.053", "pmid": "30146150", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(18)30844-3"}], "notes": [], "created": "2018-10-31T19:48:01.236Z", "modified": "2024-01-16T13:48:45.531Z"}, {"entity": "publication", "iuid": "d20710fa0ed14236b32b9fd18ef95c95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d20710fa0ed14236b32b9fd18ef95c95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d20710fa0ed14236b32b9fd18ef95c95"}}, "title": "Contribution of allelic imbalance to colorectal cancer.", "authors": [{"family": "Palin", "given": "Kimmo", "initials": "K", "orcid": "0000-0002-4621-6128", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b279cedd14f4c1eac3b917571a793b6.json"}}, {"family": "Pitk\u00e4nen", "given": "Esa", "initials": "E"}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Sahu", "given": "Biswajyoti", "initials": "B"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "V\u00e4lim\u00e4ki", "given": "Niko", "initials": "N"}, {"family": "H\u00e4nninen", "given": "Ulrika A", "initials": "UA"}, {"family": "Cajuso", "given": "Tatiana", "initials": "T"}, {"family": "Aavikko", "given": "Mervi", "initials": "M"}, {"family": "Tuupanen", "given": "Sari", "initials": "S"}, {"family": "Kilpivaara", "given": "Outi", "initials": "O"}, {"family": "van den Berg", "given": "Linda", "initials": "L"}, {"family": "Kondelin", "given": "Johanna", "initials": "J"}, {"family": "Tanskanen", "given": "Tomas", "initials": "T"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Grau", "given": "Marta", "initials": "M"}, {"family": "Rauanheimo", "given": "Heli", "initials": "H"}, {"family": "Plaketti", "given": "Roosa-Maria", "initials": "RM"}, {"family": "Taira", "given": "Aurora", "initials": "A"}, {"family": "Sulo", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Hartonen", "given": "Tuomo", "initials": "T"}, {"family": "Dave", "given": "Kashyap", "initials": "K"}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Botla", "given": "Sandeep", "initials": "S"}, {"family": "Sokolova", "given": "Maria", "initials": "M"}, {"family": "V\u00e4h\u00e4rautio", "given": "Anna", "initials": "A"}, {"family": "Gladysz", "given": "Kornelia", "initials": "K"}, {"family": "Ongen", "given": "Halit", "initials": "H", "orcid": "0000-0002-4197-5790", "researcher": {"href": "https://publications.scilifelab.se/researcher/c32fbd0537b74601b6e8d8ede15acffd.json"}}, {"family": "Dermitzakis", "given": "Emmanouil", "initials": "E", "orcid": "0000-0002-9302-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/3560d19929e94af1bb858a54e29a10cc.json"}}, {"family": "Bramsen", "given": "Jesper Bertram", "initials": "JB"}, {"family": "\u00d8rntoft", "given": "Torben Falck", "initials": "TF"}, {"family": "Andersen", "given": "Claus Lindbjerg", "initials": "CL"}, {"family": "Ristim\u00e4ki", "given": "Ari", "initials": "A"}, {"family": "Lepist\u00f6", "given": "Anna", "initials": "A"}, {"family": "Renkonen-Sinisalo", "given": "Laura", "initials": "L"}, {"family": "Mecklin", "given": "Jukka-Pekka", "initials": "JP"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}], "type": "journal article", "published": "2018-09-10", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "3664", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout and activation screens identified in total 79 genes within AI peaks regulating cell growth. Genetic and functional data implicate loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.", "doi": "10.1038/s41467-018-06132-1", "pmid": "30202008", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "CRISPR Functional Genomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-018-06132-1"}, {"db": "pmc", "key": "PMC6131244"}], "notes": [], "created": "2018-10-31T19:47:37.243Z", "modified": "2024-01-16T13:48:45.538Z"}, {"entity": "publication", "iuid": "19f23c88f5d44289a4ff88982fe8a86d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19f23c88f5d44289a4ff88982fe8a86d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19f23c88f5d44289a4ff88982fe8a86d"}}, "title": "Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Tripathy", "given": "Sucheta", "initials": "S"}, {"family": "Malar C", "given": "Mathu", "initials": "M"}, {"family": "Panda", "given": "Arijit", "initials": "A"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}], "type": "journal article", "published": "2018-09-01", "journal": {"volume": "10", "issn": "1759-6653", "issue": "9", "pages": "2432-2442", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malm\u00f6, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41\u2009Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.", "doi": "10.1093/gbe/evy162", "pmid": "30060094", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5061551"}, {"db": "pmc", "key": "PMC6152947"}], "notes": [], "created": "2018-10-31T19:48:03.537Z", "modified": "2024-01-16T13:48:45.560Z"}, {"entity": "publication", "iuid": "7859a4a903104d5da707d0e722968e8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7859a4a903104d5da707d0e722968e8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7859a4a903104d5da707d0e722968e8d"}}, "title": "The molecular genetic basis of herbivory between butterflies and their host plants.", "authors": [{"family": "Nallu", "given": "Sumitha", "initials": "S"}, {"family": "Hill", "given": "Jason A", "initials": "JA"}, {"family": "Don", "given": "Kristine", "initials": "K"}, {"family": "Sahagun", "given": "Carlos", "initials": "C"}, {"family": "Zhang", "given": "Wei", "initials": "W"}, {"family": "Meslin", "given": "Camille", "initials": "C"}, {"family": "Snell-Rood", "given": "Emilie", "initials": "E"}, {"family": "Clark", "given": "Nathan L", "initials": "NL"}, {"family": "Morehouse", "given": "Nathan I", "initials": "NI"}, {"family": "Bergelson", "given": "Joy", "initials": "J"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Kronforst", "given": "Marcus R", "initials": "MR"}], "type": "journal article", "published": "2018-09-00", "journal": {"volume": "2", "issn": "2397-334X", "issue": "9", "pages": "1418-1427", "title": "Nat Ecol Evol", "issn-l": "2397-334X"}, "abstract": "Interactions between herbivorous insects and their host plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defences and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host plants. Parallel genome-wide association studies in the cabbage white butterfly, Pieris rapae, and its host plant, Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, as well as a core set of highly conserved genes in butterflies as well as their host plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of nature's most diverse taxa, butterflies and flowering plants.", "doi": "10.1038/s41559-018-0629-9", "pmid": "30076351", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-018-0629-9"}, {"db": "pmc", "key": "PMC6149523"}, {"db": "mid", "key": "NIHMS979338"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP134094", "key": "SRP134094"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "Arabidopsis thaliana, transcriptome shotgun assembly", "key": "GGJX00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "Medicago sativa, transcriptome shotgun assembly", "key": "GGKA00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "https://www.ncbi.nlm.nih.gov/nuccore/GGJQ00000000", "key": "GGJQ00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "https://www.ncbi.nlm.nih.gov/nuccore/GGJO00000000", "key": "GGJO00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "https://www.ncbi.nlm.nih.gov/nuccore/GGJY00000000", "key": "GGJY00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "https://www.ncbi.nlm.nih.gov/nuccore/GGJZ00000000", "key": "GGJZ00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "https://www.ncbi.nlm.nih.gov/nuccore/GGKB00000000", "key": "GGKB00000000"}, {"db": "Transcriptome Shotgun Assembly Sequence Database", "description": "https://www.ncbi.nlm.nih.gov/nuccore/GGKC00000000", "key": "GGKC00000000"}], "notes": [], "created": "2018-10-31T19:46:18.340Z", "modified": "2024-01-16T13:48:45.568Z"}, {"entity": "publication", "iuid": "c802c0698b69465ab6283194d8d11d8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c802c0698b69465ab6283194d8d11d8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c802c0698b69465ab6283194d8d11d8f"}}, "title": "The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.", "authors": [{"family": "Leroux", "given": "Louis-Philippe", "initials": "LP"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Graber", "given": "Tyson E", "initials": "TE"}, {"family": "Chaparro", "given": "Visnu", "initials": "V"}, {"family": "Masvidal", "given": "Laia", "initials": "L"}, {"family": "Aguirre", "given": "Maria", "initials": "M"}, {"family": "Fonseca", "given": "Bruno D", "initials": "BD"}, {"family": "van Kempen", "given": "L\u00e9on C", "initials": "LC"}, {"family": "Alain", "given": "Tommy", "initials": "T"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Jaramillo", "given": "Maritza", "initials": "M"}], "type": "journal article", "published": "2018-09-00", "journal": {"volume": "86", "issn": "1098-5522", "issue": "9", "title": "Infect. Immun.", "issn-l": "0019-9567"}, "abstract": "The intracellular parasite ", "doi": "10.1128/IAI.00244-18", "pmid": "29967092", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "IAI.00244-18"}, {"db": "pmc", "key": "PMC6105892"}], "notes": [], "created": "2018-10-31T19:46:49.861Z", "modified": "2024-01-16T13:48:45.575Z"}, {"entity": "publication", "iuid": "5d1f0d08b17940f5b307cb09e4276c5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d1f0d08b17940f5b307cb09e4276c5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d1f0d08b17940f5b307cb09e4276c5d"}}, "title": "Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.", "authors": [{"family": "Johansson", "given": "Ulf S", "initials": "US"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Qu", "given": "Yanhua", "initials": "Y"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}], "type": "journal article", "published": "2018-09-00", "journal": {"volume": "126", "issn": "1095-9513", "issue": null, "pages": "17-22", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "The rollers (Coraciidae) constitute a relative small avian family with ca. 12 species distributed in Africa, western and southern Eurasia, and eastern Australia. In this study we examine the phylogenetic relationships of all species currently recognized in the family, including two taxa whose taxonomic status is currently contested. By using shotgun sequencing on degraded DNA from museum study skins we have been able to recover complete mitochondrial genomes as well as 15 nuclear genes for in total 16 taxa. The gene sequences were analyzed both concatenated in a maximum likelihood framework as well in a species tree approach using MP-EST. The different analytical approaches yield similar, highly supported trees and support the current division of the rollers into two genera, Coracias and Eurystomus. The only conflict relates to the placement of the Blue-bellied Roller (C. cyanogaster), where the mitochondrial, and the concatenated nuclear and mitochondrial data set, place this taxon as sister to the other Coracias species, whereas nuclear data and the species tree analysis place it as the sister taxon of C. naevia and C. spatulatus. All analyses place the Eurasian roller (C. garrulus) with the two African species, Abyssinian Roller (C. abyssinica) and Liliac-breasted Roller (C. caudatus), and place this clade as the sister group to the Asian Coracias rollers. In addition, our results support a sister group relationship between the morphologically rather dissimilar Purple Roller (C. naevia) and Racquet-tailed Roller (C. spatulatus) and also support the division of Eurystomus in an African and an Asian clade. However, within the Asian clade the Azure Roller (E. azureus) from Halmahera appears to be nested within the Dollarbird (E. orientalis), indicating that that this taxon is a morphological divergent, but a rather recent offshoot, of the widespread Dollarbird. Similarly, the Purple-winged Roller (C. temminickii) from Sulawesi group together with C. benghalensis affinis from Southeast Asia and these two in turn comprises the sister group to C. benghalensis benghalensis from India and western Asia.", "doi": "10.1016/j.ympev.2018.03.030", "pmid": "29631051", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(17)30880-1"}], "notes": [], "created": "2018-10-31T19:47:39.236Z", "modified": "2024-01-16T13:48:45.589Z"}, {"entity": "publication", "iuid": "a97fb528f0834255b1e9c8103f8ff2bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a97fb528f0834255b1e9c8103f8ff2bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a97fb528f0834255b1e9c8103f8ff2bc"}}, "title": "Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Sen", "given": "Diya", "initials": "D"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Lamour", "given": "Kurt H", "initials": "KH"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2018-09-00", "journal": {"volume": "31", "issn": "0894-0282", "issue": "9", "pages": "903-905", "title": "Mol. Plant Microbe Interact.", "issn-l": null}, "abstract": "Phytophthora colocasiae is a phytopathogenic oomycete that causes leaf blight and corm rot on taro (Colocasia esculenta), an important staple crop in the tropics. The impact of P. colocasiae is a serious concern for food security in Asian and Oceanic regions. Vietnamese strain 7290 of P. colocasiae was sequenced (Illumina) to assemble a draft genome of 56.6 Mb, comprised of 19,853 scaffolds and 19,984 predicted protein-coding genes. As in other Phytophthora species, P. colocasiae possesses numerous pathogenicity-related genes, such as the RxLR class of effectors. This draft genome sequence of P. colocasiae provides a resource to underpin the first steps in determining the molecular mechanisms of disease development in this pathosystem.", "doi": "10.1094/MPMI-12-17-0321-A", "pmid": "29558317", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "GENBANK", "description": "Phytophthora colocasiae isolate 7290, whole genome shotgun sequencing project", "key": "NSDL00000000"}], "notes": [], "created": "2018-10-31T19:48:30.191Z", "modified": "2020-01-21T13:56:11.043Z"}, {"entity": "publication", "iuid": "4d8b238ab15548f4be38b5036cf7ede1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d8b238ab15548f4be38b5036cf7ede1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d8b238ab15548f4be38b5036cf7ede1"}}, "title": "Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation", "authors": [{"family": "Costantini", "given": "Alice", "initials": "A"}, {"family": "Tournis", "given": "Symeon", "initials": "S"}, {"family": "K\u00e4mpe", "given": "Anders", "initials": "A"}, {"family": "Ul Ain", "given": "Noor", "initials": "N"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Doulgeraki", "given": "Artemis", "initials": "A"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}], "type": "journal-article", "published": "2018-09-00", "journal": {"volume": "103", "issn": "0171-967X", "issue": "3", "pages": "353-358", "title": "Calcif Tissue Int", "issn-l": "0171-967X"}, "abstract": "Osteogenesis imperfecta (OI) is a skeletal dysplasia characterized by brittle bones and extraskeletal manifestations. The disease phenotype varies greatly. Most commonly, OI arises from monoallelic mutations in one of the two genes encoding type I collagen, COL1A1 and COL1A2 and is inherited as an autosomal dominant trait. Here, we describe a consanguineous family with autosomal recessive OI caused by a novel homozygous glycine substitution in COL1A2, NM_000089.3: c.604G>A, p.(Gly202Ser), detected by whole-genome sequencing. The index patient is a 31-year-old Greek woman with severe skeletal fragility. She had mild short stature, low bone mineral density of the lumbar spine and blue sclerae. She had sustained multiple long bone and vertebral fractures since childhood and had been treated with bisphosphonates for several years. She also had an affected sister with similar clinical manifestations. Interestingly, the parents and one sister, all carriers of the COL1A2 glycine mutation, did not have manifestations of OI. In summary, we report on autosomal recessive OI caused by a homozygous glycine-to-serine substitution in COL1A2, leading to severe skeletal fragility. The mutation carriers lacked OI manifestations. This family further expands the complex genetic spectrum of OI and underscores the importance of genetic evaluation for correct genetic counselling.", "doi": "10.1007/s00223-018-0414-4", "pmid": "29572562", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-26T11:53:38.555Z", "modified": "2020-01-21T13:56:17.008Z"}, {"entity": "publication", "iuid": "1c357307784744458239c44f393eb441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c357307784744458239c44f393eb441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c357307784744458239c44f393eb441"}}, "title": "Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.", "authors": [{"family": "Tan", "given": "David J X", "initials": "DJX"}, {"family": "Chattopadhyay", "given": "Balaji", "initials": "B"}, {"family": "Garg", "given": "Kritika M", "initials": "KM"}, {"family": "Cros", "given": "Emilie", "initials": "E"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}, {"family": "Rheindt", "given": "Frank E", "initials": "FE"}], "type": "journal article", "published": "2018-08-24", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "12804", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Although edge-tolerant species are known to benefit from habitat fragmentation, less is known about the population genetic impacts fragmentation may exert on edge-tolerant species. We examined the landscape genomic structure of an edge-tolerant forest-dependent bird species, the Striped Tit-Babbler Mixornis gularis, in the heavily urbanized island of Singapore to determine if two centuries of fragmentation have led to signs of isolation and loss of population-genetic diversity in different parts of the island. We obtained a high-quality complete reference genome with 78x coverage. Using almost 4000 SNPs from double-digest RAD-Sequencing across 46 individuals, we found that the population has likely experienced a recent contraction in effective population size and presently exhibits low population genetic diversity. Using empirical and simulation-based landscape genomic analyses, we also found that the subtle population genetic structure observed in the Striped Tit-Babbler population in Singapore is likely driven by isolation by distance resulting from limited dispersal. Our results demonstrate that population genetic impoverishment and subdivision can accumulate at relatively rapid rates in edge-tolerant bird species such as the Striped Tit-Babbler as a result of fragmentation, and that subtle spatial genetic structure can be detected over fine spatial and temporal scales using relatively few multilocus genomic SNPs.", "doi": "10.1038/s41598-018-31074-5", "pmid": "30143731", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-31074-5"}, {"db": "pmc", "key": "PMC6109123"}, {"db": "BioProject", "description": "Complete genome and RAD-seq study of Mixornis gularis", "key": "PRJNA392017"}], "notes": [], "created": "2018-10-31T19:47:38.570Z", "modified": "2024-01-16T13:48:45.713Z"}, {"entity": "publication", "iuid": "66b69eace5f049459344bbb1bbc12fb1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/66b69eace5f049459344bbb1bbc12fb1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/66b69eace5f049459344bbb1bbc12fb1"}}, "title": "Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype", "authors": [{"family": "Goudarzi", "given": "Kaveh M", "initials": "KM"}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA"}, {"family": "Guo", "given": "Min", "initials": "M"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS"}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D"}], "type": "journal-article", "published": "2018-08-22", "journal": {"volume": null, "issn": "0008-5472", "issue": null, "pages": "canres.0320.2018", "title": "Cancer Res", "issn-l": "0008-5472"}, "abstract": "The homeodomain transcription factor PROX1 has been linked to several cancer types, including gliomas, but its functions remain to be further elucidated. Here we describe a functional role and the prognostic value of PROX1 in glioblastoma. Low expression of ", "doi": "10.1158/0008-5472.can-18-0320", "pmid": "30135192", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-15T10:04:43.250Z", "modified": "2020-01-21T13:56:11.196Z"}, {"entity": "publication", "iuid": "0e6079a517d040d69e5a52d2fd623ff9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e6079a517d040d69e5a52d2fd623ff9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e6079a517d040d69e5a52d2fd623ff9"}}, "title": "Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.", "authors": [{"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "M\u00e4e", "given": "Maarja Andaloussi", "initials": "MA"}, {"family": "Andrae", "given": "Johanna", "initials": "J"}, {"family": "Ando", "given": "Koji", "initials": "K"}, {"family": "Del Gaudio", "given": "Francesca", "initials": "F"}, {"family": "Nahar", "given": "Khayrun", "initials": "K"}, {"family": "Lebouvier", "given": "Thibaud", "initials": "T"}, {"family": "Lavi\u00f1a", "given": "B\u00e0rbara", "initials": "B"}, {"family": "Gouveia", "given": "Leonor", "initials": "L"}, {"family": "Sun", "given": "Ying", "initials": "Y"}, {"family": "Raschperger", "given": "Elisabeth", "initials": "E"}, {"family": "Segerstolpe", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Liu", "given": "Jianping", "initials": "J"}, {"family": "Gustafsson", "given": "Sonja", "initials": "S"}, {"family": "R\u00e4s\u00e4nen", "given": "Markus", "initials": "M"}, {"family": "Zarb", "given": "Yvette", "initials": "Y"}, {"family": "Mochizuki", "given": "Naoki", "initials": "N"}, {"family": "Keller", "given": "Annika", "initials": "A"}, {"family": "Lendahl", "given": "Urban", "initials": "U"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2018-08-21", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "5", "issue": "1", "pages": "180160"}, "abstract": "Vascular diseases are major causes of death, yet our understanding of the cellular constituents of blood vessels, including how differences in their gene expression profiles create diversity in vascular structure and function, is limited. In this paper, we describe a single-cell RNA sequencing (scRNA-seq) dataset that defines vascular and vessel-associated cell types and subtypes in mouse brain and lung. The dataset contains 3,436 single cell transcriptomes from mouse brain, which formed 15 distinct clusters corresponding to cell (sub)types, and another 1,504 single cell transcriptomes from mouse lung, which formed 17 cell clusters. In order to allow user-friendly access to our data, we constructed a searchable database (http://betsholtzlab.org/VascularSingleCells/database.html). Our dataset constitutes a comprehensive molecular atlas of vascular and vessel-associated cell types in the mouse brain and lung, and as such provides a strong foundation for future studies of vascular development and diseases.", "doi": "10.1038/sdata.2018.160", "pmid": "30129931", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "sdata2018160"}, {"db": "pmc", "key": "PMC6103262"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse brain vascular transcriptomes", "key": "GSE98816"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse lung vascular transcriptomes", "key": "GSE99235"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse brain astrocyte transcriptomes", "key": "GSE99058"}, {"db": "figshare", "description": "Single cell RNAseq of mouse brain and lung vascular and vessel-associated cell types", "key": "https://doi.org/10.6084/m9.figshare.c.4077260)."}], "notes": [], "created": "2018-10-31T13:12:57.513Z", "modified": "2024-01-16T13:48:45.720Z"}, {"entity": "publication", "iuid": "83fd3978df9b4ba18716067cbc23fec8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83fd3978df9b4ba18716067cbc23fec8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83fd3978df9b4ba18716067cbc23fec8"}}, "title": "Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.", "authors": [{"family": "Marques", "given": "Sueli", "initials": "S"}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Vanichkina", "given": "Darya Pavlovna", "initials": "DP"}, {"family": "Floriddia", "given": "Elisa Mariagrazia", "initials": "EM"}, {"family": "Munguba", "given": "Hermany", "initials": "H"}, {"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Falc\u00e3o", "given": "Ana Mendanha", "initials": "AM"}, {"family": "Meijer", "given": "Mandy", "initials": "M"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa Kristina", "initials": "\u00c5K"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}, {"family": "Taft", "given": "Ryan James", "initials": "RJ"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal article", "published": "2018-08-20", "journal": {"volume": "46", "issn": "1878-1551", "issue": "4", "pages": "504-517.e7", "title": "Dev. Cell", "issn-l": "1534-5807"}, "abstract": "Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryogenesis in the central nervous system (CNS). It is unclear whether there is a correlation between these waves and different oligodendrocyte (OL) states at adult stages. Here, we present bulk and single-cell transcriptomics resources providing insights on how transitions between these states occur. We found that post-natal OPCs from brain and spinal cord present similar transcriptional signatures. Moreover, post-natal OPC progeny of E13.5 Pdgfra+ cells present electrophysiological and transcriptional profiles similar to OPCs derived from subsequent specification waves, indicating that Pdgfra+ pre-OPCs rewire their transcriptional network during development. Single-cell RNA-seq and lineage tracing indicates that a subset of E13.5 Pdgfra+ cells originates cells of the pericyte lineage. Thus, our results indicate that embryonic Pdgfra+ cells in the CNS give rise to distinct post-natal cell lineages, including OPCs with convergent transcriptional profiles in different CNS regions.", "doi": "10.1016/j.devcel.2018.07.005", "pmid": "30078729", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Systems Biology": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1534-5807(18)30558-6"}, {"db": "pmc", "key": "PMC6104814"}, {"db": "GEO", "description": "Single-Cell RNA-seq study of E13.5 and P7 brain and Spinal Cord Pdgfra-GFP positive samples during development in Mice.", "key": "GSE95194"}, {"db": "GEO", "description": "Transcriptional convergence of oligodendrocyte lineage progenitors during development", "key": "GSE95093"}], "notes": [], "created": "2018-08-06T07:09:18.896Z", "modified": "2024-01-16T13:48:45.728Z"}, {"entity": "publication", "iuid": "7a923a1fcefd4484a6d57e3390730cd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a923a1fcefd4484a6d57e3390730cd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a923a1fcefd4484a6d57e3390730cd7"}}, "title": "BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence", "authors": [{"family": "Rosa", "given": "Jo\u00e3o", "initials": "J"}, {"family": "Fernandez-Gonzalez", "given": "Esther", "initials": "E"}, {"family": "Ducani", "given": "Cosimo", "initials": "C"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal-article", "published": "2018-08-17", "journal": {"volume": "13", "issn": "1932-6203", "issue": "8", "pages": "e0202057", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Restriction enzymes are the bread and butter of Molecular Biology. Nonetheless, how restriction enzymes recognize and cleave their target is not always clear. When developing a method for the enzymatic production of oligonucleotides, we noticed that type II endonucleases BtsCI and BseGI, which recognize the sequence GGATGNN^, perform incomplete digestions of DNA hairpins, with the top strand nick not always occurring correctly. We tested the cutting of synthetic hairpins containing all possible combinations of dinucleotides following the recognition site and our results show that all sequences containing one adenine following GGATG were digested more efficiently. We further show that the same sequence preference is also observable in double stranded DNA at higher Mg2+ concentrations and even in optimal conditions. Kinetic results show that BtsCI has a noteworthy difference in the first-rate constants between different sequences and between the two catalytic domains. An increase in Mg2+ resulted in a drastic decrease in the catalytic activity of the top (sense) strand that wasn't always accompanied by a nick in the bottom strand (antisense).", "doi": "10.1371/journal.pone.0202057", "pmid": "30118487", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Protein Science Facility (PSF)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-08-30T08:51:04.144Z", "modified": "2020-01-21T13:56:10.982Z"}, {"entity": "publication", "iuid": "68c53403732e496f9fd2f1e5affc34d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68c53403732e496f9fd2f1e5affc34d3"}}, "title": "Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YOO", "orcid": "0000-0002-2025-2198", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8675dd0fbc44f892614c848dbade8f.json"}}, {"family": "Ndegwa", "given": "Nelson", "initials": "N", "orcid": "0000-0002-5853-879X", "researcher": {"href": "https://publications.scilifelab.se/researcher/69494d497aca4285a950e335c2978135.json"}}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Johansson", "given": "Sebastian", "initials": "S"}, {"family": "Logue", "given": "J\u00fcrg Brendan", "initials": "JB"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fagerberg", "given": "Jens", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "11907", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.", "doi": "10.1038/s41598-018-29920-7", "pmid": "30093614", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-29920-7"}, {"db": "pmc", "key": "PMC6085348"}], "notes": [], "created": "2018-10-31T19:44:54.553Z", "modified": "2024-01-16T13:48:45.757Z"}, {"entity": "publication", "iuid": "244db9ef301446c5a714cc7f73d56fb7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/244db9ef301446c5a714cc7f73d56fb7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/244db9ef301446c5a714cc7f73d56fb7"}}, "title": "Molecular Architecture of the Mouse Nervous System.", "authors": [{"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Hochgerner", "given": "Hannah", "initials": "H"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Johnsson", "given": "Anna", "initials": "A"}, {"family": "Memic", "given": "Fatima", "initials": "F"}, {"family": "van der Zwan", "given": "Job", "initials": "J"}, {"family": "H\u00e4ring", "given": "Martin", "initials": "M"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Borm", "given": "Lars E", "initials": "LE"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Codeluppi", "given": "Simone", "initials": "S"}, {"family": "Furlan", "given": "Alessandro", "initials": "A"}, {"family": "Lee", "given": "Kawai", "initials": "K"}, {"family": "Skene", "given": "Nathan", "initials": "N"}, {"family": "Harris", "given": "Kenneth D", "initials": "KD"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}, {"family": "Marklund", "given": "Ulrika", "initials": "U"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "174", "issn": "1097-4172", "issue": "4", "pages": "999-1014.e22", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "The mammalian nervous system executes complex behaviors controlled by specialized, precisely positioned, and interacting cell types. Here, we used RNA sequencing of half a million single cells to create a detailed census of cell types in the mouse nervous system. We mapped cell types spatially and derived a hierarchical, data-driven taxonomy. Neurons were the most diverse and were grouped by developmental anatomical units and by the expression of neurotransmitters and neuropeptides. Neuronal diversity was driven by genes encoding cell identity, synaptic connectivity, neurotransmission, and membrane conductance. We discovered seven distinct, regionally restricted astrocyte types that obeyed developmental boundaries and correlated with the spatial distribution of key glutamate and glycine neurotransmitters. In contrast, oligodendrocytes showed a loss of regional identity followed by a secondary diversification. The resource presented here lays a solid foundation for understanding the molecular architecture of the mammalian nervous system and enables genetic manipulation of specific cell types.", "doi": "10.1016/j.cell.2018.06.021", "pmid": "30096314", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(18)30789-X"}, {"db": "pmc", "key": "PMC6086934"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP135960", "key": "SRP135960"}], "notes": [], "created": "2018-10-31T19:46:20.423Z", "modified": "2024-01-16T13:48:45.772Z"}, {"entity": "publication", "iuid": "c96afccb586a4170b645b616dc18405c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c96afccb586a4170b645b616dc18405c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c96afccb586a4170b645b616dc18405c"}}, "title": "Clonal relatedness in tumour pairs of breast cancer patients.", "authors": [{"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "Nemes", "given": "Szil\u00e1rd", "initials": "S"}, {"family": "Danielsson", "given": "Anna", "initials": "A"}, {"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Werner R\u00f6nnerman", "given": "Elisabeth", "initials": "E"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2018-08-09", "journal": {"volume": "20", "issn": "1465-542X", "issue": "1", "pages": "96", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours.\r\n\r\nThirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours. In a multi-omics approach, tumour clonality was analysed by integrating clinical characteristics (n\u00a0=\u200937), DNA copy number (n\u2009=\u200937), DNA methylation (n\u00a0=\u20098), gene expression microarray (n\u00a0=\u20097), RNA sequencing (n\u2009=\u20093), and SNP genotyping data (n\u2009=\u20093). Different statistical methods, e.g. the diagnostic similarity index (SI), were used to classify the tumours as clonally related recurrences or independent primary tumours.\r\n\r\nThe SI and hierarchical clustering showed similar tendencies and the highest concordance with the other methods. Concordant evidence for tumour clonality was found in 46% (17/37) of patients. Notably, no association was found between the current clinical guidelines and molecular tumour features.\r\n\r\nA more accurate classification of clonal relatedness between multiple breast tumours may help to mitigate treatment failure and relapse by integrating tumour-associated molecular features, clinical parameters, and statistical methods. Guidelines need to be defined with exact thresholds to standardise clonality testing in a routine diagnostic setting.", "doi": "10.1186/s13058-018-1022-y", "pmid": "30092821", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13058-018-1022-y"}, {"db": "GEO", "description": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas", "key": "GSE97293"}, {"db": "GEO", "description": "Genome-wide multi-omics profiling reveals extensive genetic complexity in 8p11-p12 amplified breast carcinomas [expression]", "key": "GSE97177"}], "notes": [], "created": "2018-08-16T15:30:10.983Z", "modified": "2024-01-16T13:48:45.779Z"}, {"entity": "publication", "iuid": "62d641cab3954c26911450b84184bd7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62d641cab3954c26911450b84184bd7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62d641cab3954c26911450b84184bd7b"}}, "title": "Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.", "authors": [{"family": "Pircs", "given": "Karolina", "initials": "K"}, {"family": "Petri", "given": "Rebecca", "initials": "R"}, {"family": "Madsen", "given": "Sofia", "initials": "S"}, {"family": "Bratt\u00e5s", "given": "Per Ludvik", "initials": "PL"}, {"family": "Vuono", "given": "Romina", "initials": "R"}, {"family": "Ottosson", "given": "Daniella R", "initials": "DR"}, {"family": "St-Amour", "given": "Isabelle", "initials": "I"}, {"family": "Hersbach", "given": "Bob A", "initials": "BA"}, {"family": "Matusiak-Br\u00fcckner", "given": "Monika", "initials": "M"}, {"family": "Lundh", "given": "Sofia Hult", "initials": "SH"}, {"family": "Peters\u00e9n", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "D\u00e9glon", "given": "Nicole", "initials": "N"}, {"family": "H\u00e9bert", "given": "S\u00e9bastien S", "initials": "SS"}, {"family": "Parmar", "given": "Malin", "initials": "M"}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Jakobsson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2018-08-07", "journal": {"volume": "24", "issn": "2211-1247", "issue": "6", "pages": "1397-1406", "title": "Cell Rep", "issn-l": null}, "abstract": "Many neurodegenerative diseases are characterized by the presence of intracellular protein aggregates, resulting in alterations in autophagy. However, the consequences of impaired autophagy for neuronal function remain poorly understood. In this study, we used cell culture and mouse models of huntingtin protein aggregation as well as post-mortem material from patients with Huntington's disease to demonstrate that Argonaute-2 (AGO2) accumulates in the presence of neuronal protein aggregates and that this is due to impaired autophagy. Accumulation of AGO2, a key factor of the RNA-induced silencing complex that executes microRNA functions, results in global alterations of microRNA levels and activity. Together, these results demonstrate that impaired autophagy found in neurodegenerative diseases not only influences protein aggregation but also directly contributes to global alterations of intracellular post-transcriptional networks.", "doi": "10.1016/j.celrep.2018.07.017", "pmid": "30089251", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2211-1247(18)31107-0"}, {"db": "GEO", "description": "Huntingtin aggregation impairs autophagy leading to Argonaute-2 accumulation and global microRNA dysregulation", "key": "GSE78928"}], "notes": [], "created": "2018-10-31T19:48:28.582Z", "modified": "2024-01-16T13:48:45.788Z"}, {"entity": "publication", "iuid": "04ade1bc910d44469483303138adb9a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04ade1bc910d44469483303138adb9a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04ade1bc910d44469483303138adb9a5"}}, "title": "Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.", "authors": [{"family": "Nascimento", "given": "Francisco J A", "initials": "FJA"}, {"family": "Lallias", "given": "Delphine", "initials": "D"}, {"family": "Bik", "given": "Holly M", "initials": "HM"}, {"family": "Creer", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2018-08-06", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "11737", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2\u2009cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18\u2009S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2\u2009g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.", "doi": "10.1038/s41598-018-30179-1", "pmid": "30082688", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-30179-1"}, {"db": "pmc", "key": "PMC6078945"}, {"db": "figshare", "description": "https://figshare.com/articles/Sample_size_effects_on_the_assessment_of_eukaryotic_diversity_and_community_structure_in_aquatic_sediments_using_high-throughput_sequencing/4993667", "key": "doi:10.6084/m9.figshare.4993667"}], "notes": [], "created": "2018-10-31T19:48:05.881Z", "modified": "2024-01-16T13:48:45.803Z"}, {"entity": "publication", "iuid": "2d325f1ceb9d4e138fce98bfee37557c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d325f1ceb9d4e138fce98bfee37557c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d325f1ceb9d4e138fce98bfee37557c"}}, "title": "Stereotypic Immune System Development in Newborn Children", "authors": [{"family": "Olin", "given": "Axel", "initials": "A"}, {"family": "Henckel", "given": "Ewa", "initials": "E"}, {"family": "Chen", "given": "Yang", "initials": "Y"}, {"family": "Lakshmikanth", "given": "Tadepally", "initials": "T", "orcid": "0000-0001-7256-5770", "researcher": {"href": "https://publications.scilifelab.se/researcher/92e81aa6b0cf4ff0a18b14098bf0fcc1.json"}}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Mikes", "given": "Jaromir", "initials": "J"}, {"family": "Gustafsson", "given": "Anna", "initials": "A"}, {"family": "Bernhardsson", "given": "Anna Karin", "initials": "AK"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Bohlin", "given": "Kajsa", "initials": "K"}, {"family": "Brodin", "given": "Petter", "initials": "P", "orcid": "0000-0002-8103-0046", "researcher": {"href": "https://publications.scilifelab.se/researcher/40097353cdb24e52bf2330eb687042bf.json"}}], "type": "journal-article", "published": "2018-08-00", "journal": {"volume": "174", "issn": "0092-8674", "issue": "5", "pages": "1277-1292.e14", "title": "Cell", "issn-l": null}, "abstract": "Epidemiological data suggest that early life exposures are key determinants of immune-mediated disease later in life. Young children are also particularly susceptible to infections, warranting more analyses of immune system development early in life. Such analyses mostly have been performed in mouse models or human cord blood samples, but these cannot account for the complex environmental exposures influencing human newborns after birth. Here, we performed longitudinal analyses in 100 newborn children, sampled up to 4 times during their first 3 months of life. From 100 \u03bcL of blood, we analyze the development of 58 immune cell populations by mass cytometry and 267 plasma proteins by immunoassays, uncovering drastic changes not predictable from cord blood measurements but following a stereotypic pattern. Preterm and term children differ at birth but converge onto a shared trajectory, seemingly driven by microbial interactions and hampered by early gut bacterial dysbiosis.", "doi": "10.1016/j.cell.2018.06.045", "pmid": "30142345", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Affinity Proteomics Stockholm": "Service", "Cellular Immunomonitoring": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6108833"}, {"db": "pii", "key": "S0092-8674(18)30848-1"}], "notes": [], "created": "2018-08-26T15:08:17.252Z", "modified": "2024-01-16T13:48:45.831Z"}, {"entity": "publication", "iuid": "1ced3bfbefa34f329fba431632461478", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ced3bfbefa34f329fba431632461478.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ced3bfbefa34f329fba431632461478"}}, "title": "RNA velocity of single cells.", "authors": [{"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Soldatov", "given": "Ruslan", "initials": "R"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Braun", "given": "Emelie", "initials": "E"}, {"family": "Hochgerner", "given": "Hannah", "initials": "H"}, {"family": "Petukhov", "given": "Viktor", "initials": "V"}, {"family": "Lidschreiber", "given": "Katja", "initials": "K"}, {"family": "Kastriti", "given": "Maria E", "initials": "ME"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Furlan", "given": "Alessandro", "initials": "A"}, {"family": "Fan", "given": "Jean", "initials": "J"}, {"family": "Borm", "given": "Lars E", "initials": "LE"}, {"family": "Liu", "given": "Zehua", "initials": "Z"}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Guo", "given": "Jimin", "initials": "J"}, {"family": "He", "given": "Xiaoling", "initials": "X"}, {"family": "Barker", "given": "Roger", "initials": "R"}, {"family": "Sundstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Cramer", "given": "Patrick", "initials": "P"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Kharchenko", "given": "Peter V", "initials": "PV"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "560", "issn": "1476-4687", "issue": "7719", "pages": "494-498", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "RNA abundance is a powerful indicator of the state of individual cells. Single-cell RNA sequencing can reveal RNA abundance with high quantitative accuracy, sensitivity and throughput", "doi": "10.1038/s41586-018-0414-6", "pmid": "30089906", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-018-0414-6"}, {"db": "pmc", "key": "PMC6130801"}, {"db": "mid", "key": "EMS78511"}], "notes": [], "created": "2018-10-31T19:46:21.118Z", "modified": "2024-01-16T13:48:45.839Z"}, {"entity": "publication", "iuid": "3609ed537d4146a28956175a3d90c112", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3609ed537d4146a28956175a3d90c112.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3609ed537d4146a28956175a3d90c112"}}, "title": "Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.", "authors": [{"family": "Th\u00f6rnqvist", "given": "Linnea", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "19", "issn": "2352-3409", "issue": null, "pages": "337-352", "title": "Data Brief", "issn-l": "2352-3409"}, "abstract": "The highly variable complementary determining region 3 (CDR3) of antibodies is generated through recombination of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes. The codons encoding the first residues of CDR3 may be derived directly from the IGHV germline gene but they may also be generated as part of the rearrangement process. Data of the nucleotide composition of these codons of rearranged genes, an indicator of the degree of contribution of the IGHV gene to CDR3 diversity, are presented in this article. Analyzed data are presented for two unrelated sets of raw sequence data. The raw data sets consisted of sequences of antibody heavy chain-encoding transcripts of six allergic subjects (European Nucleotide Archive accession number PRJEB18926), and paired antibody heavy and light chain variable region-encoding transcripts of memory B cells of three subjects (European Nucleotide Archive accession numbers SRX709625, SRX709626, and SRX709627). The nucleotide compositions of the corresponding 5'-ends of sequences encoding the CDR3 are presented for transcripts with an origin in 47 different IGHV alleles. These data have been used (Th\u00f6rnqvist and Ohlin, 2018) [1] to demonstrate the extent of incorporation of the 3' most bases of IGHV germline genes into rearranged immunoglobulin encoding sequences, and the extent whereby any difference in incorporation affects the specificity of inference of the 3'-end of IGHV genes from immunoglobulin-encoding transcripts. They have also been used to assess the effect of observed gene differences on the composition of the ascending strand of CDR3 associated to antibodies with an origin in different IGHV genes (Th\u00f6rnqvist and Ohlin, 2018) [1].", "doi": "10.1016/j.dib.2018.04.125", "pmid": "29892656", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3409(18)30478-5"}, {"db": "pmc", "key": "PMC5992955"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB18926", "key": "PRJEB18926"}], "notes": [], "created": "2018-10-31T19:47:15.063Z", "modified": "2024-01-16T13:48:45.883Z"}, {"entity": "publication", "iuid": "fa3029e4a8aa45b78d6a052ad53af728", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa3029e4a8aa45b78d6a052ad53af728.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa3029e4a8aa45b78d6a052ad53af728"}}, "title": "Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.", "authors": [{"family": "Markussen", "given": "Trine", "initials": "T"}, {"family": "Happel", "given": "Elisabeth M", "initials": "EM"}, {"family": "Teikari", "given": "Jonna E", "initials": "JE"}, {"family": "Huchaiah", "given": "Vimala", "initials": "V"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Sivonen", "given": "Kaarina", "initials": "K"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}, {"family": "Middelboe", "given": "Mathias", "initials": "M"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}], "type": "journal article", "published": "2018-08-00", "journal": {"volume": "20", "issn": "1462-2920", "issue": "8", "pages": "3083-3099", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.", "doi": "10.1111/1462-2920.14371", "pmid": "30084235", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-31T19:45:55.109Z", "modified": "2024-01-16T13:48:45.890Z"}, {"entity": "publication", "iuid": "2fb641f0015d4cf68ee3a07d329f2564", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fb641f0015d4cf68ee3a07d329f2564.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fb641f0015d4cf68ee3a07d329f2564"}}, "title": "Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy", "authors": [{"family": "Coenen-Stass", "given": "Anna M L", "initials": "AML"}, {"family": "Sork", "given": "Helena", "initials": "H"}, {"family": "Gatto", "given": "Sole", "initials": "S"}, {"family": "Godfrey", "given": "Caroline", "initials": "C"}, {"family": "Bhomra", "given": "Amarjit", "initials": "A"}, {"family": "Krjut\u0161kov", "given": "Kaarel", "initials": "K"}, {"family": "Hart", "given": "Jonathan R", "initials": "JR"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "O\u2019Donovan", "given": "Liz", "initials": "L"}, {"family": "Roos", "given": "Andreas", "initials": "A"}, {"family": "Lochm\u00fcller", "given": "Hanns", "initials": "H"}, {"family": "Puri", "given": "Pier Lorenzo", "initials": "PL"}, {"family": "Andaloussi", "given": "Samir EL", "initials": "SE"}, {"family": "Wood", "given": "Matthew J A", "initials": "MJA"}, {"family": "Roberts", "given": "Thomas C", "initials": "TC"}], "type": "journal-article", "published": "2018-08-00", "journal": {"volume": null, "issn": "2162-2531", "issue": null, "pages": null, "title": "Mol Ther Nucleic Acids", "issn-l": "2162-2531"}, "abstract": "Extracellular small RNAs (sRNAs), including microRNAs (miRNAs), are promising biomarkers for diseases such as Duchenne muscular dystrophy (DMD), although their biological relevance is largely unknown. To investigate the relationship between intracellular and extracellular sRNA levels on a global scale, we performed sRNA sequencing in four muscle types and serum from wild-type, dystrophic mdx, and mdx mice in which dystrophin protein expression was restored by exon skipping. Differentially abundant sRNAs were identified in serum (mapping to miRNA, small nuclear RNA [snRNA], and PIWI-interacting RNA [piRNA] loci). One novel candidate biomarker, miR-483, was increased in both mdx serum and muscle, and also elevated in DMD patient sera. Dystrophin restoration induced global shifts in miRNA (including miR-483) and snRNA-fragment abundance toward wild-type levels. Specific serum piRNA-like sRNAs also responded to exon skipping therapy. Absolute miRNA expression in muscle was positively correlated with abundance in the circulation, although multiple highly expressed miRNAs in muscle were not elevated in mdx serum, suggesting that both passive and selective release mechanisms contribute to serum miRNA levels. In conclusion, this study has revealed new insights into the sRNA biology of dystrophin deficiency and identified novel DMD biomarkers.", "doi": "10.1016/j.omtn.2018.08.005", "pmid": "30219269", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP102619", "key": "SRP102619"}], "notes": [], "created": "2018-08-21T11:12:55.111Z", "modified": "2024-01-16T13:48:45.897Z"}, {"entity": "publication", "iuid": "35141c274e704cbca7ce4de383f6b549", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35141c274e704cbca7ce4de383f6b549.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35141c274e704cbca7ce4de383f6b549"}}, "title": "Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.", "authors": [{"family": "Lin", "given": "Yingbo", "initials": "Y"}, {"family": "van Duyvenvoorde", "given": "Hermine A", "initials": "HA"}, {"family": "Liu", "given": "Hongyu", "initials": "H"}, {"family": "Yang", "given": "Chen", "initials": "C"}, {"family": "Warsito", "given": "Dudi", "initials": "D"}, {"family": "Yin", "given": "Chang", "initials": "C"}, {"family": "Kant", "given": "Sarina G", "initials": "SG"}, {"family": "Haglund", "given": "Felix", "initials": "F"}, {"family": "Wit", "given": "Jan M", "initials": "JM"}, {"family": "Larsson", "given": "Olle", "initials": "O"}], "type": "case reports", "published": "2018-08-00", "journal": {"volume": "179", "issn": "1479-683X", "issue": "2", "pages": "85-95", "title": "Eur. J. Endocrinol.", "issn-l": "0804-4643"}, "abstract": "The insulin-like growth factor1 receptor (IGF1R) is important in growth and development, and inactivating \n\nThe \n\nThe \n\nOur findings suggest that R1353H constitutes an activating ", "doi": "10.1530/EJE-18-0176", "pmid": "29789409", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EJE-18-0176"}], "notes": [], "created": "2018-10-31T19:46:50.538Z", "modified": "2024-01-16T13:48:45.905Z"}, {"entity": "publication", "iuid": "1fe9214171b24f35bfca0414c1502c7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fe9214171b24f35bfca0414c1502c7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fe9214171b24f35bfca0414c1502c7f"}}, "title": "BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2018-07-31", "journal": {"volume": "5", "issn": "2052-4463", "issue": null, "pages": "180146", "title": "Sci Data", "issn-l": "2052-4463"}, "abstract": "The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.", "doi": "10.1038/sdata.2018.146", "pmid": "30063227", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "sdata2018146"}, {"db": "pmc", "key": "PMC6067050"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB22997", "key": "PRJEB22997"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP058493", "key": "SRP058493"}, {"db": "figshare", "description": "BARM Annotation and Quantification Data", "key": "https://doi.org/10.6084/m9.figshare.c.3831631"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP077551", "key": "SRP077551"}], "notes": [], "created": "2018-10-31T19:45:28.762Z", "modified": "2024-01-16T13:48:45.935Z"}, {"entity": "publication", "iuid": "8a7128dc3ed34ffbbc5f62cbf077c584", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a7128dc3ed34ffbbc5f62cbf077c584.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a7128dc3ed34ffbbc5f62cbf077c584"}}, "title": "Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.", "authors": [{"family": "Berner", "given": "Christoffer", "initials": "C"}, {"family": "Bertos-Fortis", "given": "Mireia", "initials": "M"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}], "type": "journal article", "published": "2018-07-25", "journal": {"volume": "9", "issn": "1664-302X", "issue": null, "pages": "1562", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Frequencies and biomass of Baltic Sea cyanobacterial blooms are expected to be higher in future climate conditions, but also of longer duration as a result of increased sea surface temperature. Concurrently, climate predictions indicate a reduced salinity in the Baltic Sea. These climate-driven changes are expected to alter not solely the phytoplankton community but also the role of microbial communities for nutrient remineralization. Here, we present the response of summer plankton communities (filamentous cyanobacteria, picocyanobacteria, and heterotrophic bacteria) to the interplay of increasing temperature (from 16 to 18\u00b0C and 20\u00b0C) and reduced salinity (from salinity 6.9 to 5.9) in the Baltic Proper (NW Gotland Sea) using a microcosm approach. Warmer temperatures led to an earlier peak of cyanobacterial biomass, while yields were reduced. These conditions caused a decrease of nitrogen-fixers (", "doi": "10.3389/fmicb.2018.01562", "pmid": "30090087", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6068395"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP120581", "key": "SRP120581"}], "notes": [], "created": "2018-10-31T19:45:28.107Z", "modified": "2024-01-16T13:48:45.949Z"}, {"entity": "publication", "iuid": "03333639037048b1b25e62e74b907978", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03333639037048b1b25e62e74b907978.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03333639037048b1b25e62e74b907978"}}, "title": "A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.", "authors": [{"family": "Einarsdottir", "given": "Berglind O", "initials": "BO"}, {"family": "Karlsson", "given": "Joakim", "initials": "J", "orcid": "0000-0001-6332-4043", "researcher": {"href": "https://publications.scilifelab.se/researcher/6190c1a8a7d54cd6807f120e8748cfcd.json"}}, {"family": "S\u00f6derberg", "given": "Elin M V", "initials": "EMV"}, {"family": "Lindberg", "given": "Mattias F", "initials": "MF"}, {"family": "Funck-Brentano", "given": "Elisa", "initials": "E"}, {"family": "Jespersen", "given": "Henrik", "initials": "H"}, {"family": "Brynjolfsson", "given": "Siggeir F", "initials": "SF", "orcid": "0000-0003-0451-5581", "researcher": {"href": "https://publications.scilifelab.se/researcher/2411927ecc294a80ab9ce96f2c2ef48a.json"}}, {"family": "Olofsson Bagge", "given": "Roger", "initials": "R"}, {"family": "Carstam", "given": "Louise", "initials": "L"}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Wallner", "given": "Olof", "initials": "O"}, {"family": "Stierner", "given": "Ulrika", "initials": "U"}, {"family": "Berglund", "given": "Ulrika Warpman", "initials": "UW"}, {"family": "Ny", "given": "Lars", "initials": "L"}, {"family": "Nilsson", "given": "Lisa M", "initials": "LM"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Nilsson", "given": "Jonas A", "initials": "JA"}], "type": "journal article", "published": "2018-07-24", "journal": {"volume": "9", "issn": "2041-4889", "issue": "8", "pages": "810", "title": "Cell Death Dis", "issn-l": "2041-4889"}, "abstract": "Karonudib (TH1579) is a novel compound that exerts anti-tumor activities and has recently entered phase I clinical testing. The aim of this study was to conduct a pre-clinical trial in patient-derived xenografts to identify the possible biomarkers of response or resistance that could guide inclusion of patients suffering from metastatic melanoma in phase II clinical trials. Patient-derived xenografts from 31 melanoma patients with metastatic disease were treated with karonudib or a vehicle for 18 days. Treatment responses were followed by measuring tumor sizes, and the models were categorized in the response groups. Tumors were harvested and processed for RNA sequencing and protein analysis. To investigate the effect of karonudib on T-cell-mediated anti-tumor activities, tumor-infiltrating T cells were injected in mice carrying autologous tumors and the mice treated with karonudib. We show that karonudib has heterogeneous anti-tumor effect on metastatic melanoma. Thus, based on the treatment responses, we could divide the 31 patient-derived xenografts in three treatment groups: progression group (32%), suppression group (42%), and regression group (26%). Furthermore, we show that karonudib has anti-tumor effect, irrespective of major melanoma driver mutations. Also, we identify high expression of ABCB1, which codes for p-gp pumps as a resistance biomarker. Finally, we show that karonudib treatment does not hamper T-cell-mediated anti-tumor responses. These findings can be used to guide future use of karonudib in clinical use with a potential approach as precision medicine.", "doi": "10.1038/s41419-018-0865-6", "pmid": "30042422", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41419-018-0865-6"}, {"db": "pmc", "key": "PMC6057880"}], "notes": [], "created": "2018-10-31T19:46:19.734Z", "modified": "2024-01-16T13:48:45.956Z"}, {"entity": "publication", "iuid": "2d012c44ab834d82b426eccca30dbead", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d012c44ab834d82b426eccca30dbead.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d012c44ab834d82b426eccca30dbead"}}, "title": "Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Li", "given": "Lingni", "initials": "L"}, {"family": "Fridlund", "given": "Jimmy", "initials": "J"}, {"family": "Svensson", "given": "Fredrik", "initials": "F"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2018-07-17", "journal": {"volume": null, "issn": "1432-184X", "issue": null, "title": "Microb. Ecol.", "issn-l": "0095-3628"}, "abstract": "Two annual Baltic Sea phytoplankton blooms occur in spring and summer. The bloom intensity is determined by nutrient concentrations in the water, while the period depends on weather conditions. During the course of the bloom, dead cells sink to the sediment where their degradation consumes oxygen to create hypoxic zones (<\u20092\u00a0mg/L dissolved oxygen). These zones prevent the establishment of benthic communities and may result in fish mortality. The aim of the study was to determine how the spring and autumn sediment chemistry and microbial community composition changed due to degradation of diatom or cyanobacterial biomass, respectively. Results from incubation of sediment cores showed some typical anaerobic microbial processes after biomass addition such as a decrease in NO", "doi": "10.1007/s00248-018-1229-6", "pmid": "30019110", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00248-018-1229-6"}, {"db": "BioProject", "description": "Sediment surface microbial community changes due to phytoplankton addition", "key": "PRJNA323408"}], "notes": [], "created": "2018-10-31T19:47:11.562Z", "modified": "2024-01-16T13:48:45.978Z"}, {"entity": "publication", "iuid": "c5ac8923292c4f80b7f141382febd809", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5ac8923292c4f80b7f141382febd809.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5ac8923292c4f80b7f141382febd809"}}, "title": "Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.", "authors": [{"family": "Sork", "given": "Helena", "initials": "H", "orcid": "0000-0002-5390-4420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5d08dad4f2d4ee0a3e3a8f060383da5.json"}}, {"family": "Corso", "given": "Giulia", "initials": "G"}, {"family": "Krjutskov", "given": "Kaarel", "initials": "K"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Nordin", "given": "Joel Z", "initials": "JZ"}, {"family": "Wiklander", "given": "Oscar P B", "initials": "OPB"}, {"family": "Lee", "given": "Yi Xin Fiona", "initials": "YXF", "orcid": "0000-0002-9092-1932", "researcher": {"href": "https://publications.scilifelab.se/researcher/619d8471b5704b45bc8a35ee560b47f7.json"}}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO", "orcid": "0000-0002-6849-6220", "researcher": {"href": "https://publications.scilifelab.se/researcher/161d8b5fb6734b33ad5f5590edbc0cff.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Wood", "given": "Matthew J A", "initials": "MJA"}, {"family": "M\u00e4ger", "given": "Imre", "initials": "I"}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}], "type": "journal article", "published": "2018-07-17", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "10813", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Extracellular vesicles (EVs) mediate cell-to-cell communication by delivering or displaying macromolecules to their recipient cells. While certain broad-spectrum EV effects reflect their protein cargo composition, others have been attributed to individual EV-loaded molecules such as specific miRNAs. In this work, we have investigated the contents of vesicular cargo using small RNA sequencing of cells and EVs from HEK293T, RD4, C2C12, Neuro2a and C17.2. The majority of RNA content in EVs (49-96%) corresponded to rRNA-, coding- and tRNA fragments, corroborating with our proteomic analysis of HEK293T and C2C12 EVs which showed an enrichment of ribosome and translation-related proteins. On the other hand, the overall proportion of vesicular small RNA was relatively low and variable (2-39%) and mostly comprised of miRNAs and sequences mapping to piRNA loci. Importantly, this is one of the few studies, which systematically links vesicular RNA and protein cargo of vesicles. Our data is particularly useful for future work in unravelling the biological mechanisms underlying vesicular RNA and protein sorting and serves as an important guide in developing EVs as carriers for RNA therapeutics.", "doi": "10.1038/s41598-018-28485-9", "pmid": "30018314", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Global Proteomics and Proteogenomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-28485-9"}, {"db": "pmc", "key": "PMC6050237"}], "notes": [], "created": "2018-08-07T08:38:11.195Z", "modified": "2024-01-16T13:48:45.984Z"}, {"entity": "publication", "iuid": "4b83b941d3284963af77d60a44ece54d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b83b941d3284963af77d60a44ece54d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b83b941d3284963af77d60a44ece54d"}}, "title": "SECAPR\u2014a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments", "authors": [{"family": "Andermann", "given": "Tobias", "initials": "T"}, {"family": "Cano", "given": "\u00c1ngela", "initials": "\u00c1"}, {"family": "Zizka", "given": "Alexander", "initials": "A"}, {"family": "Bacon", "given": "Christine", "initials": "C"}, {"family": "Antonelli", "given": "Alexandre", "initials": "A"}], "type": "journal-article", "published": "2018-07-13", "journal": {"volume": "6", "issn": "2167-8359", "issue": null, "pages": "e5175", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": null, "doi": "10.7717/peerj.5175", "pmid": "30023140", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP131660", "key": "SRP131660"}, {"db": "Zenodo", "description": "https://zenodo.org/record/1162653#.W-wxin4h1p8", "key": "10.5281/zenodo.1162653"}], "notes": [], "created": "2018-10-31T19:53:14.255Z", "modified": "2024-01-16T13:48:45.991Z"}, {"entity": "publication", "iuid": "a439b71bb4354049aea7a38ea1251988", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a439b71bb4354049aea7a38ea1251988.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a439b71bb4354049aea7a38ea1251988"}}, "title": "EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.", "authors": [{"family": "Jeggari", "given": "Ashwini", "initials": "A"}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z"}, {"family": "Petrov", "given": "Iurii", "initials": "I"}, {"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "Ericson", "given": "Johan", "initials": "J"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}], "type": "journal article", "published": "2018-07-02", "journal": {"volume": "46", "issn": "1362-4962", "issue": "W1", "pages": "W163-W170", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The new web resource EviNet provides an easily run interface to network enrichment analysis for exploration of novel, experimentally defined gene sets. The major advantages of this analysis are (i) applicability to any genes found in the global network rather than only to those with pathway/ontology term annotations, (ii) ability to connect genes via different molecular mechanisms rather than within one high-throughput platform, and (iii) statistical power sufficient to detect enrichment of very small sets, down to individual genes. The users' gene sets are either defined prior to upload or derived interactively from an uploaded file by differential expression criteria. The pathways and networks used in the analysis can be chosen from the collection menu. The calculation is typically done within seconds or minutes and the stable URL is provided immediately. The results are presented in both visual (network graphs) and tabular formats using jQuery libraries. Uploaded data and analysis results are kept in separated project directories not accessible by other users. EviNet is available at https://www.evinet.org/.", "doi": "10.1093/nar/gky485", "pmid": "29893885", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5035166"}, {"db": "pmc", "key": "PMC6030852"}, {"db": "GEO", "description": "Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d0-d3.5]", "key": "GSE112698"}], "notes": [], "created": "2018-10-31T19:46:00.551Z", "modified": "2024-01-16T13:48:46.013Z"}, {"entity": "publication", "iuid": "30254f53a35b4096a4bc05bfa00bcbeb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30254f53a35b4096a4bc05bfa00bcbeb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30254f53a35b4096a4bc05bfa00bcbeb"}}, "title": "Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.", "authors": [{"family": "Westerholm", "given": "Maria", "initials": "M"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Singh", "given": "Abhijeet", "initials": "A"}, {"family": "Karlsson Lindsj\u00f6", "given": "Oskar", "initials": "O"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2018-07-00", "journal": {"volume": "11", "issn": "1751-7915", "issue": "4", "pages": "680-693", "title": "Microb Biotechnol", "issn-l": "1751-7915"}, "abstract": "To enrich syntrophic acetate-oxidizing bacteria (SAOB), duplicate chemostats were inoculated with sludge from syntrophic acetate oxidation (SAO)-dominated systems and continuously supplied with acetate (0.4 or 7.5\u00a0g\u00a0l", "doi": "10.1111/1751-7915.13035", "pmid": "29239113", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6011928"}, {"db": "GENBANK", "key": "KJ701175"}, {"db": "GENBANK", "key": "MG356789"}, {"db": "GENBANK", "key": "MG356790"}, {"db": "GENBANK", "key": "MG012806"}, {"db": "GENBANK", "key": "MG012840"}, {"db": "GENBANK", "key": "MG385064"}, {"db": "GENBANK", "key": "MG385074"}], "notes": [], "created": "2018-10-31T19:48:31.526Z", "modified": "2020-01-21T13:56:10.989Z"}, {"entity": "publication", "iuid": "ae5e7844daac458eab752c808de67349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae5e7844daac458eab752c808de67349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae5e7844daac458eab752c808de67349"}}, "title": "CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response.", "authors": [{"family": "Haapaniemi", "given": "Emma", "initials": "E"}, {"family": "Botla", "given": "Sandeep", "initials": "S"}, {"family": "Persson", "given": "Jenna", "initials": "J", "orcid": "0000-0002-0208-8080", "researcher": {"href": "https://publications.scilifelab.se/researcher/395e4bc2719b44aeadd51137ee85631a.json"}}, {"family": "Schmierer", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9082-7022", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ee96f9eb454850be6db3318b28479f.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2018-07-00", "journal": {"volume": "24", "issn": "1546-170X", "issue": "7", "pages": "927-930", "title": "Nat. Med.", "issn-l": "1078-8956"}, "abstract": "Here, we report that genome editing by CRISPR-Cas9 induces a p53-mediated DNA damage response and cell cycle arrest in immortalized human retinal pigment epithelial cells, leading to a selection against cells with a functional p53 pathway. Inhibition of p53 prevents the damage response and increases the rate of homologous recombination from a donor template. These results suggest that p53 inhibition may improve the efficiency of genome editing of untransformed cells and that p53 function should be monitored when developing cell-based therapies utilizing CRISPR-Cas9.", "doi": "10.1038/s41591-018-0049-z", "pmid": "29892067", "labels": {"Protein Science Facility (PSF)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "CRISPR Functional Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41591-018-0049-z"}], "notes": [], "created": "2018-06-20T14:33:07.211Z", "modified": "2021-07-06T14:41:17.286Z"}, {"entity": "publication", "iuid": "12c76ece8d6343d1beeb7137840accd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12c76ece8d6343d1beeb7137840accd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12c76ece8d6343d1beeb7137840accd9"}}, "title": "Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity", "authors": [{"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Friedrich", "given": "Stefanie", "initials": "S"}, {"family": "Marklund", "given": "Maja", "initials": "M"}, {"family": "Bergenstr\u00e5hle", "given": "Joseph", "initials": "J"}, {"family": "Tarish", "given": "Firas", "initials": "F"}, {"family": "Tanoglidi", "given": "Anna", "initials": "A"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Salme\u0301n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Ogris", "given": "Christoph", "initials": "C"}, {"family": "Wallenborg", "given": "Karolina", "initials": "K"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "St\u00e5hl", "given": "Patrik", "initials": "P"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal-article", "published": "2018-06-20", "journal": {"volume": "9", "issn": "2041-1723", "issue": "1", "pages": "2419", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.", "doi": "10.1038/s41467-018-04724-5", "pmid": "29925878", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6010471"}, {"db": "pii", "key": "10.1038/s41467-018-04724-5"}], "notes": [], "created": "2018-10-31T19:44:55.262Z", "modified": "2024-01-16T13:48:46.097Z"}, {"entity": "publication", "iuid": "0e1b3f3ba66e44708551ca9d3cbaf781", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e1b3f3ba66e44708551ca9d3cbaf781.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e1b3f3ba66e44708551ca9d3cbaf781"}}, "title": "Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.", "authors": [{"family": "Lundmark", "given": "Anna", "initials": "A", "orcid": "0000-0002-3655-3710", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c320c868d5d4eb09bed08fa3836f7e8.json"}}, {"family": "Gerasimcik", "given": "Natalija", "initials": "N"}, {"family": "B\u00e5ge", "given": "Tove", "initials": "T"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2018-06-19", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "9370", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Periodontitis is a highly prevalent chronic inflammatory disease of the periodontium, leading ultimately to tooth loss. In order to characterize the gene expression of periodontitis-affected gingival tissue, we have here simultaneously quantified and localized gene expression in periodontal tissue using spatial transcriptomics, combining RNA sequencing with histological analysis. Our analyses revealed distinct clusters of gene expression, which were identified to correspond to epithelium, inflamed areas of connective tissue, and non-inflamed areas of connective tissue. Moreover, 92 genes were identified as significantly up-regulated in inflamed areas of the gingival connective tissue compared to non-inflamed tissue. Among these, immunoglobulin lambda-like polypeptide 5 (IGLL5), signal sequence receptor subunit 4 (SSR4), marginal zone B and B1 cell specific protein (MZB1), and X-box binding protein 1 (XBP1) were the four most highly up-regulated genes. These genes were also verified as significantly higher expressed in gingival tissue of patients with periodontitis compared to healthy controls, using reverse transcription quantitative polymerase chain reaction. Moreover, the protein expressions of up-regulated genes were verified in gingival biopsies by immunohistochemistry. In summary, in this study, we report distinct gene expression signatures within periodontitis-affected gingival tissue, as well as specific genes that are up-regulated in inflamed areas compared to non-inflamed areas of gingival tissue. The results obtained from this study may add novel information on the genes and cell types contributing to pathogenesis of the chronic inflammatory disease periodontitis.", "doi": "10.1038/s41598-018-27627-3", "pmid": "29921943", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-27627-3"}, {"db": "pmc", "key": "PMC6008462"}], "notes": [], "created": "2018-10-31T19:44:55.950Z", "modified": "2024-01-16T13:48:46.104Z"}, {"entity": "publication", "iuid": "768c0a397b7f434a8c5c02c6d5cfaeb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/768c0a397b7f434a8c5c02c6d5cfaeb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/768c0a397b7f434a8c5c02c6d5cfaeb4"}}, "title": "Investigating Holocene human population history in North Asia using ancient mitogenomes.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "S\u00fcmer", "given": "Arev Pelin", "initials": "AP"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Shergin", "given": "Dmitrij", "initials": "D"}, {"family": "Ivanov", "given": "Grigorij Leonidovich", "initials": "GL"}, {"family": "Kichigin", "given": "Dmitrii", "initials": "D"}, {"family": "Pestereva", "given": "Kjunnej", "initials": "K"}, {"family": "Volkov", "given": "Denis", "initials": "D"}, {"family": "Mandryka", "given": "Pavel", "initials": "P"}, {"family": "Kharinskii", "given": "Artur", "initials": "A"}, {"family": "Tishkin", "given": "Alexey", "initials": "A"}, {"family": "Ineshin", "given": "Evgenij", "initials": "E"}, {"family": "Kovychev", "given": "Evgeniy", "initials": "E"}, {"family": "Stepanov", "given": "Aleksandr", "initials": "A"}, {"family": "Alekseev", "given": "Aanatolij", "initials": "A"}, {"family": "Fedoseeva", "given": "Svetlana Aleksandrovna", "initials": "SA"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-06-12", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8969", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.", "doi": "10.1038/s41598-018-27325-0", "pmid": "29895902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-27325-0"}, {"db": "pmc", "key": "PMC5997703"}], "notes": [], "created": "2018-10-31T19:48:02.044Z", "modified": "2024-01-16T13:48:46.130Z"}, {"entity": "publication", "iuid": "b5e4c3ebecf6493fa7dcfa4e9bc61c14", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5e4c3ebecf6493fa7dcfa4e9bc61c14.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5e4c3ebecf6493fa7dcfa4e9bc61c14"}}, "title": "Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.", "authors": [{"family": "H\u00e4ring", "given": "Martin", "initials": "M"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Hochgerner", "given": "Hannah", "initials": "H"}, {"family": "Rinwa", "given": "Puneet", "initials": "P"}, {"family": "Jakobsson", "given": "Jon E T", "initials": "JET"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Sharma", "given": "Nilesh", "initials": "N"}, {"family": "Borgius", "given": "Lotta", "initials": "L"}, {"family": "Kiehn", "given": "Ole", "initials": "O"}, {"family": "Lagerstr\u00f6m", "given": "Malin C", "initials": "MC"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}], "type": "journal article", "published": "2018-06-00", "journal": {"volume": "21", "issn": "1546-1726", "issue": "6", "pages": "869-880", "title": "Nat. Neurosci.", "issn-l": "1097-6256"}, "abstract": "The dorsal horn of the spinal cord is critical to processing distinct modalities of noxious and innocuous sensation, but little is known of the neuronal subtypes involved, hampering efforts to deduce principles governing somatic sensation. Here we used single-cell RNA sequencing to classify sensory neurons in the mouse dorsal horn. We identified 15 inhibitory and 15 excitatory molecular subtypes of neurons, equaling the complexity in cerebral cortex. Validating our classification scheme in vivo and matching cell types to anatomy of the dorsal horn by spatial transcriptomics reveals laminar enrichment for each of the cell types. Neuron types, when combined, define a multilayered organization with like neurons layered together. Employing our scheme, we find that heat and cold stimuli activate discrete sets of both excitatory and inhibitory neuron types. This work provides a systematic and comprehensive molecular classification of spinal cord sensory neurons, enabling functional interrogation of sensory processing.", "doi": "10.1038/s41593-018-0141-1", "pmid": "29686262", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-018-0141-1"}], "notes": [], "created": "2018-10-31T19:46:19.015Z", "modified": "2024-01-16T13:48:46.184Z"}, {"entity": "publication", "iuid": "952c936b5ab4478c9b58bb9e9749446f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/952c936b5ab4478c9b58bb9e9749446f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/952c936b5ab4478c9b58bb9e9749446f"}}, "title": "Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).", "authors": [{"family": "Bl\u00e5hed", "given": "Ida-Maria", "initials": "IM"}, {"family": "K\u00f6nigsson", "given": "Helena", "initials": "H"}, {"family": "Ericsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Spong", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2018-05-30", "journal": {"volume": "13", "issn": "1932-6203", "issue": "5", "pages": "e0197364", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Monitoring of wild animal populations is challenging, yet reliable information about population processes is important for both management and conservation efforts. Access to molecular markers, such as SNPs, enables population monitoring through genotyping of various DNA sources. We have developed 96 high quality SNP markers for individual identification of moose (Alces alces), an economically and ecologically important top-herbivore in boreal regions. Reduced representation libraries constructed from 34 moose were high-throughput de novo sequenced, generating nearly 50 million read pairs. About 50 000 stacks of aligned reads containing one or more SNPs were discovered with the Stacks pipeline. Several quality criteria were applied on the candidate SNPs to find markers informative on the individual level and well representative for the population. An empirical validation by genotyping of sequenced individuals and additional moose, resulted in the selection of a final panel of 86 high quality autosomal SNPs. Additionally, five sex-specific SNPs and five SNPs for sympatric species diagnostics are included in the panel. The genotyping error rate was 0.002 for the total panel and probability of identities were low enough to separate individuals with high confidence. Moreover, the autosomal SNPs were highly informative also for population level analyses. The potential applications of this SNP panel are thus many including investigations of population size, sex ratios, relatedness, reproductive success and population structure. Ideally, SNP-based studies could improve today's population monitoring and increase our knowledge about moose population dynamics.", "doi": "10.1371/journal.pone.0197364", "pmid": "29847564", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-39125"}, {"db": "pmc", "key": "PMC5976195"}, {"db": "Zenodo", "description": "SNPs for population monitoring of moose (Alces alces)", "key": "https://doi.org/10.5281/zenodo.1237474"}], "notes": [], "created": "2018-10-31T19:44:59.410Z", "modified": "2024-01-16T13:48:46.266Z"}, {"entity": "publication", "iuid": "f9a8fbd98d754cffa1879583683d108c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9a8fbd98d754cffa1879583683d108c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9a8fbd98d754cffa1879583683d108c"}}, "title": "SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.", "authors": [{"family": "Jord\u00e1n-Pla", "given": "Antonio", "initials": "A"}, {"family": "Yu", "given": "Simei", "initials": "S"}, {"family": "Waldholm", "given": "Johan", "initials": "J"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK"}, {"family": "Visa", "given": "Neus", "initials": "N"}], "type": "journal article", "published": "2018-05-18", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "367", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes.\n\nHere we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in S2 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SWI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes.\n\nThis study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SWI/SNF through ATPase-dependent and ATPase-independent mechanisms have specialized roles in different cellular and developmental processes.", "doi": "10.1186/s12864-018-4746-2", "pmid": "29776334", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-018-4746-2"}, {"db": "pmc", "key": "PMC5960078"}, {"db": "GEO", "description": "The distribution of Brahma in the genome of Drosophila melanogaster S2 cells and the roles of Brahma in transcription and pre-mRNA processin", "key": "GSE95236"}], "notes": [], "created": "2018-10-31T19:46:23.156Z", "modified": "2024-01-16T13:48:46.291Z"}, {"entity": "publication", "iuid": "6d67c0449e5843b2a82f8e00b62832e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d67c0449e5843b2a82f8e00b62832e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d67c0449e5843b2a82f8e00b62832e5"}}, "title": "Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.", "authors": [{"family": "Jaff", "given": "Nasren", "initials": "N"}, {"family": "Grankvist", "given": "Rikard", "initials": "R"}, {"family": "Muhl", "given": "Lars", "initials": "L"}, {"family": "Chireh", "given": "Arvin", "initials": "A"}, {"family": "Sandell", "given": "Mikael", "initials": "M"}, {"family": "Jonsson", "given": "Stefan", "initials": "S"}, {"family": "Arnberg", "given": "Fabian", "initials": "F"}, {"family": "Eriksson", "given": "Ulf", "initials": "U"}, {"family": "Holmin", "given": "Staffan", "initials": "S"}], "type": "journal article", "published": "2018-05-14", "journal": {"volume": null, "issn": "1432-1920", "issue": null, "title": "Neuroradiology", "issn-l": "0028-3940"}, "abstract": "In mechanical thrombectomy (MT) for ischemic stroke, endothelial cells (ECs) from intracranial blood vessels adhere to the stent retriever device and can be harvested. However, understanding the molecular biology and the role of the endothelium in different pathological conditions remains insufficient. The purpose of the study was to characterize and analyze the molecular aspect of harvested ECs using cell culture and transcriptomic techniques in an MT swine model relevant to clinical ischemic stroke.\n\nIn swine, preformed thrombi were injected into the external carotid and subclavian arteries to occlude their branches. MT was performed according to clinical routine. The stent retriever device and thrombus were treated with cell dissociation buffer. The resulting cell suspension was analyzed by immunohistochemistry and was cultured. Cultured cells were analyzed using single-cell RNA sequencing (scRNA-seq) after fluorescence-activated cell sorting (FACS).\n\nA total number of 37 samples were obtained containing CD31-positive cells. Cell culture was successful in 90% of samples, and the cells expressed multiple typical EC protein markers. Eighty-nine percent of the sorted cells yielded high-quality transcriptomes, and single-cell transcriptomes from cultured cells showed that they expressed typical endothelial gene patterns. Gene expression analysis of ECs from an occluded artery did not show distinctive clustering into subtypes.\n\nECs harvested during MT can be cultured and analyzed using single-cell transcriptomic techniques. This analysis can be implemented in clinical practice to study the EC gene expression of comorbidities, such as hypertension, diabetes mellitus, and metabolic syndrome, in patients suffering from acute ischemic stroke.", "doi": "10.1007/s00234-018-2033-1", "pmid": "29761220", "labels": {"Eukaryotic Single Cell Genomics (ESCG)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00234-018-2033-1"}, {"db": "pmc", "key": "PMC5995995"}], "notes": [], "created": "2018-10-31T19:48:34.971Z", "modified": "2024-01-16T13:48:46.308Z"}, {"entity": "publication", "iuid": "b0b81e150aa848f1bc76a3ffd4185fdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0b81e150aa848f1bc76a3ffd4185fdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0b81e150aa848f1bc76a3ffd4185fdf"}}, "title": "Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.", "authors": [{"family": "Parris", "given": "Toshima Z", "initials": "TZ"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Engqvist", "given": "Hanna", "initials": "H"}, {"family": "Biermann", "given": "Jana", "initials": "J"}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K"}, {"family": "Nemes", "given": "Szil\u00e1rd", "initials": "S"}, {"family": "Forssell-Aronsson", "given": "Eva", "initials": "E"}, {"family": "Solinas", "given": "Giovanni", "initials": "G"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2018-05-08", "journal": {"volume": "9", "issn": "1949-2553", "issue": "35", "pages": "24140-24154", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Genomic instability contributes to the neoplastic phenotype by deregulating key cancer-related genes, which in turn can have a detrimental effect on patient outcome. DNA amplification of the 8p11-p12 genomic region has clinical and biological implications in multiple malignancies, including breast carcinoma where the amplicon has been associated with tumor progression and poor prognosis. However, oncogenes driving increased cancer-related death and recurrent genetic features associated with the 8p11-p12 amplicon remain to be identified. In this study, DNA copy number and transcriptome profiling data for 229 primary invasive breast carcinomas (corresponding to 185 patients) were evaluated in conjunction with clinicopathological features to identify putative oncogenes in 8p11-p12 amplified samples. Illumina paired-end whole transcriptome sequencing and whole-genome SNP genotyping were subsequently performed on 23 samples showing high-level regional 8p11-p12 amplification to characterize recurrent genetic variants (SNPs and indels), expressed gene fusions, gene expression profiles and allelic imbalances. We now show previously undescribed chromothripsis-like patterns spanning the 8p11-p12 genomic region and allele-specific DNA amplification events. In addition, recurrent amplification-specific genetic features were identified, including genetic variants in the HIST1H1E and UQCRHL genes and fusion transcripts containing MALAT1 non-coding RNA, which is known to be a prognostic indicator for breast cancer and stimulated by estrogen. In summary, these findings highlight novel candidate targets for improved treatment of 8p11-p12 amplified breast carcinomas.", "doi": "10.18632/oncotarget.25329", "pmid": "29844878", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "25329"}, {"db": "pmc", "key": "PMC5963621"}], "notes": [], "created": "2018-10-31T19:48:00.521Z", "modified": "2024-01-16T13:48:46.330Z"}, {"entity": "publication", "iuid": "a344bd74d02542a7bc490b8a4cbc1206", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a344bd74d02542a7bc490b8a4cbc1206.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a344bd74d02542a7bc490b8a4cbc1206"}}, "title": "O6-methylguanine\u2013induced transcriptional mutagenesis reduces p53 tumor-suppressor function", "authors": [{"family": "Ezerskyte", "given": "Monika", "initials": "M"}, {"family": "Paredes", "given": "Jo\u00e3o A", "initials": "JA"}, {"family": "Malvezzi", "given": "Stefano", "initials": "S"}, {"family": "Burns", "given": "John A", "initials": "JA"}, {"family": "Margison", "given": "Geoffrey P", "initials": "GP"}, {"family": "Olsson", "given": "Magnus", "initials": "M"}, {"family": "Scicchitano", "given": "David A", "initials": "DA"}, {"family": "Dreij", "given": "Kristian", "initials": "K"}], "type": "journal article", "published": "2018-05-01", "journal": {"volume": "115", "issn": "1091-6490", "issue": "18", "pages": "4731-4736", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Altered protein function due to mutagenesis plays an important role in disease development. This is perhaps most evident in tumorigenesis and the associated loss or gain of function of tumor-suppressor genes and oncogenes. The extent to which lesion-induced transcriptional mutagenesis (TM) influences protein function and its contribution to the development of disease is not well understood. In this study, the impact of O6-methylguanine on the transcription fidelity of p53 and the subsequent effects on the protein\u2019s function as a regulator of cell death and cell-cycle arrest were examined in human cells. Levels of TM were determined by RNA-sequencing. In cells with active DNA repair, misincorporation of uridine opposite the lesion occurred in 0.14% of the transcripts and increased to 14.7% when repair by alkylguanine\u2013DNA alkyltransferase was compromised. Expression of the dominant-negative p53 R248W mutant due to TM significantly reduced the transactivation of several established p53 target genes that mediate the tumor-suppressor function, including CDKN1A (p21) and BBC3 (PUMA). This resulted in deregulated signaling through the retinoblastoma protein and loss of G1/S cell-cycle checkpoint function. In addition, we observed impaired activation of apoptosis coupled to the reduction of the tumor-suppressor functions of p53. Taking these findings together, this work provides evidence that TM can induce phenotypic changes in mammalian cells that have important implications for the role of TM in tumorigenesis.", "doi": "10.1073/pnas.1721764115", "pmid": "29666243", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "1721764115"}], "notes": [], "created": "2018-04-20T07:29:36.693Z", "modified": "2024-01-16T13:48:46.353Z"}, {"entity": "publication", "iuid": "7d9c18c050494beda6356c70a748d7d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d9c18c050494beda6356c70a748d7d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d9c18c050494beda6356c70a748d7d6"}}, "title": "Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.", "authors": [{"family": "Westbury", "given": "Michael V", "initials": "MV"}, {"family": "Hartmann", "given": "Stefanie", "initials": "S"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Wiesel", "given": "Ingrid", "initials": "I"}, {"family": "Leo", "given": "Viyanna", "initials": "V"}, {"family": "Welch", "given": "Rebecca", "initials": "R"}, {"family": "Parker", "given": "Daniel M", "initials": "DM"}, {"family": "Sicks", "given": "Florian", "initials": "F"}, {"family": "Ludwig", "given": "Arne", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2018-05-01", "journal": {"volume": "35", "issn": "1537-1719", "issue": "5", "pages": "1225-1237", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started \u223c1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.", "doi": "10.1093/molbev/msy037", "pmid": "29528428", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "4924857"}, {"db": "pmc", "key": "PMC5913678"}], "notes": [], "created": "2018-10-31T19:46:53.968Z", "modified": "2021-07-07T20:31:10.844Z"}, {"entity": "publication", "iuid": "928af491ca2748b486065f9afcf6164e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/928af491ca2748b486065f9afcf6164e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/928af491ca2748b486065f9afcf6164e"}}, "title": "Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-\u03b2 signaling", "authors": [{"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fe4902c355449e4812008d4ad7a37e0.json"}}, {"family": "Pieber", "given": "Melanie", "initials": "M", "orcid": "0000-0002-4522-2489", "researcher": {"href": "https://publications.scilifelab.se/researcher/054b79afd3ec48d9adfb723b9ca0d3ae.json"}}, {"family": "Parsa", "given": "Roham", "initials": "R", "orcid": "0000-0002-0864-6098", "researcher": {"href": "https://publications.scilifelab.se/researcher/034a292f99404db0886159fdb225bfd6.json"}}, {"family": "Grommisch", "given": "David", "initials": "D", "orcid": "0000-0002-2666-1419", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba4e40cb43e64713b48caa02a0941d1a.json"}}, {"family": "Ewing", "given": "Ewoud", "initials": "E", "orcid": "0000-0001-8644-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/aea9350a4f864d8e8781ab111b4f9273.json"}}, {"family": "Kular", "given": "Lara", "initials": "L"}, {"family": "Han", "given": "Jinming", "initials": "J", "orcid": "0000-0002-6084-3275", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0f73f656d114874bcfd64efd97883cb.json"}}, {"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b85d1ae8136464788be19d62a8863d7.json"}}, {"family": "Nijssen", "given": "Jik", "initials": "J"}, {"family": "Hedlund", "given": "Eva", "initials": "E", "orcid": "0000-0001-6347-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/d517e76df2e944e09ddbe87b7e0329af.json"}}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b824181455243b19f4aa145a4545870.json"}}, {"family": "Berglund", "given": "Rasmus", "initials": "R"}, {"family": "Forteza", "given": "Maria J", "initials": "MJ"}, {"family": "Ketelhuth", "given": "Daniel F J", "initials": "DFJ"}, {"family": "Butovsky", "given": "Oleg", "initials": "O"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Zhang", "given": "Xing Mei", "initials": "XM"}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b0733d3c25145139f42cad897d6726b.json"}}], "type": "journal-article", "published": "2018-05-00", "journal": {"volume": "19", "issn": "1529-2908", "issue": "5", "pages": "1-7", "title": "Nat. Immunol.", "issn-l": null}, "abstract": "The cytokine transforming growth factor-\u03b2 (TGF-\u03b2) regulates the development and homeostasis of several tissue-resident macrophage populations, including microglia. TGF-\u03b2 is not critical for microglia survival but is required for the maintenance of the microglia-specific homeostatic gene signature1,2. Under defined host conditions, circulating monocytes can compete for the microglial niche and give rise to long-lived monocyte-derived macrophages residing in the central nervous system (CNS)3-5. Whether monocytes require TGF-\u03b2 for colonization of the microglial niche and maintenance of CNS integrity is unknown. We found that abrogation of TGF-\u03b2 signaling in CX3CR1+ monocyte-derived macrophages led to rapid onset of a progressive and fatal demyelinating motor disease characterized by myelin-laden giant macrophages throughout the spinal cord. Tgfbr2-deficient macrophages were characterized by high expression of genes encoding proteins involved in antigen presentation, inflammation and phagocytosis. TGF-\u03b2 is thus crucial for the functional integration of monocytes into the CNS microenvironment.", "doi": "10.1038/s41590-018-0091-5", "pmid": "29662171", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1586138"}, {"db": "pmc", "key": "PMC7309278"}, {"db": "pii", "key": "10.1038/s41590-018-0091-5"}], "notes": [], "created": "2018-10-31T19:46:22.446Z", "modified": "2024-01-16T13:48:46.428Z"}, {"entity": "publication", "iuid": "946c4387c3ec41da986b55efd91f63fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/946c4387c3ec41da986b55efd91f63fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/946c4387c3ec41da986b55efd91f63fd"}}, "title": "Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen.", "authors": [{"family": "Felten", "given": "Judith", "initials": "J", "orcid": "0000-0002-0444-822X", "researcher": {"href": "https://publications.scilifelab.se/researcher/add6fe81af494256ab942e9eeca979b0.json"}}, {"family": "Vahala", "given": "Jorma", "initials": "J"}, {"family": "Love", "given": "Jonathan", "initials": "J"}, {"family": "Gorzs\u00e1s", "given": "Andr\u00e1s", "initials": "A"}, {"family": "R\u00fcggeberg", "given": "Markus", "initials": "M"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Le\u015bniewska", "given": "Joanna", "initials": "J"}, {"family": "Kangasj\u00e4rvi", "given": "Jaakko", "initials": "J"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Mellerowicz", "given": "Ewa J", "initials": "EJ", "orcid": "0000-0001-6817-1031", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9bf45f4790e4360b19ec021469cfad2.json"}}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2018-05-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "218", "issue": "3", "pages": "999-1014", "issn-l": "0028-646X"}, "abstract": "The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. We report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild-type and ethylene-insensitive hybrid aspen trees (Populus tremula \u00d7 tremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild-type and ethylene-insensitive trees. We demonstrate that ACC and ethylene induce gelatinous layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (Ethylene Response Factors (ERFs), ETHYLENE INSENSITIVE 3/ETHYLENE INSENSITIVE3-LIKE1 (EIN3/EIL1)) and wood formation. G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.", "doi": "10.1111/nph.15078", "pmid": "29528503", "labels": {"Cryo-EM": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2019-01-10T21:37:37.272Z", "modified": "2021-12-06T13:45:20.936Z"}, {"entity": "publication", "iuid": "58825a68ec3c48ff88d9c006248ff996", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58825a68ec3c48ff88d9c006248ff996.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58825a68ec3c48ff88d9c006248ff996"}}, "title": "Full Mitogenomes in the Critically Endangered K\u0101k\u0101p\u014d Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.", "authors": [{"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Robertson", "given": "Bruce C", "initials": "BC", "orcid": "0000-0002-5348-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/765ee347a5f04b29b28a17f14f707231.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2018-04-19", "journal": {"volume": "9", "issn": "2073-4425", "issue": "4", "title": "Genes", "pages": "220", "issn-l": "2073-4425"}, "abstract": "Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered k\u0101k\u0101p\u014d (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of k\u0101k\u0101p\u014d contributed to a rapid loss of genetic diversity following severe population declines.", "doi": "10.3390/genes9040220", "pmid": "29671759", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5924562"}, {"db": "pii", "key": "genes9040220"}], "notes": [], "created": "2018-10-31T19:46:53.308Z", "modified": "2023-06-19T12:48:48.519Z"}, {"entity": "publication", "iuid": "e0e299f2920c45afa3763b218f36089f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0e299f2920c45afa3763b218f36089f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0e299f2920c45afa3763b218f36089f"}}, "title": "Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.", "authors": [{"family": "La Fleur", "given": "Linn\u00e9a", "initials": "L"}, {"family": "Boura", "given": "Vanessa F", "initials": "VF"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Victor", "initials": "V"}, {"family": "Mattsson", "given": "Johanna S M", "initials": "JSM"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Persson", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Karlsson", "given": "Mikael C I", "initials": "MCI"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2018-04-18", "journal": {"volume": null, "issn": "1097-0215", "issue": null, "pages": null, "title": "Int. J. Cancer", "issn-l": "0020-7136"}, "abstract": "Tumor-associated macrophages (TAMs) are attractive targets for immunotherapy. Recently, studies in animal models showed that treatment with an anti-TAM antibody directed against the scavenger receptor MARCO resulted in suppression of tumor growth and metastatic dissemination. Here we investigated the expression of MARCO in relation to other macrophage markers and immune pathways in a non-small cell lung cancer (NSCLC) cohort (n\u2009=\u2009352). MARCO, CD68, CD163, MSR1 and programmed death ligand-1 (PD-L1) were analyzed by immunohistochemistry and immunofluorescence, and associations to other immune cells and regulatory pathways were studied in a subset of cases (n\u2009=\u2009199) with available RNA-seq data. We observed a large variation in macrophage density between cases and a strong correlation between CD68 and CD163, suggesting that the majority of TAMs present in NSCLC exhibit a protumor phenotype. Correlation to clinical data only showed a weak trend toward worse survival for patients with high macrophage infiltration. Interestingly, MARCO was expressed on a distinct subpopulation of TAMs, which tended to aggregate in close proximity to tumor cell nests. On the transcriptomic level, we found a positive association between MARCO gene expression and general immune response pathways including strong links to immunosuppressive TAMs, T-cell infiltration and immune checkpoint molecules. Indeed, a higher macrophage infiltration was seen in tumors expressing PD-L1, and macrophages residing within tumor cell nests co-expressed MARCO and PD-L1. Thus, MARCO is a potential new immune target for anti-TAM treatment in a subset of NSCLC patients, possibly in combination with available immune checkpoint inhibitors.", "doi": "10.1002/ijc.31545", "pmid": "29667169", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2018-10-31T19:47:13.069Z", "modified": "2024-01-16T13:48:46.503Z"}, {"entity": "publication", "iuid": "50e6a1add56143eaafa43557ad8e0879", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50e6a1add56143eaafa43557ad8e0879.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50e6a1add56143eaafa43557ad8e0879"}}, "title": "Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.", "authors": [{"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Sullivan", "given": "Devin", "initials": "D"}, {"family": "Hases", "given": "Linnea", "initials": "L"}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Al-Khalili", "given": "Cristina", "initials": "C"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Williams", "given": "Cecilia", "initials": "C"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2018-04-13", "journal": {"volume": "9", "issn": "1949-2553", "issue": "28", "pages": "19730-19744", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing their surrounding vasculature network. Transformed cancer cells are known to exhibit phenotypic alterations, enabling continuous proliferation despite a limited oxygen supply. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O", "doi": "10.18632/oncotarget.24808", "pmid": "29731978", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "24808"}, {"db": "pmc", "key": "PMC5929421"}, {"db": "GEO", "description": "Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia", "key": "GSE109367"}], "notes": [], "created": "2018-10-31T19:45:26.772Z", "modified": "2024-01-16T13:48:46.535Z"}, {"entity": "publication", "iuid": "68f3101baf804ebb96b6b7ccbc42246e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68f3101baf804ebb96b6b7ccbc42246e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68f3101baf804ebb96b6b7ccbc42246e"}}, "title": "Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.", "authors": [{"family": "Jokipii-Lukkari", "given": "Soile", "initials": "S"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Prestele", "given": "Jakob", "initials": "J"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2018-04-00", "journal": {"volume": "176", "issn": "1532-2548", "issue": "4", "pages": "2851-2870", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": "Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation, and tracheid cell death in woody tissues of Norway spruce (", "doi": "10.1104/pp.17.01590", "pmid": "29487121", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "pp.17.01590"}, {"db": "pmc", "key": "PMC5884607"}], "notes": [], "created": "2018-10-31T19:45:26.083Z", "modified": "2024-01-16T13:48:46.566Z"}, {"entity": "publication", "iuid": "7ebdc6d50af84a17b6832f33022db953", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ebdc6d50af84a17b6832f33022db953.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ebdc6d50af84a17b6832f33022db953"}}, "title": "The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.", "authors": [{"family": "Th\u00f6rnqvist", "given": "Linnea", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2018-04-00", "journal": {"volume": "96", "issn": "1872-9142", "issue": null, "pages": "61-68", "title": "Mol. Immunol.", "issn-l": "0161-5890"}, "abstract": "Inference of antibody gene repertoires using transcriptome data has emerged as an alternative approach to the complex process of sequencing of adaptive immune receptor germline gene loci. The diversity introduced during rearrangement of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes has however been identified as potentially affecting inference specificity. In this study, we have addressed this issue by analysing the nucleotide composition of unmutated human immunoglobulin heavy chains-encoding transcripts, focusing on the 3\u00f6 most bases of 47 IGHV germline genes. Although transcripts derived from some of the germline genes predominately incorporated the germline encoded base even at position 320, the last base of most IGHV genes, transcripts originating in other genes presented other nucleotides to the same extent at this position. In transcripts derived from two of the germline genes, IGHV3-13*01 and IGHV4-30-2*01, the predominating nucleotide (G) was in fact not that of the gene (A). Hence, we suggest that inference of IGHV genes should be limited to bases preceding nucleotide 320, as inference beyond this would jeopardize the specificity of the inference process. The different degree of incorporation of the final base of the IGHV gene directly influences the distribution of amino acids of the ascending strand of the third complementarity determining region of the heavy chain. Thereby it influences the nature of this specificity-determining part of the antibody population. In addition, we also present data that indicate the existence of a common so far un-recognized allelic variant of IGHV3-7 that carries an A318G difference in relation to IGHV3-7*02.", "doi": "10.1016/j.molimm.2018.02.013", "pmid": "29499482", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0161-5890(18)30043-9"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB18926", "key": "PRJEB18926"}], "notes": [], "created": "2018-10-31T19:47:15.710Z", "modified": "2024-01-16T13:48:46.574Z"}, {"entity": "publication", "iuid": "30a4cdde170142558ffc1542e890e661", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30a4cdde170142558ffc1542e890e661.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30a4cdde170142558ffc1542e890e661"}}, "title": "Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.", "authors": [{"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Kerr", "given": "Alastair", "initials": "A"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Hon", "given": "Chung-Chau", "initials": "CC"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Arner", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2018-04-00", "journal": {"volume": "30", "issn": "2352-3964", "issue": null, "pages": "248-260", "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "Long non-coding RNAs (lncRNAs) belong to a recently discovered class of molecules proposed to regulate various cellular processes. Here, we systematically analyzed their expression in human subcutaneous white adipose tissue (WAT) and found that a limited set was differentially expressed in obesity and/or the insulin resistant state. Two lncRNAs herein termed adipocyte-specific metabolic related lncRNAs, ASMER-1 and ASMER-2 were enriched in adipocytes and regulated by both obesity and insulin resistance. Knockdown of either ASMER-1 or ASMER-2 by antisense oligonucleotides in in vitro differentiated human adipocytes revealed that both genes regulated adipogenesis, lipid mobilization and adiponectin secretion. The observed effects could be attributed to crosstalk between ASMERs and genes within the master regulatory pathways for adipocyte function including PPARG and INSR. Altogether, our data demonstrate that lncRNAs are modulators of the metabolic and secretory functions in human fat cells and provide an emerging link between WAT and common metabolic conditions.", "doi": "10.1016/j.ebiom.2018.03.010", "pmid": "29580841", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(18)30094-X"}, {"db": "pmc", "key": "PMC5952343"}], "notes": [], "created": "2018-10-31T19:45:57.783Z", "modified": "2024-01-16T13:48:46.606Z"}, {"entity": "publication", "iuid": "a2eb1c912dac479f8c9ecfd57d465144", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2eb1c912dac479f8c9ecfd57d465144.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2eb1c912dac479f8c9ecfd57d465144"}}, "title": "Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.", "authors": [{"family": "Arkani", "given": "Samara", "initials": "S"}, {"family": "Cao", "given": "Jia", "initials": "J"}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Barker", "given": "Gillian", "initials": "G"}, {"family": "Holmdahl", "given": "Gundela", "initials": "G"}, {"family": "Clementsson Kockum", "given": "Christina", "initials": "C"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2018-03-29", "journal": {"volume": "5", "issn": "2054-345X", "issue": null, "pages": "18009", "title": "Hum Genome Var", "issn-l": "2054-345X"}, "abstract": "Bladder exstrophy is a congenital closure defect of the urinary bladder with a profound effect on morbidity. Although the malformation is usually sporadic, a genetic background is supported by an increased recurrence risk in relatives, higher concordance rates in monozygotic twins and several associated chromosomal aberrations. Recently, the", "doi": "10.1038/hgv.2018.9", "pmid": "29619236", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5874392"}, {"db": "ArrayExpress", "description": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5143/", "key": "E-MTAB-5143"}], "notes": [], "created": "2018-10-31T19:44:57.444Z", "modified": "2024-01-16T13:48:46.642Z"}, {"entity": "publication", "iuid": "4a8a1e43244646b49fbc30a515991b04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a8a1e43244646b49fbc30a515991b04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a8a1e43244646b49fbc30a515991b04"}}, "title": "AMYCNE: Confident copy number assessment using whole genome sequencing data.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Andersson-Assarsson", "given": "Johanna C", "initials": "JC"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "evaluation studies", "published": "2018-03-26", "journal": {"volume": "13", "issn": "1932-6203", "issue": "3", "pages": "e0189710", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Copy number variations (CNVs) within the human genome have been linked to a diversity of inherited diseases and phenotypic traits. The currently used methodology to measure copy numbers has limited resolution and/or precision, especially for regions with more than 4 copies. Whole genome sequencing (WGS) offers an alternative data source to allow for the detection and characterization of the copy number across different genomic regions in a single experiment. A plethora of tools have been developed to utilize WGS data for CNV detection. None of these tools are designed specifically to accurately estimate copy numbers of complex regions in a small cohort or clinical setting. Herein, we present AMYCNE (automatic modeling functionality for copy number estimation), a CNV analysis tool using WGS data. AMYCNE is multifunctional and performs copy number estimation of complex regions, annotation of VCF files, and CNV detection on individual samples. The performance of AMYCNE was evaluated using AMY1A ddPCR measurements from 86 unrelated individuals. In addition, we validated the accuracy of AMYCNE copy number predictions on two additional genes (FCGR3A and FCGR3B) using datasets available through the 1000 genomes consortium. Finally, we simulated levels of mosaic loss and gain of chromosome X and used this dataset for benchmarking AMYCNE. The results show a high concordance between AMYCNE and ddPCR, validating the use of AMYCNE to measure tandem AMY1 repeats with high accuracy. This opens up new possibilities for the use of WGS for accurate copy number determination of other complex regions in the genome in small cohorts or single individuals.", "doi": "10.1371/journal.pone.0189710", "pmid": "29579039", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-18300"}, {"db": "pmc", "key": "PMC5868770"}], "notes": [], "created": "2018-10-31T19:44:58.110Z", "modified": "2024-01-16T13:48:46.682Z"}, {"entity": "publication", "iuid": "9d8c6492c6d34cd3a2e13bf84615f0b4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d8c6492c6d34cd3a2e13bf84615f0b4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d8c6492c6d34cd3a2e13bf84615f0b4"}}, "title": "Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb", "authors": [{"family": "Rasmussen", "given": "Pil U", "initials": "PU"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Blanchet", "given": "F Guillaume", "initials": "FG"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}, {"family": "Tack", "given": "Ayco J M", "initials": "AJM"}], "type": "journal-article", "published": "2018-03-24", "journal": {"volume": null, "issn": "0028-646X", "issue": null, "pages": null, "title": "New Phytol", "issn-l": "0028-646X"}, "abstract": "Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c.\u00a030\u00a0cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.", "doi": "10.1111/nph.15088", "pmid": "29573431", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP132598", "key": "SRP132598"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP132591", "key": "SRP132591"}], "notes": [], "created": "2018-06-25T13:56:23.626Z", "modified": "2024-01-16T13:48:46.698Z"}, {"entity": "publication", "iuid": "f5f88e9b9b0841d8accf11d2ef19650a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5f88e9b9b0841d8accf11d2ef19650a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5f88e9b9b0841d8accf11d2ef19650a"}}, "title": "Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.", "authors": [{"family": "Dias", "given": "David Oliveira", "initials": "DO"}, {"family": "Kim", "given": "Hoseok", "initials": "H"}, {"family": "Holl", "given": "Daniel", "initials": "D"}, {"family": "Werne Solnestam", "given": "Beata", "initials": "B"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Carl\u00e9n", "given": "Marie", "initials": "M"}, {"family": "G\u00f6ritz", "given": "Christian", "initials": "C"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2018-03-22", "journal": {"volume": "173", "issn": "1097-4172", "issue": "1", "pages": "153-165.e22", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "CNS injury often severs axons. Scar tissue that forms locally at the lesion site is thought to block axonal regeneration, resulting in permanent functional deficits. We report that inhibiting the generation of progeny by a subclass of pericytes led to decreased fibrosis and extracellular matrix deposition after spinal cord injury in mice. Regeneration of raphespinal and corticospinal tract axons was enhanced and sensorimotor function recovery improved following spinal cord injury in animals with attenuated pericyte-derived scarring. Using optogenetic stimulation, we demonstrate that regenerated corticospinal tract axons integrated into the local spinal cord circuitry below the lesion site. The number of regenerated axons correlated with improved sensorimotor function recovery. In conclusion, attenuation of pericyte-derived fibrosis represents a promising therapeutic approach to facilitate recovery following CNS injury.", "doi": "10.1016/j.cell.2018.02.004", "pmid": "29502968", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(18)30148-X"}, {"db": "pmc", "key": "PMC5871719"}], "notes": [], "created": "2018-10-31T19:46:01.240Z", "modified": "2024-01-16T13:48:46.716Z"}, {"entity": "publication", "iuid": "adbb3f0858c64bf782b0320bc06f1884", "links": {"self": {"href": "https://publications.scilifelab.se/publication/adbb3f0858c64bf782b0320bc06f1884.json"}, "display": {"href": "https://publications.scilifelab.se/publication/adbb3f0858c64bf782b0320bc06f1884"}}, "title": "Ethylene-Related Gene Expression Networks in Wood Formation.", "authors": [{"family": "Seyfferth", "given": "Carolin", "initials": "C"}, {"family": "Wessels", "given": "Bernard", "initials": "B"}, {"family": "Jokipii-Lukkari", "given": "Soile", "initials": "S"}, {"family": "Sundberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Felten", "given": "Judith", "initials": "J"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2018-03-14", "journal": {"volume": "9", "issn": "1664-462X", "issue": null, "pages": "272", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (", "doi": "10.3389/fpls.2018.00272", "pmid": "29593753", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5861219"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB11181", "key": "ERP012528"}], "notes": [], "created": "2018-10-31T19:45:23.194Z", "modified": "2024-01-16T13:48:46.764Z"}, {"entity": "publication", "iuid": "5005480d5a954e4d95e4f2a549db1442", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5005480d5a954e4d95e4f2a549db1442.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5005480d5a954e4d95e4f2a549db1442"}}, "title": "High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.", "authors": [{"family": "Tran", "given": "Anh Nhi", "initials": "AN"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Ivanov \u00d6fverholm", "given": "Ingegerd", "initials": "I"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "evaluation studies", "published": "2018-03-12", "journal": {"volume": "13", "issn": "1932-6203", "issue": "3", "pages": "e0193928", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The detection of recurrent somatic chromosomal rearrangements is standard of care for most leukemia types. Even though karyotype analysis-a low-resolution genome-wide chromosome analysis-is still the gold standard, it often needs to be complemented with other methods to increase resolution. To evaluate the feasibility and applicability of mate pair whole genome sequencing (MP-WGS) to detect structural chromosomal rearrangements in the diagnostic setting, we sequenced ten bone marrow samples from leukemia patients with recurrent rearrangements. Samples were selected based on cytogenetic and FISH results at leukemia diagnosis to include common rearrangements of prognostic relevance. Using MP-WGS and in-house bioinformatic analysis all sought rearrangements were successfully detected. In addition, unexpected complexity or additional, previously undetected rearrangements was unraveled in three samples. Finally, the MP-WGS analysis pinpointed the location of chromosome junctions at high resolution and we were able to identify the exact exons involved in the resulting fusion genes in all samples and the specific junction at the nucleotide level in half of the samples. The results show that our approach combines the screening character from karyotype analysis with the specificity and resolution of cytogenetic and molecular methods. As a result of the straightforward analysis and high-resolution detection of clinically relevant rearrangements, we conclude that MP-WGS is a feasible method for routine leukemia diagnostics of structural chromosomal rearrangements.", "doi": "10.1371/journal.pone.0193928", "pmid": "29529047", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-38103"}, {"db": "pmc", "key": "PMC5846771"}, {"db": "SRA", "description": "https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP121435", "key": "SRP121435"}], "notes": [], "created": "2018-10-31T19:44:58.756Z", "modified": "2024-01-16T13:48:46.771Z"}, {"entity": "publication", "iuid": "a569320043c3473aa82310813a5d97e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a569320043c3473aa82310813a5d97e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a569320043c3473aa82310813a5d97e3"}}, "title": "Global analysis of A-to-I RNA editing reveals association with common disease variants", "authors": [{"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Sukhavasi", "given": "Katyayani", "initials": "K"}, {"family": "Jain", "given": "Rajeev", "initials": "R"}, {"family": "Jain", "given": "Anamika", "initials": "A"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Giannarelli", "given": "Chiara", "initials": "C"}, {"family": "Kovacic", "given": "Jason C", "initials": "JC"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Skogsberg", "given": "Josefin", "initials": "J"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}], "type": "journal-article", "published": "2018-03-06", "journal": {"volume": "6", "issn": "2167-8359", "issue": null, "pages": "e4466", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "RNA editing modifies transcripts and may alter their regulation or function. In humans, the most common modification is adenosine to inosine (A-to-I). We examined the global characteristics of RNA editing in 4,301 human tissue samples. More than 1.6 million A-to-I edits were identified in 62% of all protein-coding transcripts. mRNA recoding was extremely rare; only 11 novel recoding sites were uncovered. Thirty single nucleotide polymorphisms from genome-wide association studies were associated with RNA editing; one that influences type 2 diabetes (rs2028299) was associated with editing in ", "doi": "10.7717/peerj.4466", "pmid": "29527417", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-10-26T05:48:37.219Z", "modified": "2020-01-21T13:56:10.968Z"}, {"entity": "publication", "iuid": "f4129bf82a9946f3a6dbd7f23437a2d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4129bf82a9946f3a6dbd7f23437a2d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4129bf82a9946f3a6dbd7f23437a2d8"}}, "title": "Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.", "authors": [{"family": "Reza", "given": "Salim H", "initials": "SH"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Ramachandran", "given": "Prashanth", "initials": "P"}, {"family": "Dalman", "given": "Kerstin", "initials": "K"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Minina", "given": "Elena A", "initials": "EA"}, {"family": "Bozhkov", "given": "Peter V", "initials": "PV"}], "type": "journal article", "published": "2018-03-02", "journal": {"volume": "13", "issn": "1932-6203", "issue": "3", "pages": "e0192945", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The terminal differentiation and elimination of the embryo-suspensor is the earliest manifestation of programmed cell death (PCD) during plant ontogenesis. Molecular regulation of suspensor PCD remains poorly understood. Norway spruce (Picea abies) embryos provide a powerful model for studying embryo development because of their large size, sequenced genome, and the possibility to obtain a large number of embryos at a specific developmental stage through somatic embryogenesis. Here, we have carried out global gene expression analysis of the Norway spruce embryo-suspensor versus embryonal mass (a gymnosperm analogue of embryo proper) using RNA sequencing. We have identified that suspensors have enhanced expression of the NAC domain-containing transcription factors, XND1 and ANAC075, previously shown to be involved in the initiation of developmental PCD in Arabidiopsis. The analysis has also revealed enhanced expression of Norway spruce homologues of the known executioners of both developmental and stress-induced cell deaths, such as metacaspase 9 (MC9), cysteine endopeptidase-1 (CEP1) and ribonuclease 3 (RNS3). Interestingly, a spruce homologue of bax inhibitor-1 (PaBI-1, for Picea abies BI-1), an evolutionarily conserved cell death suppressor, was likewise up-regulated in the embryo-suspensor. Since Arabidopsis BI-1 so far has been implicated only in the endoplasmic reticulum (ER)-stress induced cell death, we investigated its role in embryogenesis and suspensor PCD using RNA interference (RNAi). We have found that PaBI-1-deficient lines formed a large number of abnormal embryos with suppressed suspensor elongation and disturbed polarity. Cytochemical staining of suspensor cells has revealed that PaBI-1 deficiency suppresses vacuolar cell death and induces necrotic type of cell death previously shown to compromise embryo development. This study demonstrates that a large number of cell-death components are conserved between angiosperms and gymnosperms and establishes a new role for BI-1 in the progression of vacuolar cell death.", "doi": "10.1371/journal.pone.0192945", "pmid": "29499063", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-39048"}, {"db": "pmc", "key": "PMC5834160"}, {"db": "ENA", "description": "sequences", "key": "PRJEB22154"}], "notes": [], "created": "2018-10-31T19:45:25.282Z", "modified": "2024-01-16T13:48:46.786Z"}, {"entity": "publication", "iuid": "1e9fa1105f644bd08c671f3fc5fccf8f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e9fa1105f644bd08c671f3fc5fccf8f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e9fa1105f644bd08c671f3fc5fccf8f"}}, "title": "Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.", "authors": [{"family": "James", "given": "Tojo", "initials": "T"}, {"family": "Lind\u00e9n", "given": "Magdalena", "initials": "M"}, {"family": "Morikawa", "given": "Hiromasa", "initials": "H"}, {"family": "Fernandes", "given": "Sunjay Jude", "initials": "SJ"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Brandi", "given": "Maya", "initials": "M"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Tegn\u00e9r", "given": "Jesper", "initials": "J"}, {"family": "Khademi", "given": "Mohsen", "initials": "M"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2018-03-01", "journal": {"volume": "27", "issn": "1460-2083", "issue": "5", "pages": "912-928", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Despite advancements in genetic studies, it is difficult to understand and characterize the functional relevance of disease-associated genetic variants, especially in the context of a complex multifactorial disease such as multiple sclerosis (MS). As a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells from MS patients (n\u2009=\u2009145) to identify eQTLs in regions centered on 109 MS risk single nucleotide polymorphisms and 7 associated human leukocyte antigen variants. We identified 77 statistically significant eQTL associations, including pseudogenes and non-coding RNAs. Thirty-eight out of 40 testable eQTL effects were colocalized with the disease association signal. As many eQTLs are tissue specific, we aimed to detail their significance in different cell types. Approximately 70% of the eQTLs were replicated and characterized in at least one major peripheral blood mononuclear cell-derived cell type. Furthermore, 40% of eQTLs were found to be more pronounced in MS patients compared with non-inflammatory neurological diseases patients. In addition, we found two single nucleotide polymorphisms to be significantly associated with the proportions of three different cell types. Mapping to enhancer histone marks and predicted transcription factor binding sites added additional functional evidence for eight eQTL regions. As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. This study provides many novel and validated targets for future functional characterization of MS and other diseases.", "doi": "10.1093/hmg/ddy001", "pmid": "29325110", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4792999"}], "notes": [], "created": "2018-10-31T19:45:24.566Z", "modified": "2024-01-16T13:48:46.800Z"}, {"entity": "publication", "iuid": "7181577c666445399213897f443fc9bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7181577c666445399213897f443fc9bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7181577c666445399213897f443fc9bc"}}, "title": "Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.", "authors": [{"family": "J\u00f8nsson", "given": "Knud Andreas", "initials": "KA"}, {"family": "Blom", "given": "Mozes P K", "initials": "MPK"}, {"family": "P\u00e4ckert", "given": "Martin", "initials": "M"}, {"family": "Ericson", "given": "Per G P", "initials": "PGP"}, {"family": "Irestedt", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2018-03-00", "journal": {"volume": "120", "issn": "1095-9513", "issue": null, "pages": "28-32", "title": "Mol. Phylogenet. Evol.", "issn-l": "1055-7903"}, "abstract": "Molecular studies have revealed a number of cases in which traditional assessments of evolutionary relationships have been incorrect. This has implications not only for systematics and taxonomy but also for our understanding of how diversity patterns on Earth have been formed. Here, we use high-throughput sequencing technology to obtain molecular data from the holotype specimen of the elusive Eutrichomyias rowleyi, which is endemic to the Indonesian island of Sangihe. We show that E. rowleyi unexpectedly is a member of the family Lamproliidae, which dates back some 20 Million years and only include two other species, Lamprolia victoriae from Fiji and Chaetorhynchus papuensis from New Guinea. Tectonic reconstructions suggest that the Melanesian island arc, which included land masses on the northern edge of the Australian plate (present day New Guinea) stretched as a string of islands from the Philippines (including proto-Sangihe) to Fiji from 25 to 20\u202fMy. Consequently, our results are indicative of an ancient distribution along the Melanesian island arc followed by relictualization, which led to members of the Lamproliidae to be distributed on widely separated islands across the Indo-Pacific.", "doi": "10.1016/j.ympev.2017.11.021", "pmid": "29199105", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1055-7903(17)30354-8"}], "notes": [], "created": "2018-10-31T19:47:40.662Z", "modified": "2024-01-16T13:48:46.840Z"}, {"entity": "publication", "iuid": "a57b479d505e4345b6e7544d06510423", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a57b479d505e4345b6e7544d06510423.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a57b479d505e4345b6e7544d06510423"}}, "title": "First de novo whole genome sequencing and assembly of the pink-footed goose.", "authors": [{"family": "Pujolar", "given": "J M", "initials": "JM"}, {"family": "Dal\u00e9n", "given": "L", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Olsen", "given": "R A", "initials": "RA"}, {"family": "Hansen", "given": "M M", "initials": "MM"}, {"family": "Madsen", "given": "J", "initials": "J"}], "type": "journal article", "published": "2018-03-00", "journal": {"volume": "110", "issn": "1089-8646", "issue": "2", "title": "Genomics", "pages": "75-79", "issn-l": "0888-7543"}, "abstract": "Annotated genomes can provide new perspectives on the biology of species. We present the first de novo whole genome sequencing for the pink-footed goose. In order to obtain a high-quality de novo assembly the strategy used was to combine one short insert paired-end library with two mate-pair libraries. The pink-footed goose genome was assembled de novo using three different assemblers and an assembly evaluation was subsequently performed in order to choose the best assembler. For our data, ALLPATHS-LG performed the best, since the assembly produced covers most of the genome, while introducing the fewest errors. A total of 26,134 genes were annotated, with bird species accounting for virtually all BLAST hits. We also estimated the substitution rate in the pink-footed goose, which can be of use in future demographic studies, by using a comparative approach with the genome of the chicken, the mallard and the swan goose. A substitution rate of 1.38\u00d710-7 per nucleotide per generation was obtained when comparing the genomes of the two closely-related goose species (the pink-footed and the swan goose). Altogether, we provide a valuable tool for future genomic studies aiming at particular genes and regions of the pink-footed goose genome as well as other bird species.", "doi": "10.1016/j.ygeno.2017.08.008", "pmid": "28860085", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0888-7543(17)30075-7"}], "notes": [], "created": "2017-11-03T16:21:37.795Z", "modified": "2021-07-07T20:31:10.893Z"}, {"entity": "publication", "iuid": "17f2d493f234469ea9a824378dfb489c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17f2d493f234469ea9a824378dfb489c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17f2d493f234469ea9a824378dfb489c"}}, "title": "A molecular atlas of cell types and zonation in the brain vasculature.", "authors": [{"family": "Vanlandewijck", "given": "Michael", "initials": "M"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "M\u00e4e", "given": "Maarja Andaloussi", "initials": "MA"}, {"family": "Andrae", "given": "Johanna", "initials": "J"}, {"family": "Ando", "given": "Koji", "initials": "K"}, {"family": "Del Gaudio", "given": "Francesca", "initials": "F"}, {"family": "Nahar", "given": "Khayrun", "initials": "K"}, {"family": "Lebouvier", "given": "Thibaud", "initials": "T"}, {"family": "Lavi\u00f1a", "given": "B\u00e0rbara", "initials": "B"}, {"family": "Gouveia", "given": "Leonor", "initials": "L"}, {"family": "Sun", "given": "Ying", "initials": "Y"}, {"family": "Raschperger", "given": "Elisabeth", "initials": "E"}, {"family": "R\u00e4s\u00e4nen", "given": "Markus", "initials": "M"}, {"family": "Zarb", "given": "Yvette", "initials": "Y"}, {"family": "Mochizuki", "given": "Naoki", "initials": "N"}, {"family": "Keller", "given": "Annika", "initials": "A"}, {"family": "Lendahl", "given": "Urban", "initials": "U"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}], "type": "journal article", "published": "2018-02-22", "journal": {"volume": "554", "issn": "1476-4687", "issue": "7693", "pages": "475-480", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Cerebrovascular disease is the third most common cause of death in developed countries, but our understanding of the cells that compose the cerebral vasculature is limited. Here, using vascular single-cell transcriptomics, we provide molecular definitions for the principal types of blood vascular and vessel-associated cells in the adult mouse brain. We uncover the transcriptional basis of the gradual phenotypic change (zonation) along the arteriovenous axis and reveal unexpected cell type differences: a seamless continuum for endothelial cells versus a punctuated continuum for mural cells. We also provide insight into pericyte organotypicity and define a population of perivascular fibroblast-like cells that are present on all vessel types except capillaries. Our work illustrates the power of single-cell transcriptomics to decode the higher organizational principles of a tissue and may provide the initial chapter in a molecular encyclopaedia of the mammalian vasculature.", "doi": "10.1038/nature25739", "pmid": "29443965", "labels": {"National Genomics Infrastructure": "Service", "Eukaryotic Single Cell Genomics (ESCG)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nature25739"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse brain vascular transcriptomes", "key": "GSE98816"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse brain astrocyte transcriptomes", "key": "GSE99058"}, {"db": "GEO", "description": "Single cell RNA-seq of mouse lung vascular transcriptomes", "key": "GSE99235"}], "notes": [], "created": "2018-10-31T13:12:24.088Z", "modified": "2024-01-16T13:48:46.900Z"}, {"entity": "publication", "iuid": "abfca60b81f644029343286d33478c2b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abfca60b81f644029343286d33478c2b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abfca60b81f644029343286d33478c2b"}}, "title": "Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T.", "authors": [{"family": "Christel", "given": "Stephan", "initials": "S", "orcid": "0000-0003-0021-2452", "researcher": {"href": "https://publications.scilifelab.se/researcher/9db0f79d5ee144308ccb724e51959bc8.json"}}, {"family": "Herold", "given": "Malte", "initials": "M", "orcid": "0000-0003-2627-0159", "researcher": {"href": "https://publications.scilifelab.se/researcher/70759c28794141fbb123901947534ec4.json"}}, {"family": "Bellenberg", "given": "S\u00f6ren", "initials": "S"}, {"family": "El Hajjami", "given": "Mohamed", "initials": "M"}, {"family": "Buetti-Dinh", "given": "Antoine", "initials": "A", "orcid": "0000-0002-6469-0296", "researcher": {"href": "https://publications.scilifelab.se/researcher/071a99356d6f4650a6707dc84777a66c.json"}}, {"family": "Pivkin", "given": "Igor V", "initials": "IV"}, {"family": "Sand", "given": "Wolfgang", "initials": "W"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Poetsch", "given": "Ansgar", "initials": "A"}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal article", "published": "2018-02-01", "journal": {"volume": "84", "issn": "1098-5336", "issue": "3", "pages": "e02091-17", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilumT) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilumT to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCELeptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilumT coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilumT for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.", "doi": "10.1128/AEM.02091-17", "pmid": "29150517", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "AEM.02091-17"}, {"db": "pmc", "key": "PMC5772234"}], "notes": [], "created": "2018-01-10T09:45:06.893Z", "modified": "2021-06-21T15:01:28.616Z"}, {"entity": "publication", "iuid": "da4544017fa94bc88722701573cf2617", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da4544017fa94bc88722701573cf2617.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da4544017fa94bc88722701573cf2617"}}, "title": "T cells are influenced by a long non-coding RNA in the autoimmune associated  PTPN2  locus", "authors": [{"family": "Houtman", "given": "Miranda", "initials": "M"}, {"family": "Shchetynsky", "given": "Klementy", "initials": "K"}, {"family": "Chemin", "given": "Karine", "initials": "K"}, {"family": "Hensvold", "given": "Aase Haj", "initials": "AH"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Eloranta", "given": "Maija Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Uebe", "given": "Steffen", "initials": "S"}, {"family": "Catrina", "given": "Anca Irinel", "initials": "AI"}, {"family": "Malmstr\u00f6m", "given": "Vivianne", "initials": "V"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal-article", "published": "2018-02-00", "journal": {"volume": "90", "issn": "0896-8411", "issue": null, "pages": "28-38", "title": "Journal of Autoimmunity", "issn-l": "0896-8411"}, "abstract": "Non-coding SNPs in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) locus have been linked with several autoimmune diseases, including rheumatoid arthritis, type I diabetes, and inflammatory bowel disease. However, the functional consequences of these SNPs are poorly characterized. Herein, we show in blood cells that SNPs in the PTPN2 locus are highly correlated with DNA methylation levels at four CpG sites downstream of PTPN2 and expression levels of the long non-coding RNA (lncRNA) LINC01882 downstream of these CpG sites. We observed that LINC01882 is mainly expressed in T cells and that anti-CD3/CD28 activated na\u00efve CD4", "doi": "10.1016/j.jaut.2018.01.003", "pmid": "29398253", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2018-04-04T11:31:11.341Z", "modified": "2024-01-16T13:48:46.962Z"}, {"entity": "publication", "iuid": "6d6d2546a79e49f9bd07debf8066d5be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6d2546a79e49f9bd07debf8066d5be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6d2546a79e49f9bd07debf8066d5be"}}, "title": "In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.", "authors": [{"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "31", "issn": "1530-0285", "issue": "2", "title": "Mod. Pathol.", "pages": "253-263", "issn-l": "0893-3952"}, "abstract": "Antibodies are important tools in anatomical pathology and research, but the quality of in situ protein detection by immunohistochemistry greatly depends on the choice of antibodies and the abundance of the targeted proteins. Many antibodies used in scientific research do not meet requirements for specificity and sensitivity. Accordingly, methods that improve antibody performance and produce quantitative data can greatly advance both scientific investigations and clinical diagnostics based on protein expression and in situ localization. We demonstrate here protocols for antibody labeling that allow specific protein detection in tissues via bright-field in situ proximity ligation assays, where each protein molecule must be recognized by two antibodies. We further demonstrate that single polyclonal antibodies or purified serum preparations can be used for these dual recognition assays. The requirement for protein recognition by pairs of antibody conjugates can significantly improve specificity of protein detection over single-binder assays.", "doi": "10.1038/modpathol.2017.102", "pmid": "28937142", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "PLA and Single Cell Proteomics": "Technology development", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "modpathol2017102"}], "notes": [], "created": "2017-11-03T07:29:13.291Z", "modified": "2023-04-14T13:56:07.652Z"}, {"entity": "publication", "iuid": "c9af84ed6e2e41d4830e9f77a67c002f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9af84ed6e2e41d4830e9f77a67c002f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9af84ed6e2e41d4830e9f77a67c002f"}}, "title": "Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.", "authors": [{"family": "Leal", "given": "Luis", "initials": "L"}, {"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Dinc\u0103", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "27", "issn": "1365-294X", "issue": "4", "pages": "935-948", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L.\u00a0sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.", "doi": "10.1111/mec.14501", "pmid": "29411442", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "BioProject", "description": "SRA experiments", "key": "PRJEB24745"}, {"db": "ArrayExpress", "description": "RNA-seq data", "key": "E\u2010MTAB\u20106454"}], "notes": [], "created": "2018-10-31T19:46:48.334Z", "modified": "2020-01-21T13:56:17.397Z"}, {"entity": "publication", "iuid": "9439e7c2f56b4cd58c60f2b0e2442fbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9439e7c2f56b4cd58c60f2b0e2442fbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9439e7c2f56b4cd58c60f2b0e2442fbe"}}, "title": "Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.", "authors": [{"family": "Hochgerner", "given": "Hannah", "initials": "H"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "21", "issn": "1546-1726", "issue": "2", "pages": "290-299", "title": "Nat. Neurosci.", "issn-l": "1097-6256"}, "abstract": "The dentate gyrus of the hippocampus is a brain region in which neurogenesis persists into adulthood; however, the relationship between developmental and adult dentate gyrus neurogenesis has not been examined in detail. Here we used single-cell RNA sequencing to reveal the molecular dynamics and diversity of dentate gyrus cell types in perinatal, juvenile, and adult mice. We found distinct quiescent and proliferating progenitor cell types, linked by transient intermediate states to neuroblast stages and fully mature granule cells. We observed shifts in the molecular identity of quiescent and proliferating radial glia and granule cells during the postnatal period that were then maintained through adult stages. In contrast, intermediate progenitor cells, neuroblasts, and immature granule cells were nearly indistinguishable at all ages. These findings demonstrate the fundamental similarity of postnatal and adult neurogenesis in the hippocampus and pinpoint the early postnatal transformation of radial glia from embryonic progenitors to adult quiescent stem cells.", "doi": "10.1038/s41593-017-0056-2", "pmid": "29335606", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41593-017-0056-2"}], "notes": [], "created": "2018-10-31T19:46:21.779Z", "modified": "2024-01-16T13:48:47.020Z"}, {"entity": "publication", "iuid": "10afe8c5b9054810970c6b6a732dd11d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10afe8c5b9054810970c6b6a732dd11d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10afe8c5b9054810970c6b6a732dd11d"}}, "title": "Activating FGFR1 Mutations in Sporadic Pheochromocytomas.", "authors": [{"family": "Welander", "given": "Jenny", "initials": "J"}, {"family": "\u0141ysiak", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Brauckhoff", "given": "Michael", "initials": "M"}, {"family": "Brunaud", "given": "Laurent", "initials": "L"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P", "orcid": "0000-0001-9867-8706", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fc163b9a08421180f7f235af3897f4.json"}}, {"family": "Gimm", "given": "Oliver", "initials": "O"}], "type": "journal article", "published": "2018-02-00", "journal": {"volume": "42", "issn": "1432-2323", "issue": "2", "title": "World J Surg", "pages": "482-489", "issn-l": "0364-2313"}, "abstract": "Pheochromocytomas are neuroendocrine tumors of the adrenal glands. Up to 40% of the cases are caused by germline mutations in one of at least 15 susceptibility genes, making them the human neoplasms with the highest degree of heritability. Recurrent somatic alterations are found in about 50% of the more common sporadic tumors with NF1 being the most common mutated gene (20-25%). In many sporadic tumors, however, a genetic explanation is still lacking.\n\nWe investigated the genomic landscape of sporadic pheochromocytomas with whole-exome sequencing of 16 paired tumor and normal DNA samples and extended confirmation analysis in 2 additional cohorts comprising a total of 80 sporadic pheochromocytomas.\n\nWe discovered on average 33 non-silent somatic variants per tumor. One of the recurrently mutated genes was FGFR1, encoding the fibroblast growth factor receptor 1, which was recently revealed as an oncogene in pediatric brain tumors. Including a subsequent analysis of a larger cohort, activating FGFR1 mutations were detected in three of 80 sporadic pheochromocytomas (3.8%). Gene expression microarray profiling showed that these tumors clustered with NF1-, RET,- and HRAS-mutated pheochromocytomas, indicating activation of the MAPK and PI3K-AKT signal transduction pathways.\n\nBesides RET and HRAS, FGFR1 is only the third protooncogene found to be recurrently mutated in pheochromocytomas. The results advance our biological understanding of pheochromocytoma and suggest that somatic FGFR1 activation is an important event in a subset of sporadic pheochromocytomas.", "doi": "10.1007/s00268-017-4320-0", "pmid": "29159601", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00268-017-4320-0"}, {"db": "pmc", "key": "PMC5762800"}], "notes": [], "created": "2018-01-10T09:45:08.337Z", "modified": "2021-07-06T15:11:23.659Z"}, {"entity": "publication", "iuid": "cddd0536b8af495a92e67d2c2bdedb91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cddd0536b8af495a92e67d2c2bdedb91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cddd0536b8af495a92e67d2c2bdedb91"}}, "title": "Discovering viral genomes in human metagenomic data by predicting unknown protein families.", "authors": [{"family": "Barrientos-Somarribas", "given": "Mauricio", "initials": "M"}, {"family": "Messina", "given": "David N", "initials": "DN"}, {"family": "Pou", "given": "Christian", "initials": "C"}, {"family": "Lysholm", "given": "Fredrik", "initials": "F"}, {"family": "Bjerkner", "given": "Annelie", "initials": "A"}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2018-01-08", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "28", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families. We applied this method to 17 virus-enriched libraries originating from human nasopharyngeal aspirates, serum, feces, and cerebrospinal fluid samples. This resulted in 32 predicted putative novel gene families. Some families showed detectable homology to sequences in metagenomics datasets and protein databases after reannotation. Notably, one predicted family matches an ORF from the highly variable Torque Teno virus (TTV). Furthermore, follow-up from a predicted ORFan resulted in the complete reconstruction of a novel circular genome. Its organisation suggests that it most likely corresponds to a novel bacteriophage in the microviridae family, hence it was named bacteriophage HFM.", "doi": "10.1038/s41598-017-18341-7", "pmid": "29311716", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-18341-7"}, {"db": "pmc", "key": "PMC5758519"}, {"db": "European Nucleotide Archive", "description": "https://www.ebi.ac.uk/ena/data/view/PRJEB17838", "key": "PRJEB17838"}], "notes": [], "created": "2018-10-31T19:44:53.198Z", "modified": "2024-01-16T13:48:47.101Z"}, {"entity": "publication", "iuid": "95528cb576024dc288a66fc3d60df598", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95528cb576024dc288a66fc3d60df598.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95528cb576024dc288a66fc3d60df598"}}, "title": "Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.", "authors": [{"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Tzelepis", "given": "Georgios", "initials": "G"}, {"family": "Bejai", "given": "Sarosh", "initials": "S"}, {"family": "Ilb\u00e4ck", "given": "Jonas", "initials": "J"}, {"family": "Schwelm", "given": "Arne", "initials": "A"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2018-01-03", "journal": {"volume": "19", "issn": "1471-2164", "issue": "1", "pages": "14", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed.\n\nThe draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70\u00a0Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1-1-1 and MAT1-2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species.\n\nThe established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.", "doi": "10.1186/s12864-017-4407-x", "pmid": "29298673", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-4407-x"}, {"db": "pmc", "key": "PMC5753508"}], "notes": [], "created": "2018-10-31T19:45:58.528Z", "modified": "2024-01-16T13:48:47.117Z"}, {"entity": "publication", "iuid": "0ca940c36d6046a58ed5be6686d2d5ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ca940c36d6046a58ed5be6686d2d5ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ca940c36d6046a58ed5be6686d2d5ee"}}, "title": "Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.", "authors": [{"family": "Low", "given": "G W", "initials": "GW"}, {"family": "Chattopadhyay", "given": "B", "initials": "B"}, {"family": "Garg", "given": "K M", "initials": "KM"}, {"family": "Irestedt", "given": "M", "initials": "M"}, {"family": "Ericson", "given": "Pgp", "initials": "P"}, {"family": "Yap", "given": "G", "initials": "G"}, {"family": "Tang", "given": "Q", "initials": "Q"}, {"family": "Wu", "given": "S", "initials": "S"}, {"family": "Rheindt", "given": "F E", "initials": "FE"}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "120", "issn": "1365-2540", "issue": "2", "pages": "138-153", "title": "Heredity (Edinb)", "issn-l": "0018-067X"}, "abstract": "Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an invasive population of the Javan Myna Acridotheres javanicus across the island of Singapore. We inferred limited population subdivision at a micro-geographic level, a genetic patch size (~13-14\u2009km) indicative of a pronounced dispersal ability, and barely an increase in effective population size since introduction despite an increase of four to five orders of magnitude in actual population size, suggesting that low population-genetic diversity following a bottleneck has not impeded establishment success. Landscape genomic analyses identified urban features, such as low-rise neighborhoods, that constitute pronounced barriers to gene flow. Based on our data, we consider an approach targeting the complete eradication of Javan Mynas across Singapore to be unfeasible. Instead, a mixed approach of localized mitigation measures taking into account urban geographic features and planning policy may be the most promising avenue to reducing the adverse impacts of this urban pest. Our study demonstrates how genomic methods can directly inform the management and control of invasive species, even in geographically limited datasets with high gene flow rates.", "doi": "10.1038/s41437-017-0026-1", "pmid": "29225353", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-017-0026-1"}, {"db": "pmc", "key": "PMC5837122"}], "notes": [], "created": "2018-10-31T19:47:39.988Z", "modified": "2024-01-16T13:48:47.154Z"}, {"entity": "publication", "iuid": "79a097bcd5394e09a35047c3eb9dac7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79a097bcd5394e09a35047c3eb9dac7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79a097bcd5394e09a35047c3eb9dac7a"}}, "title": "Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "S\u00e1nchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah M", "initials": "GM"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Eriksson", "given": "Gunilla", "initials": "G"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Sj\u00f6lander", "given": "Anders", "initials": "A"}, {"family": "Jansen Sellevold", "given": "Berit", "initials": "B"}, {"family": "J\u00f8rgensen", "given": "Roger", "initials": "R"}, {"family": "Claes", "given": "Peter", "initials": "P"}, {"family": "Shriver", "given": "Mark D", "initials": "MD"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Netea", "given": "Mihai G", "initials": "MG"}, {"family": "Apel", "given": "Jan", "initials": "J"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2018-01-00", "journal": {"volume": "16", "issn": "1545-7885", "issue": "1", "pages": "e2003703", "title": "PLoS Biol.", "issn-l": "1544-9173"}, "abstract": "Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57\u00d7 coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.", "doi": "10.1371/journal.pbio.2003703", "pmid": "29315301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5760011"}, {"db": "pii", "key": "pbio.2003703"}], "notes": [], "created": "2018-01-11T10:03:24.352Z", "modified": "2024-01-16T13:48:47.193Z"}, {"entity": "publication", "iuid": "4aec1dba6cd84d518d4a8fcd4450b703", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4aec1dba6cd84d518d4a8fcd4450b703.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4aec1dba6cd84d518d4a8fcd4450b703"}}, "title": "Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.", "authors": [{"family": "Zhao", "given": "Jin J", "initials": "JJ", "orcid": "0000-0001-8367-8391", "researcher": {"href": "https://publications.scilifelab.se/researcher/fad3b22c21064a85a351f549bedfc36e.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Zander", "given": "Cecilia S", "initials": "CS"}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Georgii-Hemming", "given": "Patrik", "initials": "P"}, {"family": "M\u00e5nsson", "given": "Else", "initials": "E"}, {"family": "Brandberg", "given": "G\u00f6ran", "initials": "G"}, {"family": "S\u00e4vmarker", "given": "Helena E", "initials": "HE"}, {"family": "Frykholm", "given": "Carina", "initials": "C"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2018-01-00", "journal": {"volume": "177", "issn": "1552-485X", "issue": "1", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "pages": "10-20", "issn-l": "1552-4841"}, "abstract": "Intellectual Disability (ID) is a clinically heterogeneous condition that affects 2-3% of population worldwide. In recent years, exome sequencing has been a successful strategy for studies of genetic causes of ID, providing a growing list of both candidate and validated ID genes. In this study, exome sequencing was performed on 28 ID patients in 27 patient-parent trios with the aim to identify de novo variants (DNVs) in known and novel ID associated genes. We report the identification of 25 DNVs out of which five were classified as pathogenic or likely pathogenic. Among these, a two base pair deletion was identified in the PUF60 gene, which is one of three genes in the critical region of the 8q24.3 microdeletion syndrome (Verheij syndrome). Our result adds to the growing evidence that PUF60 is responsible for the majority of the symptoms reported for carriers of a microdeletion across this region. We also report variants in several genes previously not associated with ID, including a de novo missense variant in NAA15. We highlight NAA15 as a novel candidate ID gene based on the vital role of NAA15 in the generation and differentiation of neurons in neonatal brain, the fact that the gene is highly intolerant to loss of function and coding variation, and previously reported DNVs in neurodevelopmental disorders.", "doi": "10.1002/ajmg.b.32574", "pmid": "28990276", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5765476"}], "notes": [], "created": "2017-11-02T16:04:48.503Z", "modified": "2024-01-16T13:48:47.230Z"}, {"entity": "publication", "iuid": "de5cef0f77da4349b6fd836ac8b9887a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de5cef0f77da4349b6fd836ac8b9887a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de5cef0f77da4349b6fd836ac8b9887a"}}, "title": "Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish.", "authors": [{"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Kurtoglu", "given": "Deniz", "initials": "D"}, {"family": "Armenio", "given": "Miriam", "initials": "M"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Papadogiannakis", "given": "Nikos", "initials": "N"}, {"family": "Gustavsson", "given": "Peter", "initials": "P"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-12-28", "journal": {"volume": null, "issn": "1098-1004", "issue": null, "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Congenital malformations affecting the neural tube can present as isolated malformations or occur in association with other developmental abnormalities and syndromes. Using high resolution copy number screening in 66 fetuses with neural tube defects we identified 6 fetuses with likely pathogenic mutations, three aneuploidies (one trisomy 13 and two trisomy 18) and three deletions previously reported in NTDs (one 22q11.2 deletion and two 1p36 deletions) corresponding to 9% of the cohort. In addition, we identified five rare deletions and two duplications of uncertain significance including a rare intragenic heterozygous in-frame WDR63 deletion in a fetus with occipital encephalocele. Whole genome sequencing verified the deletion and excluded known pathogenic variants. The deletion spans exons 14-17 resulting in the expression of a protein missing the third and fourth WD-repeat domains. These findings were supported by CRISPR/Cas9 mediated somatic deletions in zebrafish. Injection of two different sgRNA-pairs targeting relevant intronic regions resulted in a deletion mimicking the human deletion and a concomitant increase of abnormal embryos with body and brain malformations (41%, n\u00a0=\u00a0161 and 62%, n\u00a0=\u00a0224 respectively), including a sac-like brain protrusion (7% and 9%, p\u00a0<\u00a00.01). Similar results were seen with overexpression of RNA encoding the deleted variant in zebrafish (Total abnormal;46%, n\u00a0=\u00a0255, P\u00a0<\u00a00.001) compared to overexpression of an equivalent amount of wild-type RNA (Total abnormal;3%, n\u00a0=\u00a0177). We predict the in-frame WDR63 deletion to result in a dominant negative or gain of function form of WDR63. These are the first findings supporting a role for WDR63 in encephalocele formation. This article is protected by copyright. All rights reserved.", "doi": "10.1002/humu.23388", "pmid": "29285825", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-10T09:44:17.066Z", "modified": "2020-01-21T13:56:11.002Z"}, {"entity": "publication", "iuid": "fef10a717b6948448b27dd4db58ce148", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fef10a717b6948448b27dd4db58ce148.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fef10a717b6948448b27dd4db58ce148"}}, "title": "Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils.", "authors": [{"family": "H\u00f6gfors-R\u00f6nnholm", "given": "Eva", "initials": "E"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Dalhem", "given": "Krister", "initials": "K"}, {"family": "Lillhonga", "given": "Tom", "initials": "T"}, {"family": "Engblom", "given": "Sten", "initials": "S"}, {"family": "\u00d6sterholm", "given": "Peter", "initials": "P"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-12-26", "journal": {"volume": "625", "issn": "1879-1026", "issue": null, "pages": "39-49", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "Naturally occurring sulfide rich deposits are common along the northern Baltic Sea coast that when exposed to air, release large amounts of acid and metals into receiving water bodies. This causes severe environmental implications for agriculture, forestry, and building of infrastructure. In this study, we investigated the efficiency of ultrafine-grained calcium carbonate and peat (both separately and in combination) to mitigate acid and metal release. The experiments were carried out aerobically that mimicked summer conditions when the groundwater level is low and acid sulfate soils are exposed to oxygen, and anaerobically that is similar to autumn to spring conditions. The ultrafine-grained calcium carbonate dissipated well in the soil and its effect alone and when mixed with peat raised the pH and reduced pyrite dissolution while peat alone was similar to the controls and did not halt metal and acid release. High throughput 16S rRNA gene sequencing identified populations most similar to characterized acidophiles in the control and peat treated incubations while the acidophilic like populations were altered in the calcium carbonate alone and calcium carbonate plus peat treated acid sulfate soils. Coupled with the geochemistry data, it was suggested that the acidophiles were inactivated by the high pH in the presence of calcium carbonate but catalyzed pyrite dissolution in the controls and peat incubations. In conclusion, the anaerobic conditions during winter would likely be sufficient to mitigate acid production and metal release from acid sulfate soils and in the summer, treatment with calcium carbonate was the best mitigation method.", "doi": "10.1016/j.scitotenv.2017.12.287", "pmid": "29287211", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(17)33720-8"}, {"db": "BioProject", "description": "16S rRNA gene raw reads. Community analysis of the microbiome of acid sulfate soils before and after remediation attempts by different treatments.", "key": "PRJNA407753"}], "notes": [], "created": "2018-01-10T09:45:06.241Z", "modified": "2020-01-21T13:56:11.012Z"}, {"entity": "publication", "iuid": "0d4095789678406cba65e6ce25b7b0a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d4095789678406cba65e6ce25b7b0a9"}}, "title": "Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.", "authors": [{"family": "Elewa", "given": "Ahmed", "initials": "A"}, {"family": "Wang", "given": "Heng", "initials": "H"}, {"family": "Talavera-L\u00f3pez", "given": "Carlos", "initials": "C"}, {"family": "Joven", "given": "Alberto", "initials": "A"}, {"family": "Brito", "given": "Gon\u00e7alo", "initials": "G", "orcid": "0000-0003-2134-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0196703e4df4518b212ed1f3322e811.json"}}, {"family": "Kumar", "given": "Anoop", "initials": "A"}, {"family": "Hameed", "given": "L Shahul", "initials": "LS"}, {"family": "Penrad-Mobayed", "given": "May", "initials": "M"}, {"family": "Yao", "given": "Zeyu", "initials": "Z"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Abbas", "given": "Yamen", "initials": "Y"}, {"family": "Abdullayev", "given": "Ilgar", "initials": "I"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-4624-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/d85416dce306436ab0c4cdeea22a1f59.json"}}, {"family": "Simon", "given": "Andr\u00e1s", "initials": "A"}], "type": "journal article", "published": "2017-12-22", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "2286", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "Salamanders exhibit an extraordinary ability among vertebrates to regenerate complex body parts. However, scarce genomic resources have limited our understanding of regeneration in adult salamanders. Here, we present the ~20 Gb genome and transcriptome of the Iberian ribbed newt Pleurodeles waltl, a tractable species suitable for laboratory research. We find that embryonic stem cell-specific miRNAs mir-93b and mir-427/430/302, as well as Harbinger DNA transposons carrying the Myb-like proto-oncogene have expanded dramatically in the Pleurodeles waltl genome and are co-expressed during limb regeneration. Moreover, we find that a family of salamander methyltransferases is expressed specifically in adult appendages. Using CRISPR/Cas9 technology to perturb transcription factors, we demonstrate that, unlike the axolotl, Pax3 is present and necessary for development and that contrary to mammals, muscle regeneration is normal without functional Pax7 gene. Our data provide a foundation for comparative genomic studies that generate models for the uneven distribution of regenerative capacities among vertebrates.", "doi": "10.1038/s41467-017-01964-9", "pmid": "29273779", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-01964-9"}, {"db": "pmc", "key": "PMC5741667"}], "notes": [], "created": "2018-01-10T09:44:17.789Z", "modified": "2021-07-07T11:44:07.846Z"}, {"entity": "publication", "iuid": "a2f292fd15964c09bf55b71f9a64af47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2f292fd15964c09bf55b71f9a64af47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2f292fd15964c09bf55b71f9a64af47"}}, "title": "Discovery of the fourth mobile sulfonamide resistance gene.", "authors": [{"family": "Razavi", "given": "Mohammad", "initials": "M"}, {"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "Gillings", "given": "Michael R", "initials": "MR"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Joakim Larsson", "given": "D G", "initials": "DG"}], "type": "journal article", "published": "2017-12-15", "journal": {"volume": "5", "issn": "2049-2618", "issue": "1", "pages": "160", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Over the past 75\u00a0years, human pathogens have acquired antibiotic resistance genes (ARGs), often from environmental bacteria. Integrons play a major role in the acquisition of antibiotic resistance genes. We therefore hypothesized that focused exploration of integron gene cassettes from microbial communities could be an efficient way to find novel mobile resistance genes. DNA from polluted Indian river sediments were amplified using three sets of primers targeting class 1 integrons and sequenced by long- and short-read technologies to maintain both accuracy and context.\n\nUp to 89% of identified open reading frames encode known resistance genes, or variations thereof (>\u20091000). We identified putative novel ARGs to aminoglycosides, beta-lactams, trimethoprim, rifampicin, and chloramphenicol, including several novel OXA variants, providing reduced susceptibility to carbapenems. One dihydropteroate synthase gene, with less than 34% amino acid identity to the three known mobile sulfonamide resistance genes (sul1-3), provided complete resistance when expressed in Escherichia coli. The mobilized gene, here named sul4, is the first mobile sulfonamide resistance gene discovered since 2003. Analyses of adjacent DNA suggest that sul4 has been decontextualized from a set of chromosomal genes involved in folate synthesis in its original host, likely within the phylum Chloroflexi. The presence of an insertion sequence common region element could provide mobility to the entire integron. Screening of 6489 metagenomic datasets revealed that sul4 is already widespread in seven countries across Asia and Europe.\n\nOur findings show that exploring integrons from environmental communities with a history of antibiotic exposure can provide an efficient way to find novel, mobile resistance genes. The mobilization of a fourth sulfonamide resistance gene is likely to provide expanded opportunities for sulfonamide resistance to spread, with potential impacts on both human and animal health.", "doi": "10.1186/s40168-017-0379-y", "pmid": "29246178", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0379-y"}, {"db": "pmc", "key": "PMC5732528"}, {"db": "BioProject", "description": "Sediment metagenome. Amplicon sequencing of gene cassettes from polluted sediments.", "key": "PRJNA400874"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv2 dihydropteroate synthase (sul4) and quaternary ammonium compound efflux genes, complete cds", "key": "MG649394"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv3 OXA-2-like protein gene, complete cds; and QacE delta gene, partial cds", "key": "MG649395"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv4 dihydrofolate reductase (drfb2) gene, partial cds; arr-6-like protein gene, complete cds; and class 1 integron integrase gene, partial cds", "key": "MG649396"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv5 class 1 integron integrase gene, partial cds; and OXA-10-like protein gene, complete cds", "key": "MG649397"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv6 chloramphenicol O-acetyltransferase gene, complete cds", "key": "MG649398"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv7 QacE delta gene, partial cds; and OXA-46-like protein gene, complete cds", "key": "MG649399"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv9 OXA-2-like protein gene, complete cds; and QacE delta gene, partial cds", "key": "MG649400"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv10 CARB-PSE gene, partial cds; and dfrA-like protein gene, complete cds", "key": "MG649401"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv8 ISCR20-like protein, dihydropteroate synthase (sul4), and hypothetical protein genes, complete cds", "key": "MG649402"}, {"db": "GENBANK", "description": "Uncultured bacterium clone riv11 qacE gene, partial cds; and molecular chaperone, qacE, and aminoglycoside nucleotidyltransferase AadA genes, complete cds", "key": "MG649403"}], "notes": [], "created": "2018-01-10T09:45:03.356Z", "modified": "2020-01-21T13:56:11.019Z"}, {"entity": "publication", "iuid": "8f6ae3f4a79d4fa49e24d158da645cd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f6ae3f4a79d4fa49e24d158da645cd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f6ae3f4a79d4fa49e24d158da645cd7"}}, "title": "Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.", "authors": [{"family": "Zhang", "given": "Wang", "initials": "W"}, {"family": "Ambikan", "given": "Anoop T", "initials": "AT"}, {"family": "Sperk", "given": "Maike", "initials": "M"}, {"family": "van Domselaar", "given": "Robert", "initials": "R"}, {"family": "Nowak", "given": "Piotr", "initials": "P"}, {"family": "Noyan", "given": "Kajsa", "initials": "K"}, {"family": "Russom", "given": "Aman", "initials": "A"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}, {"family": "Neogi", "given": "Ujjwal", "initials": "U"}], "type": "journal article", "published": "2017-12-12", "journal": {"volume": null, "issn": "2352-3964", "issue": null, "title": "EBioMedicine", "issn-l": "2352-3964"}, "abstract": "A small subset of HIV-1 infected individuals, the \"Elite Controllers\" (EC), can control viral replication and restrain progression to immunodeficiency without antiretroviral therapy (ART). In this study, a cross-sectional transcriptomics and targeted proteomics analysis were performed in a well-defined Swedish cohort of untreated EC (n=19), treatment na\u00efve patients with viremia (VP, n=32) and HIV-1-negative healthy controls (HC, n=23). The blood transcriptome identified 151 protein-coding genes that were differentially expressed (DE) in VP compared to EC. Genes like CXCR6 and SIGLEC1 were downregulated in EC compared to VP. A definite distinction in gene expression between males and females among all patient-groups were observed. The gene expression profile between female EC and the healthy females was similar but did differ between male EC and healthy males. At targeted proteomics analysis, 90% (29/32) of VPs clustered together while EC and HC clustered separately from VP. Among the soluble factors, 33 were distinctive to be statistically significant (False discovery rate=0.02). Cell surface receptor signaling pathway, programmed cell death, response to cytokine and cytokine-mediated signaling seem to synergistically play an essential role in HIV-1 control in EC.", "doi": "10.1016/j.ebiom.2017.11.031", "pmid": "29269040", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3964(17)30473-5"}, {"db": "BioProject", "description": "Transcriptomic analysis to map mechanisms of viral replication control in HIV-1 positive Elite Controllers", "key": "PRJNA420459"}, {"db": "SRA", "description": "Transcriptomic analysis to map mechanisms of viral replication control in HIV-1 positive Elite Controllers", "key": "SRP125882"}], "notes": [], "created": "2018-01-10T09:45:01.949Z", "modified": "2020-01-21T13:56:11.033Z"}, {"entity": "publication", "iuid": "a1e96d19911348b0881541e490d67a58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1e96d19911348b0881541e490d67a58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1e96d19911348b0881541e490d67a58"}}, "title": "A Unique ISR Program Determines Cellular Responses to Chronic Stress.", "authors": [{"family": "Guan", "given": "Bo-Jhih", "initials": "BJ"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Jobava", "given": "Raul", "initials": "R"}, {"family": "Elroy-Stein", "given": "Orna", "initials": "O"}, {"family": "Valasek", "given": "Leos S", "initials": "LS"}, {"family": "Cargnello", "given": "Marie", "initials": "M"}, {"family": "Gao", "given": "Xing-Huang", "initials": "XH"}, {"family": "Krokowski", "given": "Dawid", "initials": "D"}, {"family": "Merrick", "given": "William C", "initials": "WC"}, {"family": "Kimball", "given": "Scot R", "initials": "SR"}, {"family": "Komar", "given": "Anton A", "initials": "AA"}, {"family": "Koromilas", "given": "Antonis E", "initials": "AE"}, {"family": "Wynshaw-Boris", "given": "Anthony", "initials": "A"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Hatzoglou", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2017-12-07", "journal": {"volume": "68", "issn": "1097-4164", "issue": "5", "pages": "885-900.e6", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "The integrated stress response (ISR) is a homeostatic mechanism induced by endoplasmic reticulum (ER) stress. In acute/transient ER stress, decreased global protein synthesis and increased uORF mRNA translation are followed by normalization of protein synthesis. Here, we report a dramatically different response during chronic ER stress. This chronic ISR program is characterized by persistently elevated uORF mRNA translation and concurrent gene expression reprogramming, which permits simultaneous stress sensing and proteostasis. The program includes PERK-dependent switching to an eIF3-dependent translation initiation mechanism, resulting in partial, but not complete, translational recovery, which, together with transcriptional reprogramming, selectively bolsters expression of proteins with ER functions. Coordination of transcriptional and translational reprogramming prevents ER dysfunction and inhibits \"foamy cell\" development, thus establishing a molecular basis for understanding human diseases associated with ER dysfunction.", "doi": "10.1016/j.molcel.2017.11.007", "pmid": "29220654", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S1097-2765(17)30842-0"}, {"db": "pmc", "key": "PMC5730339"}, {"db": "mid", "key": "NIHMS919694"}, {"db": "GEO", "description": "A unique ISR Program Determines Cellular Responses to Chronic Stress", "key": "GSE90070"}], "notes": [], "created": "2018-01-10T09:45:07.638Z", "modified": "2020-01-21T13:56:11.026Z"}, {"entity": "publication", "iuid": "812369ae8ecd493db7a2b7cb3c8387f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/812369ae8ecd493db7a2b7cb3c8387f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/812369ae8ecd493db7a2b7cb3c8387f9"}}, "title": "Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis).", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Shipilina", "given": "Daria", "initials": "D"}, {"family": "Marova", "given": "Irina", "initials": "I"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}], "type": "journal article", "published": "2017-12-04", "journal": {"volume": "7", "issn": "2160-1836", "issue": "12", "pages": "3983-3998", "title": "G3 (Bethesda)", "issn-l": "2160-1836"}, "abstract": "Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European ( Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)-two recently diverged species which differ in morphology, plumage, song, habitat, and migration-to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that postdivergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.", "doi": "10.1534/g3.117.300152", "pmid": "29054864", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "g3.117.300152"}, {"db": "pmc", "key": "PMC5714495"}], "notes": [], "created": "2017-11-03T16:22:15.701Z", "modified": "2021-06-21T14:59:08.098Z"}, {"entity": "publication", "iuid": "5dc932db5ed947d5912b3f59db7f4023", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5dc932db5ed947d5912b3f59db7f4023.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5dc932db5ed947d5912b3f59db7f4023"}}, "title": "Inflammatory infiltrates in parathyroid tumors.", "authors": [{"family": "Haglund", "given": "Felix", "initials": "F"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Nilsson", "given": "Inga-Lena", "initials": "IL"}, {"family": "H\u00f6\u00f6g", "given": "Anders", "initials": "A"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}], "type": "comparative study", "published": "2017-12-00", "journal": {"volume": "177", "issn": "1479-683X", "issue": "6", "pages": "445-453", "title": "Eur. J. Endocrinol.", "issn-l": "0804-4643"}, "abstract": "Inflammatory infiltrates are sometimes present in solid tumors and may be coupled to clinical behavior or etiology. Infectious viruses contribute to tumorigenesis in a significant fraction of human neoplasias.\n\nCharacterize inflammatory infiltrates and possible viral transcription in primary hyperparathyroidism.\n\nFrom the period 2007 to 2016, a total of 55 parathyroid tumors (51 adenomas and 4 hyperplasias) with prominent inflammatory infiltrates were identified from more than 2000 parathyroid tumors in the pathology archives, and investigated by immunohistochemistry for CD4, CD8, CD20 and CD45 and scored as +0, +1 or +2. Clinicopathological data were compared to 142 parathyroid adenomas without histological evidence of inflammation. Transcriptome sequencing was performed for 13 parathyroid tumors (four inflammatory, 9 non-inflammatory) to identify potential viral transcripts.\n\nTumors had prominent germinal center-like nodular (+2) lymphocytic infiltrates consisting of T and B lymphocytes (31%) and/or diffuse (+1-2) infiltrates of predominantly CD8+ T lymphocytes (84%). In the majority of cases with adjacent normal parathyroid tissue, the normal rim was unaffected by the inflammatory infiltrates (96%). Presence of inflammatory infiltrates was associated with higher levels of serum-PTH (P\u2005=\u20050.007) and oxyphilic differentiation (P\u2005=\u20050.002). Co-existent autoimmune disease was observed in 27% of patients with inflammatory infiltrates, which in turn was associated with oxyphilic differentiation (P\u2005=\u20050.041). Additionally, prescription of anti-inflammatory drugs was associated with lower serum ionized calcium (P\u2005=\u20050.037).\n\nNo evidence of virus-like sequences in the parathyroid tumors could be found by transcriptome sequencing, suggesting that other factors may contribute to attract the immune system to the parathyroid tumor tissue.", "doi": "10.1530/EJE-17-0277", "pmid": "28855268", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EJE-17-0277"}, {"db": "pmc", "key": "PMC5642267"}], "notes": [], "created": "2017-11-03T16:20:58.775Z", "modified": "2024-01-16T13:48:47.280Z"}, {"entity": "publication", "iuid": "1b64378122df401ea8d44baa1f502671", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64378122df401ea8d44baa1f502671.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64378122df401ea8d44baa1f502671"}}, "title": "A female Viking warrior confirmed by genomics.", "authors": [{"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0001-8964-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3a47cc07e9d4b8592dba430785681b5.json"}}, {"family": "Zachrisson", "given": "Torun", "initials": "T"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Sobrado", "given": "Veronica", "initials": "V"}, {"family": "Price", "given": "Neil", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}], "type": "historical article", "published": "2017-12-00", "journal": {"volume": "164", "issn": "1096-8644", "issue": "4", "title": "Am. J. Phys. Anthropol.", "pages": "853-860", "issn-l": "0002-9483"}, "abstract": "The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.\n\nGenome-wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern-day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.\n\nThe genomic results revealed the lack of a Y-chromosome and thus a female biological sex, and the mtDNA analyses support a single-individual origin of sampled elements. The genetic affinity is close to present-day North Europeans, and within Sweden to the southern and south-central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.\n\nThe identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time-period. The results call for caution against generalizations regarding social orders in past societies.", "doi": "10.1002/ajpa.23308", "pmid": "28884802", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5724682"}], "notes": [], "created": "2017-11-03T16:18:39.012Z", "modified": "2024-01-16T13:48:47.310Z"}, {"entity": "publication", "iuid": "dcdd0e77f81742ba8bd8593d8b5a6659", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcdd0e77f81742ba8bd8593d8b5a6659.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcdd0e77f81742ba8bd8593d8b5a6659"}}, "title": "Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.", "authors": [{"family": "Karthik", "given": "Govindasamy-Muralidharan", "initials": "GM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "L\u00f6vrot", "given": "John", "initials": "J"}, {"family": "Ullah", "given": "Ikram", "initials": "I"}, {"family": "Alkodsi", "given": "Amjad", "initials": "A"}, {"family": "Ma", "given": "Ran", "initials": "R"}, {"family": "Wedlund", "given": "Lena", "initials": "L"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Frisell", "given": "Jan", "initials": "J"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-11-29", "journal": {"volume": "17", "issn": "1471-2407", "issue": "1", "pages": "802", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Transcriptomic profiling of breast tumors provides opportunity for subtyping and molecular-based patient stratification. In diagnostic applications the specimen profiled should be representative of the expression profile of the whole tumor and ideally capture properties of the most aggressive part of the tumor. However, breast cancers commonly exhibit intra-tumor heterogeneity at molecular, genomic and in phenotypic level, which can arise during tumor evolution. Currently it is not established to what extent a random sampling approach may influence molecular breast cancer diagnostics.\n\nIn this study we applied RNA-sequencing to quantify gene expression in 43 pieces (2-5 pieces per tumor) from 12 breast tumors (Cohort 1). We determined molecular subtype and transcriptomic grade for all tumor pieces and analysed to what extent pieces originating from the same tumors are concordant or discordant with each other. Additionally, we validated our finding in an independent cohort consisting of 19 pieces (2-6 pieces per tumor) from 6 breast tumors (Cohort 2) profiled using microarray technique. Exome sequencing was also performed on this cohort, to investigate the extent of intra-tumor genomic heterogeneity versus the intra-tumor molecular subtype classifications.\n\nMolecular subtyping was consistent in 11 out of 12 tumors and transcriptomic grade assignments were consistent in 11 out of 12 tumors as well. Molecular subtype predictions revealed consistent subtypes in four out of six patients in this cohort 2. Interestingly, we observed extensive intra-tumor genomic heterogeneity in these tumor pieces but not in their molecular subtype classifications.\n\nOur results suggest that macroscopic intra-tumoral transcriptomic heterogeneity is limited and unlikely to have an impact on molecular diagnostics for most patients.", "doi": "10.1186/s12885-017-3815-2", "pmid": "29187174", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12885-017-3815-2"}, {"db": "pmc", "key": "PMC5708109"}], "notes": [], "created": "2018-01-10T09:45:04.700Z", "modified": "2020-01-21T13:56:11.065Z"}, {"entity": "publication", "iuid": "04e76f0947204c27a9f2e4e51b7d1713", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e76f0947204c27a9f2e4e51b7d1713.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e76f0947204c27a9f2e4e51b7d1713"}}, "title": "STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.", "authors": [{"family": "Hochgerner", "given": "Hannah", "initials": "H", "orcid": "0000-0002-7739-666X", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b8fc33efd44cfb2bb60a3f250a518.json"}}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Hodge", "given": "Rebecca", "initials": "R"}, {"family": "Mikes", "given": "Jaromir", "initials": "J", "orcid": "0000-0002-9941-7855", "researcher": {"href": "https://publications.scilifelab.se/researcher/21c127bffa7c4a01af7fad8ba6bac90b.json"}}, {"family": "Heskol", "given": "Abeer", "initials": "A"}, {"family": "Hubschle", "given": "Hermann", "initials": "H"}, {"family": "Lin", "given": "Philip", "initials": "P"}, {"family": "Picelli", "given": "Simone", "initials": "S"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Ratz", "given": "Michael", "initials": "M"}, {"family": "Dunne", "given": "Jude", "initials": "J"}, {"family": "Husain", "given": "Syed", "initials": "S"}, {"family": "Lein", "given": "Ed", "initials": "E", "orcid": "0000-0001-9012-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd450c764a4431aa798630053343cd6.json"}}, {"family": "Srinivasan", "given": "Maithreyan", "initials": "M"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "journal article", "published": "2017-11-27", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "16327", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Single-cell RNA-seq has become routine for discovering cell types and revealing cellular diversity, but archived human brain samples still pose a challenge to current high-throughput platforms. We present STRT-seq-2i, an addressable 9600-microwell array platform, combining sampling by limiting dilution or FACS, with imaging and high throughput at competitive cost. We applied the platform to fresh single mouse cortical cells and to frozen post-mortem human cortical nuclei, matching the performance of a previous lower-throughput platform while retaining a high degree of flexibility, potentially also for other high-throughput applications.", "doi": "10.1038/s41598-017-16546-4", "pmid": "29180631", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Cellular Immunomonitoring": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5703850"}, {"db": "pii", "key": "10.1038/s41598-017-16546-4"}], "notes": [], "created": "2018-01-10T09:45:09.064Z", "modified": "2024-01-21T18:00:22.804Z"}, {"entity": "publication", "iuid": "dd3127485e334ad7b4b073d0399d4d33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd3127485e334ad7b4b073d0399d4d33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd3127485e334ad7b4b073d0399d4d33"}}, "title": "Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Feuerborn", "given": "Tatiana", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "van der Plicht", "given": "Johannes", "initials": "J"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Tikhonov", "given": "Alexei", "initials": "A"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2017-11-20", "journal": {"volume": "27", "issn": "1879-0445", "issue": "22", "pages": "3505-3510.e3", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. We hypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.", "doi": "10.1016/j.cub.2017.09.064", "pmid": "29103934", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(17)31264-2"}], "notes": [], "created": "2017-11-03T13:20:53.917Z", "modified": "2021-07-07T20:31:10.935Z"}, {"entity": "publication", "iuid": "86b4dfef19e14e50a0aa6009e61cb8e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86b4dfef19e14e50a0aa6009e61cb8e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86b4dfef19e14e50a0aa6009e61cb8e7"}}, "title": "Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.", "authors": [{"family": "Hammarsj\u00f6", "given": "A", "initials": "A"}, {"family": "Wang", "given": "Z", "initials": "Z"}, {"family": "Vaz", "given": "R", "initials": "R"}, {"family": "Taylan", "given": "F", "initials": "F"}, {"family": "Sedghi", "given": "M", "initials": "M"}, {"family": "Girisha", "given": "K M", "initials": "KM"}, {"family": "Chitayat", "given": "D", "initials": "D"}, {"family": "Neethukrishna", "given": "K", "initials": "K"}, {"family": "Shannon", "given": "P", "initials": "P"}, {"family": "Godoy", "given": "R", "initials": "R"}, {"family": "Gowrishankar", "given": "K", "initials": "K"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Nasiri", "given": "J", "initials": "J"}, {"family": "Baktashian", "given": "M", "initials": "M"}, {"family": "Newton", "given": "P T", "initials": "PT"}, {"family": "Guo", "given": "L", "initials": "L"}, {"family": "Hofmeister", "given": "W", "initials": "W"}, {"family": "Pettersson", "given": "M", "initials": "M"}, {"family": "Chagin", "given": "A S", "initials": "AS"}, {"family": "Nishimura", "given": "G", "initials": "G"}, {"family": "Yan", "given": "L", "initials": "L"}, {"family": "Matsumoto", "given": "N", "initials": "N"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Miyake", "given": "N", "initials": "N"}, {"family": "Grigelioniene", "given": "G", "initials": "G"}, {"family": "Ikegawa", "given": "S", "initials": "S"}], "type": "journal article", "published": "2017-11-14", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "15585", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The skeletal ciliopathies are a heterogeneous group of disorders with a significant clinical and genetic variability and the main clinical features are thoracic hypoplasia and short tubular bones. To date, 25 genes have been identified in association with skeletal ciliopathies. Mutations in the KIAA0753 gene have recently been associated with Joubert syndrome\u00a0(JBTS) and orofaciodigital (OFD) syndrome. We report biallelic pathogenic variants in KIAA0753 in four patients with short-rib type skeletal dysplasia. The manifestations in our patients are variable and ranging from fetal lethal to viable and moderate skeletal dysplasia with narrow thorax and abnormal metaphyses. We demonstrate that KIAA0753 is expressed in normal fetal human growth plate and show that the affected fetus, with a compound heterozygous frameshift and a nonsense mutation in KIAA0753, has an abnormal proliferative zone and a broad hypertrophic zone. The importance of KIAA0753 for normal skeletal development is further confirmed by our findings that zebrafish embryos homozygous for a nonsense mutation in kiaa0753 display altered cartilage patterning.", "doi": "10.1038/s41598-017-15442-1", "pmid": "29138412", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-15442-1"}, {"db": "pmc", "key": "PMC5686170"}], "notes": [], "created": "2018-01-10T09:44:15.685Z", "modified": "2020-01-21T13:56:11.126Z"}, {"entity": "publication", "iuid": "63a7fc722c47447b9dc981a289d38084", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a7fc722c47447b9dc981a289d38084.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a7fc722c47447b9dc981a289d38084"}}, "title": "Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Gillingwater", "given": "Thomas H", "initials": "TH"}, {"family": "MacCallum", "given": "Malcolm", "initials": "M"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Dobney", "given": "Keith", "initials": "K"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}], "type": "journal article", "published": "2017-11-06", "journal": {"volume": "27", "issn": "1879-0445", "issue": "21", "pages": "3396-3402.e5", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE) yielded sufficient autosomal genome coverage (0.21\u00d7 to 3.93\u00d7) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.", "doi": "10.1016/j.cub.2017.09.059", "pmid": "29107554", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(17)31257-5"}], "notes": [], "created": "2018-01-10T09:44:16.403Z", "modified": "2023-06-20T15:54:27.159Z"}, {"entity": "publication", "iuid": "880eebdde88d41dc834023c786093f68", "links": {"self": {"href": "https://publications.scilifelab.se/publication/880eebdde88d41dc834023c786093f68.json"}, "display": {"href": "https://publications.scilifelab.se/publication/880eebdde88d41dc834023c786093f68"}}, "title": "Unique case of cerebrotendinous xanthomatosis revisited: All the mutations responsible for this disease are present in the CYP27A1 gene.", "authors": [{"family": "Jiao", "given": "H", "initials": "H"}, {"family": "Olin", "given": "M", "initials": "M"}, {"family": "Hansson", "given": "M", "initials": "M"}, {"family": "Eggertsen", "given": "G", "initials": "G"}, {"family": "Eriksson", "given": "M", "initials": "M"}, {"family": "Angelin", "given": "B", "initials": "B"}, {"family": "Bj\u00f6rkhem", "given": "I", "initials": "I"}], "type": "letter", "published": "2017-11-02", "journal": {"volume": null, "issn": "1365-2796", "issue": null, "title": "J. Intern. Med.", "issn-l": "0954-6820"}, "abstract": null, "doi": "10.1111/joim.12709", "pmid": "29095540", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2018-01-10T09:45:02.667Z", "modified": "2020-01-21T13:56:11.145Z"}, {"entity": "publication", "iuid": "f32d433317a047abadcdd972d785fce2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f32d433317a047abadcdd972d785fce2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f32d433317a047abadcdd972d785fce2"}}, "title": "Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.", "authors": [{"family": "Marathe", "given": "Nachiket P", "initials": "NP"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Gaikwad", "given": "Swapnil S", "initials": "SS"}, {"family": "Jonsson", "given": "Viktor", "initials": "V"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DGJ"}], "type": "journal article", "published": "2017-11-01", "journal": {"volume": "124", "issn": "1879-2448", "issue": null, "pages": "388-397", "title": "Water Res.", "issn-l": "0043-1354"}, "abstract": "Efficient sewage treatment is critical for limiting environmental transmission of antibiotic-resistant bacteria. In many low and middle income countries, however, large proportions of sewage are still released untreated into receiving water bodies. In-depth knowledge of how such discharges of untreated urban waste influences the environmental resistome is largely lacking. Here, we highlight the impact of uncontrolled discharge of partially treated and/or untreated wastewater on the structure of bacterial communities and resistome of sediments collected from Mutha river flowing through Pune city in India. Using shotgun metagenomics, we found a wide array (n\u00a0=\u00a0175) of horizontally transferable antibiotic resistance genes (ARGs) including carbapenemases such as NDM, VIM, KPC, OXA-48 and IMP types. The relative abundance of total ARGs was 30-fold higher in river sediments within the city compared to upstream sites. Forty four ARGs, including the tet(X) gene conferring resistance to tigecycline, OXA-58 and GES type carbapenemases, were significantly more abundant in city sediments, while two ARGs were more common at upstream sites. The recently identified mobile colistin resistance gene mcr-1 was detected only in one of the upstream samples, but not in city samples. In addition to ARGs, higher abundances of various mobile genetic elements were found in city samples, including integron-associated integrases and ISCR transposases, as well as some biocide/metal resistance genes. Virulence toxin genes as well as bacterial genera comprising many pathogens were more abundant here; the genus Acinetobacter, which is often associated with multidrug resistance and nosocomial infections, comprised up to 29% of the 16S rRNA reads, which to our best knowledge is unmatched in any other deeply sequenced metagenome. There was a strong correlation between the abundance of Acinetobacter and the OXA-58 carbapenemase gene. Our study shows that uncontrolled discharge of untreated urban waste can contribute to an overall increase of the abundance and diversity of ARGs in the environment, including those conferring resistance to last-resort antibiotics.", "doi": "10.1016/j.watres.2017.07.060", "pmid": "28780361", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0043-1354(17)30633-4"}, {"db": "MG-RAST", "description": "raw metagenomic sequencing data", "key": "19878"}], "notes": [], "created": "2017-11-03T16:22:29.646Z", "modified": "2024-01-16T13:48:47.324Z"}, {"entity": "publication", "iuid": "3696fbf5832447b98e3ff70736927e22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3696fbf5832447b98e3ff70736927e22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3696fbf5832447b98e3ff70736927e22"}}, "title": "Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Lona Durazo", "given": "Frida", "initials": "F"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "17", "issn": "1755-0998", "issue": "6", "title": "Mol Ecol Resour", "pages": "e111-e121", "issn-l": "1755-098X"}, "abstract": "Population-scale molecular studies of endangered and cryptic species are often limited by access to high-quality samples. The use of noninvasively collected samples or museum-preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300-fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla-generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double-barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field-collected faecal samples is a robust and reliable approach for population-wide studies of nonmodel organisms.", "doi": "10.1111/1755-0998.12699", "pmid": "28675688", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:21:38.460Z", "modified": "2024-01-16T13:48:47.331Z"}, {"entity": "publication", "iuid": "f892ff63669141bc8f46e7fd8d8fde48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f892ff63669141bc8f46e7fd8d8fde48"}}, "title": "SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Dahlberg", "given": "Johan", "initials": "J"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Karlsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-8949-2587", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df14bf33f3342408d624caa70d45b7c.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Viklund", "given": "Johan", "initials": "J"}, {"family": "K\u00e4h\u00e4ri", "given": "Andreas Kusalananda", "initials": "AK"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Che", "given": "Huiwen", "initials": "H"}, {"family": "Thutkawkorapin", "given": "Jessada", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Dahlberg", "given": "Mats", "initials": "M"}, {"family": "Hagberg", "given": "Jonas", "initials": "J", "orcid": "0000-0003-2370-6025", "researcher": {"href": "https://publications.scilifelab.se/researcher/181649773b3e451981f5ffb2da4c60b9.json"}}, {"family": "Jareborg", "given": "Niclas", "initials": "N", "orcid": "0000-0002-4520-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09533c4bd4174ecab9ba866d22a1e585.json"}}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Jonasson", "given": "Inger", "initials": "I"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Magnusson", "given": "Patrik Ke", "initials": "PK"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "25", "issn": "1476-5438", "issue": "11", "pages": "1253-1260", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website https://swefreq.nbis.se. A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.", "doi": "10.1038/ejhg.2017.130", "pmid": "28832569", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ejhg2017130"}, {"db": "pmc", "key": "PMC5765326"}], "notes": [], "created": "2017-08-24T14:18:14.989Z", "modified": "2024-01-16T13:48:47.338Z"}, {"entity": "publication", "iuid": "b616130aa5e24ecab64baeba6c16c0a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b616130aa5e24ecab64baeba6c16c0a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b616130aa5e24ecab64baeba6c16c0a8"}}, "title": "Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.", "authors": [{"family": "Svartstr\u00f6m", "given": "Olov", "initials": "O"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Terrapon", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3693-6017", "researcher": {"href": "https://publications.scilifelab.se/researcher/08f47757224649faa4a6e81854b8578f.json"}}, {"family": "Lombard", "given": "Vincent", "initials": "V"}, {"family": "de Bruijn", "given": "Ino", "initials": "I"}, {"family": "Malmsten", "given": "Jonas", "initials": "J", "orcid": "0000-0003-1868-3746", "researcher": {"href": "https://publications.scilifelab.se/researcher/31afb191067641c9b2190aa36db6d225.json"}}, {"family": "Dalin", "given": "Ann-Marie", "initials": "AM"}, {"family": "El Muller", "given": "Emilie", "initials": "E"}, {"family": "Shah", "given": "Pranjul", "initials": "P"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Henrissat", "given": "Bernard", "initials": "B"}, {"family": "Aspeborg", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8576-4370", "researcher": {"href": "https://publications.scilifelab.se/researcher/973b41980bd34391aa3be4e54b19ff2f.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "11", "pages": "2538-2551", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes. Unlike in other ruminants, Spirochaetes constituted a significant proportion of the community and our analyses indicate that the corresponding strains are primarily pectin digesters. Pectin-degrading genes were also common in MAGs of Ruminococcus, Fibrobacteres and Bacteroidetes and were overall overrepresented in the moose microbiome compared with other ruminants. Phylogenomic analyses revealed several clades within the Bacteriodetes without previously characterized genomes. Several of these MAGs encoded a large numbers of dockerins, a module usually associated with cellulosomes. The Bacteroidetes dockerins were often linked to CAZymes and sometimes encoded inside polysaccharide utilization loci, which has never been reported before. The almost 100 CAZyme-annotated genomes reconstructed in this study provide an in-depth view of an efficient lignocellulose-degrading microbiome and prospects for developing enzyme technology for biorefineries.", "doi": "10.1038/ismej.2017.108", "pmid": "28731473", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "EMS73237"}, {"db": "pmc", "key": "PMC5648042"}, {"db": "pii", "key": "ismej2017108"}], "notes": [], "created": "2017-11-03T16:11:39.460Z", "modified": "2024-01-16T13:48:47.346Z"}, {"entity": "publication", "iuid": "6fde580c283e4ad29b2f0f852b9d8da2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fde580c283e4ad29b2f0f852b9d8da2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fde580c283e4ad29b2f0f852b9d8da2"}}, "title": "High abundance and expression of transposases in bacteria from the Baltic Sea.", "authors": [{"family": "Vigil-Stenman", "given": "Theoden", "initials": "T"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Ekman", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "11", "issn": "1751-7370", "issue": "11", "pages": "2611-2623", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200\u2009\u03bcm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.", "doi": "10.1038/ismej.2017.114", "pmid": "28731472", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ismej2017114"}, {"db": "pmc", "key": "PMC5649170"}], "notes": [], "created": "2017-11-03T16:19:50.532Z", "modified": "2024-01-16T13:48:47.354Z"}, {"entity": "publication", "iuid": "10631255696544f194076164c1ab4128", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10631255696544f194076164c1ab4128.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10631255696544f194076164c1ab4128"}}, "title": "Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age.", "authors": [{"family": "Pujolar", "given": "J M", "initials": "JM", "orcid": "0000-0001-6406-583X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6671dcfa12b94390807a1c2a175f451d.json"}}, {"family": "Dal\u00e9n", "given": "L", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Hansen", "given": "M M", "initials": "MM", "orcid": "0000-0001-5372-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc21c1cf8e074f35a012494cdef48424.json"}}, {"family": "Madsen", "given": "J", "initials": "J"}], "type": "journal article", "published": "2017-11-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "22", "title": "Mol. Ecol.", "pages": "6270-6283", "issn-l": "0962-1083"}, "abstract": "We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, demographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the last glacial maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese, (2) the decline inferred during the Middle Ages is due to human persecution, and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.", "doi": "10.1111/mec.14374", "pmid": "28980346", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "BioProject", "description": "RAD-sequencing", "key": "PRJNA400851"}, {"db": "Dryad", "description": "Genotype data", "key": "https://doi.org/10.5061/dryad.c4r81"}], "notes": [], "created": "2017-11-03T16:21:37.140Z", "modified": "2021-07-07T20:31:10.703Z"}, {"entity": "publication", "iuid": "37e3547dbecb415db8dc52713feb0b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37e3547dbecb415db8dc52713feb0b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37e3547dbecb415db8dc52713feb0b69"}}, "title": "Efficient protein production by yeast requires global tuning of metabolism.", "authors": [{"family": "Huang", "given": "Mingtao", "initials": "M"}, {"family": "Bao", "given": "Jichen", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-10-25", "journal": {"volume": "8", "issn": "2041-1723", "issue": "1", "pages": "1131", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion.", "doi": "10.1038/s41467-017-00999-2", "pmid": "29070809", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-017-00999-2"}, {"db": "pmc", "key": "PMC5656615"}, {"db": "ENA", "description": "raw RNA-seq", "key": "ERP019558"}], "notes": [], "created": "2017-11-03T16:22:28.292Z", "modified": "2024-01-16T13:48:47.390Z"}, {"entity": "publication", "iuid": "293919f0d9c348b6b68db3fa0960d649", "links": {"self": {"href": "https://publications.scilifelab.se/publication/293919f0d9c348b6b68db3fa0960d649.json"}, "display": {"href": "https://publications.scilifelab.se/publication/293919f0d9c348b6b68db3fa0960d649"}}, "title": "Polysome-profiling in small tissue samples.", "authors": [{"family": "Liang", "given": "Shuo", "initials": "S"}, {"family": "Bellato", "given": "Hermano Martins", "initials": "HM"}, {"family": "Lorent", "given": "Julie", "initials": "J"}, {"family": "Lupinacci", "given": "Fernanda C S", "initials": "FCS"}, {"family": "Oertlin", "given": "Christian", "initials": "C"}, {"family": "van Hoef", "given": "Vincent", "initials": "V"}, {"family": "Andrade", "given": "Victor P", "initials": "VP"}, {"family": "Roff\u00e9", "given": "Mart\u00edn", "initials": "M"}, {"family": "Masvidal", "given": "Laia", "initials": "L"}, {"family": "Hajj", "given": "Glaucia N M", "initials": "GNM"}, {"family": "Larsson", "given": "Ola", "initials": "O"}], "type": "journal article", "published": "2017-10-23", "journal": {"volume": null, "issn": "1362-4962", "issue": null, "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Polysome-profiling is commonly used to study translatomes and applies laborious extraction of efficiently translated mRNA (associated with >3 ribosomes) from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for efficiently translated mRNA in only one or two fractions, thereby reducing sample handling 5-10-fold. The technique generates polysome-associated RNA with a quality reflecting the starting material and, when coupled with smart-seq2 single-cell RNA sequencing, translatomes in small tissues from biobanks can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associates with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in biobanks.", "doi": "10.1093/nar/gkx940", "pmid": "29069469", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4561642"}, {"db": "BioProject", "description": "raw RNA-seq", "key": "PRJNA390060"}], "notes": [], "created": "2017-11-03T16:22:26.268Z", "modified": "2024-01-16T13:48:47.401Z"}, {"entity": "publication", "iuid": "0531312ee42d448cb3d9ac4c140ea664", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0531312ee42d448cb3d9ac4c140ea664.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0531312ee42d448cb3d9ac4c140ea664"}}, "title": "Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.", "authors": [{"family": "Asp", "given": "Michaela", "initials": "M", "orcid": "0000-0001-5941-7220", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf1751a54e274e60b77290464b4d9733.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Felldin", "given": "Ulrika", "initials": "U"}, {"family": "L\u00f6fling", "given": "Marie", "initials": "M"}, {"family": "Fernandez Navarro", "given": "Jos\u00e9", "initials": "J"}, {"family": "Maaskola", "given": "Jonas", "initials": "J"}, {"family": "Eriksson", "given": "Maria J", "initials": "MJ"}, {"family": "Persson", "given": "Bengt", "initials": "B", "orcid": "0000-0003-3165-5344", "researcher": {"href": "https://publications.scilifelab.se/researcher/38f116ef0ed146419cb18e742c270c4a.json"}}, {"family": "Corbascio", "given": "Matthias", "initials": "M"}, {"family": "Persson", "given": "Hans", "initials": "H"}, {"family": "Linde", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-9039-6023", "researcher": {"href": "https://publications.scilifelab.se/researcher/632b5a1e903240d5a0bf0ccbe13a1890.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-10-11", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "12941", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.", "doi": "10.1038/s41598-017-13462-5", "pmid": "29021611", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-13462-5"}, {"db": "pmc", "key": "PMC5636908"}], "notes": [], "created": "2017-11-03T16:20:56.701Z", "modified": "2024-01-16T13:48:47.424Z"}, {"entity": "publication", "iuid": "8407c40d77d04cb2bde84500f396cddc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8407c40d77d04cb2bde84500f396cddc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8407c40d77d04cb2bde84500f396cddc"}}, "title": "Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Sachpazidou", "given": "Varvara", "initials": "V"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Hylander", "given": "Samuel", "initials": "S"}], "type": "journal article", "published": "2017-10-11", "journal": {"volume": "284", "issn": "1471-2954", "issue": "1864", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "An important characteristic of marine sediments is the oxygen concentration that affects many central metabolic processes. There has been a widespread increase in hypoxia in coastal systems (referred to as 'dead zones') mainly caused by eutrophication. Hence, it is central to understand the metabolism and ecology of eukaryotic life in sediments during changing oxygen conditions. Therefore, we sampled coastal 'dead zone' Baltic Sea sediment during autumn and spring, and analysed the eukaryotic metatranscriptome from field samples and after incubation in the dark under oxic or anoxic conditions. Bacillariophyta (diatoms) dominated the eukaryotic metatranscriptome in spring and were also abundant during autumn. A large fraction of the diatom RNA reads was associated with the photosystems suggesting a constitutive expression in darkness. Microscope observation showed intact diatom cells and these would, if hatched, represent a significant part of the pelagic phytoplankton biomass. Oxygenation did not significantly change the relative proportion of diatoms nor resulted in any major shifts in metabolic 'signatures'. By contrast, diatoms rapidly responded when exposed to light suggesting that light is limiting diatom development in hypoxic sediments. Hence, it is suggested that diatoms in hypoxic sediments are on 'standby' to exploit the environment if they reach suitable habitats.", "doi": "10.1098/rspb.2017.1617", "pmid": "28978732", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "rspb.2017.1617"}, {"db": "pmc", "key": "PMC5647304"}, {"db": "BioProject", "description": "Raw metatranscriptomic RNA data", "key": "PRJNA347538"}, {"db": "BioProject", "description": "Raw metagenome, 16S rRNA and metatranscriptome sequence data", "key": "PRJNA322450"}], "notes": [], "created": "2017-11-03T16:21:54.440Z", "modified": "2024-01-16T13:48:47.434Z"}, {"entity": "publication", "iuid": "7288c350f11e45b4986bd6fa6331f24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7288c350f11e45b4986bd6fa6331f24d"}}, "title": "Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.", "authors": [{"family": "Talla", "given": "Venkat", "initials": "V"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Kalsoom", "given": "Faheema", "initials": "F"}, {"family": "Dinca", "given": "Vlad", "initials": "V"}, {"family": "Vila", "given": "Roger", "initials": "R"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}], "type": "journal article", "published": "2017-10-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "10", "pages": "2491-2505", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643\u2009Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72\u2009Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.", "doi": "10.1093/gbe/evx163", "pmid": "28981642", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "4091610"}, {"db": "BioProject", "description": "Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (Leptidea) butterflies.", "key": "PRJEB21838"}, {"db": "GENBANK", "description": "Leptidea sinapis, whole genome shotgun sequencing project", "key": "FZQP00000000"}], "notes": [], "created": "2017-10-30T09:27:46.367Z", "modified": "2024-01-16T13:48:47.456Z"}, {"entity": "publication", "iuid": "3f6086e7614a4402bcc94904e166a97e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f6086e7614a4402bcc94904e166a97e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f6086e7614a4402bcc94904e166a97e"}}, "title": "NorWood: a gene expression resource for evo-devo studies of conifer wood development.", "authors": [{"family": "Jokipii-Lukkari", "given": "Soile", "initials": "S"}, {"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Tuominen", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2017-10-00", "journal": {"volume": "216", "issn": "1469-8137", "issue": "2", "pages": "482-494", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development. RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks. Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P.\u00a0abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A.\u00a0thaliana and P.\u00a0tremula, but not in P.\u00a0abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P.\u00a0abies. The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P.\u00a0abies.", "doi": "10.1111/nph.14458", "pmid": "28186632", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "ENA", "description": "raw RNA-seq", "key": "ERP017340"}], "notes": [], "created": "2017-11-03T16:21:20.692Z", "modified": "2024-01-16T13:48:47.485Z"}, {"entity": "publication", "iuid": "cd261cbdf4ce4347baaaf237956dccdd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd261cbdf4ce4347baaaf237956dccdd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd261cbdf4ce4347baaaf237956dccdd"}}, "title": "Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny", "authors": [{"family": "Rydin", "given": "Catarina", "initials": "C"}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Bremer", "given": "Birgitta", "initials": "B"}], "type": "journal-article", "published": "2017-10-00", "journal": {"volume": "104", "issn": "0002-9122", "issue": "10", "pages": "1522-1532", "title": "Am. J. Bot.", "issn-l": null}, "abstract": null, "doi": "10.3732/ajb.1700255", "pmid": "29885222", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:38.978Z", "modified": "2024-01-16T13:48:47.493Z"}, {"entity": "publication", "iuid": "d23e11e266a14e9d9e84db92232867a5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d23e11e266a14e9d9e84db92232867a5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d23e11e266a14e9d9e84db92232867a5"}}, "title": "Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria.", "authors": [{"family": "Quin", "given": "Jaclyn E", "initials": "JE"}, {"family": "Bujila", "given": "Ioana", "initials": "I"}, {"family": "Ch\u00e9rif", "given": "Mariama", "initials": "M"}, {"family": "Sanou", "given": "Guillaume S", "initials": "GS"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Vafa Homann", "given": "Manijeh", "initials": "M"}, {"family": "Rolicka", "given": "Anna", "initials": "A"}, {"family": "Sirima", "given": "Sodiomon B", "initials": "SB"}, {"family": "O'Connell", "given": "Mary A", "initials": "MA"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Troye-Blomberg", "given": "Marita", "initials": "M"}, {"family": "Nebie", "given": "Issa", "initials": "I"}, {"family": "\u00d6stlund Farrants", "given": "Ann-Kristin", "initials": "AK"}], "type": "journal article", "published": "2017-09-19", "journal": {"volume": "6", "issn": "2050-084X", "issue": null, "title": "Elife", "issn-l": "2050-084X"}, "abstract": "The Fulani ethnic group has relatively better protection from Plasmodium falciparum malaria, as reflected by fewer symptomatic cases of malaria, lower infection rates, and lower parasite densities compared to sympatric ethnic groups. However, the basis for this lower susceptibility to malaria by the Fulani is unknown. The incidence of classic malaria resistance genes are lower in the Fulani than in other sympatric ethnic populations, and targeted SNP analyses of other candidate genes involved in the immune response to malaria have not been able to account for the observed difference in the Fulani susceptibility to P.falciparum. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani to elucidate the mechanisms that confer the lower susceptibility to P.falciparum malaria. When we compared uninfected and infected Fulani individuals, in contrast to uninfected and infected individuals from the sympatric ethnic group Mossi, we observed a key difference: a strong transcriptional response was only detected in the monocyte fraction of the Fulani, where over 1000 genes were significantly differentially expressed upon P.falciparum infection.", "doi": "10.7554/eLife.29156", "pmid": "28923166", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5629023"}, {"db": "GEO", "description": "Sequence data", "key": "GSE100563"}], "notes": [], "created": "2017-11-03T16:19:28.128Z", "modified": "2020-01-21T13:56:11.453Z"}, {"entity": "publication", "iuid": "05b4dacde1b34c7db34d7a6b147d1346", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05b4dacde1b34c7db34d7a6b147d1346.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05b4dacde1b34c7db34d7a6b147d1346"}}, "title": "Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.", "authors": [{"family": "Yu", "given": "Nancy Y", "initials": "NY"}, {"family": "Bieder", "given": "Andrea", "initials": "A"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Mileti", "given": "Enrichetta", "initials": "E"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Fredholm", "given": "Bertil B", "initials": "BB"}, {"family": "Falk", "given": "Anna", "initials": "A"}, {"family": "Tapia-P\u00e1ez", "given": "Isabel", "initials": "I"}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2017-09-13", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "11458", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Caffeine is a widely consumed psychoactive substance, but little is known about the effects of caffeine stimulation on global gene expression changes in neurons. Here, we conducted gene expression profiling of human neuroepithelial stem cell-derived neurons, stimulated with normal consumption levels of caffeine (3\u2009\u03bcM and 10\u2009\u03bcM), over a period of 9\u2009h. We found dosage-dependent activation of immediate early genes after 1\u2009h. Neuronal projection development processes were up-regulated and negative regulation of axon extension processes were down-regulated at 3\u2009h. In addition, genes involved in extracellular matrix organization, response for wound healing, and regulation of immune system processes were down-regulated by caffeine at 3\u2009h. This study identified novel genes within the neuronal projection guidance pathways that respond to acute caffeine stimulation and suggests potential mechanisms for the effects of caffeine on neuronal cells.", "doi": "10.1038/s41598-017-11574-6", "pmid": "28904364", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-11574-6"}, {"db": "pmc", "key": "PMC5597620"}, {"db": "BioProject", "description": "raw RNA-seq", "key": "PRJEB20092"}], "notes": [], "created": "2017-11-03T16:18:37.631Z", "modified": "2024-01-16T13:48:47.529Z"}, {"entity": "publication", "iuid": "4a316c8916a44647a751f72482d76147", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a316c8916a44647a751f72482d76147.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a316c8916a44647a751f72482d76147"}}, "title": "Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2017-09-04", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": "1561", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.", "doi": "10.3389/fmicb.2017.01561", "pmid": "28928718", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5591341"}], "notes": [], "created": "2017-11-03T16:11:38.776Z", "modified": "2024-01-16T13:48:47.543Z"}, {"entity": "publication", "iuid": "f57321685c0b4169a4414640c3787e7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f57321685c0b4169a4414640c3787e7f"}}, "title": "The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.", "authors": [{"family": "Evkaikina", "given": "Anastasiia I", "initials": "AI"}, {"family": "Berke", "given": "Lidija", "initials": "L"}, {"family": "Romanova", "given": "Marina A", "initials": "MA"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Ivanova", "given": "Alexandra N", "initials": "AN"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}, {"family": "Pawlowski", "given": "Katharina", "initials": "K"}, {"family": "Voitsekhovskaja", "given": "Olga V", "initials": "OV"}], "type": "journal article", "published": "2017-09-01", "journal": {"volume": "9", "issn": "1759-6653", "issue": "9", "pages": "2444-2460", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls-that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap-not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY.We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants.The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509-514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.", "doi": "10.1093/gbe/evx169", "pmid": "28957460", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4097580"}, {"db": "pmc", "key": "PMC5622374"}, {"db": "BioProject", "description": "DNA sequencing data", "key": "PRJNA281995"}], "notes": [], "created": "2017-11-03T16:20:59.430Z", "modified": "2024-01-16T13:48:47.550Z"}, {"entity": "publication", "iuid": "481f7584fddd4db2a5d9f3833a7ed7e8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/481f7584fddd4db2a5d9f3833a7ed7e8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/481f7584fddd4db2a5d9f3833a7ed7e8"}}, "title": "Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.", "authors": [{"family": "Azimi", "given": "Alireza", "initials": "A"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Costa Svedman", "given": "Fernanda", "initials": "F"}, {"family": "Caramuta", "given": "Stefano", "initials": "S"}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15f303cb2044cfa81719700137e3603.json"}}, {"family": "Frostvik Stolt", "given": "Marianne", "initials": "M"}, {"family": "Kanter", "given": "Lena", "initials": "L"}, {"family": "Kharaziha", "given": "Pedram", "initials": "P"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Hertzman Johansson", "given": "Carolina", "initials": "C"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Egyhazi Brage", "given": "Suzanne", "initials": "S", "orcid": "0000-0002-0524-2346", "researcher": {"href": "https://publications.scilifelab.se/researcher/40eddeacb66f490089dbf72978d20721.json"}}], "type": "journal article", "published": "2017-08-31", "journal": {"volume": "8", "issn": "2041-4889", "issue": "8", "pages": "e3029", "title": "Cell Death Dis", "issn-l": "2041-4889"}, "abstract": "A majority of patients with BRAF-mutated metastatic melanoma respond to therapy with BRAF inhibitors (BRAFi), but relapses are common owing to acquired resistance. To unravel BRAFi resistance mechanisms we have performed gene expression and mass spectrometry based proteome profiling of the sensitive parental A375 BRAF V600E-mutated human melanoma cell line and of daughter cell lines with induced BRAFi resistance. Increased expression of two novel resistance candidates, aminopeptidase-N (CD13/ANPEP) and ETS transcription factor FLI1 was observed in the BRAFi-resistant daughter cell lines. In addition, increased levels of the previously reported resistance mediators, receptor tyrosine kinase ephrine receptor A2 (EPHA2) and the hepatocyte growth factor receptor MET were also identified. The expression of these proteins was assessed in matched tumor samples from melanoma patients obtained before BRAFi and after disease progression. MET was overexpressed in all progression samples while the expression of the other candidates varied between the individual patients. Targeting CD13/ANPEP by a blocking antibody induced apoptosis in both parental A375- and BRAFi-resistant daughter cells as well as in melanoma cells with intrinsic BRAFi resistance and led to dephosphorylation of EPHA2 on S897, previously demonstrated to cause inhibition of the migratory capacity. AKT and RSK, both reported to induce EPHA2 S897 phosphorylation, were also dephosphorylated after inhibition of CD13/ANPEP. FLI1 silencing also caused decreases in EPHA2 S897 phosphorylation and in total MET protein expression. In addition, silencing of FLI1 sensitized the resistant cells to BRAFi. Furthermore, we show that BRAFi in combination with the multi kinase inhibitor dasatinib can abrogate BRAFi resistance and decrease both EPHA2 S897 phosphorylation and total FLI1 protein expression. This is the first report presenting CD13/ANPEP and FLI1 as important mediators of resistance to BRAF inhibition with potential as drug targets in BRAFi refractory melanoma.", "doi": "10.1038/cddis.2017.406", "pmid": "29048432", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "Clinical Proteomics Mass spectrometry": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "cddis2017406"}, {"db": "pmc", "key": "PMC5596587"}], "notes": [], "created": "2017-10-17T07:53:20.719Z", "modified": "2021-07-08T11:36:54.639Z"}, {"entity": "publication", "iuid": "c000b2d71662419d80ada5c60423b8dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c000b2d71662419d80ada5c60423b8dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c000b2d71662419d80ada5c60423b8dd"}}, "title": "Identification of NCAN as a candidate gene for developmental dyslexia.", "authors": [{"family": "Einarsdottir", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "Peyrard-Janvid", "given": "Myriam", "initials": "M"}, {"family": "Darki", "given": "Fahimeh", "initials": "F"}, {"family": "Tuulari", "given": "Jetro J", "initials": "JJ"}, {"family": "Merisaari", "given": "Harri", "initials": "H", "orcid": "0000-0002-8515-5399", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca8ef9e0084e48db88fd47fd51dd23a4.json"}}, {"family": "Karlsson", "given": "Linnea", "initials": "L"}, {"family": "Scheinin", "given": "Noora M", "initials": "NM"}, {"family": "Saunavaara", "given": "Jani", "initials": "J"}, {"family": "Parkkola", "given": "Riitta", "initials": "R"}, {"family": "Kantoj\u00e4rvi", "given": "Katri", "initials": "K"}, {"family": "\u00c4mm\u00e4l\u00e4", "given": "Antti-Jussi", "initials": "AJ"}, {"family": "Yiu-Lin Yu", "given": "Nancy", "initials": "N", "orcid": "0000-0001-8321-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7b0ebe0de64edca6546aff2292c376.json"}}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Nopola-Hemmi", "given": "Jaana", "initials": "J"}, {"family": "Karlsson", "given": "Hasse", "initials": "H"}, {"family": "Paunio", "given": "Tiina", "initials": "T"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}, {"family": "Leinonen", "given": "Eira", "initials": "E"}, {"family": "Kere", "given": "Juha", "initials": "J", "orcid": "0000-0003-1974-0271", "researcher": {"href": "https://publications.scilifelab.se/researcher/102085fb1c3147ceaf8dcb7651df1303.json"}}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9294", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A whole-genome linkage analysis in a Finnish pedigree of eight cases with developmental dyslexia (DD) revealed several regions shared by the affected individuals. Analysis of coding variants from two affected individuals identified rs146011974G > A (Ala1039Thr), a rare variant within the NCAN gene co-segregating with DD in the pedigree. This variant prompted us to consider this gene as a putative candidate for DD. The RNA expression pattern of the NCAN gene in human tissues was highly correlated (R > 0.8) with that of the previously suggested DD susceptibility genes KIAA0319, CTNND2, CNTNAP2 and GRIN2B. We investigated the association of common variation in NCAN to brain structures in two data sets: young adults (Brainchild study, Sweden) and infants (FinnBrain study, Finland). In young adults, we found associations between a common genetic variant in NCAN, rs1064395, and white matter volume in the left and right temporoparietal as well as the left inferior frontal brain regions. In infants, this same variant was found to be associated with cingulate and prefrontal grey matter volumes. Our results suggest NCAN as a new candidate gene for DD and indicate that NCAN variants affect brain structure.", "doi": "10.1038/s41598-017-10175-7", "pmid": "28839234", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-10175-7"}, {"db": "pmc", "key": "PMC5570950"}], "notes": [], "created": "2017-10-17T09:24:33.409Z", "modified": "2024-01-16T13:48:47.593Z"}, {"entity": "publication", "iuid": "5521219aa1794ec98838a8591df79469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5521219aa1794ec98838a8591df79469"}}, "title": "Cerium oxide nanoparticles inhibit differentiation of neural stem cells.", "authors": [{"family": "Gliga", "given": "Anda R", "initials": "AR"}, {"family": "Edoff", "given": "Karin", "initials": "K"}, {"family": "Caputo", "given": "Fanny", "initials": "F"}, {"family": "K\u00e4llman", "given": "Thomas", "initials": "T"}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}, {"family": "Ghibelli", "given": "Lina", "initials": "L"}, {"family": "Traversa", "given": "Enrico", "initials": "E"}, {"family": "Ceccatelli", "given": "Sandra", "initials": "S"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2017-08-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "9284", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Cerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific \u03b23-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.", "doi": "10.1038/s41598-017-09430-8", "pmid": "28839176", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Integrated Microscopy Technologies Stockholm": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-09430-8"}, {"db": "pmc", "key": "PMC5570910"}, {"db": "ArrayExpress", "description": "raw RNA-seq", "key": "E-MTAB-4398"}], "notes": [], "created": "2017-10-05T09:22:50.002Z", "modified": "2021-07-05T13:48:51.542Z"}, {"entity": "publication", "iuid": "04d609a90c47487388785c1d3bb89419", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04d609a90c47487388785c1d3bb89419.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04d609a90c47487388785c1d3bb89419"}}, "title": "Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae).", "authors": [{"family": "Haddad", "given": "Nizar", "initials": "N", "orcid": "0000-0003-0250-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ff610b5673c4050a4e4377c48b2a372.json"}}, {"family": "Adjlane", "given": "Noureddine", "initials": "N"}, {"family": "Loucif-Ayad", "given": "Wahida", "initials": "W"}, {"family": "Dash", "given": "Abhinandita", "initials": "A"}, {"family": "S", "given": "Naganeeswaran", "initials": "N"}, {"family": "Rajashekar", "given": "Balaji", "initials": "B"}, {"family": "Al-Nakeeb", "given": "Kosai", "initials": "K", "orcid": "0000-0003-3432-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d87f93200b4f0ba3480a0f975e9cd9.json"}}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}], "type": "journal article", "published": "2017-08-22", "journal": {"volume": "2", "issn": "2380-2359", "issue": "2", "pages": "548-549", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "We present the complete mitochondrial genome of honey bee subspecies, Apis mellifera sahariensis (Apidae) belonging to the African lineage. The assembled circular genome has a length of 16,569 bp which comprises 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and AT rich region.", "doi": "10.1080/23802359.2017.1365647", "pmid": "33473895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1365647"}, {"db": "pmc", "key": "PMC7800622"}], "notes": [], "created": "2017-11-03T15:53:39.359Z", "modified": "2021-06-21T15:45:29.250Z"}, {"entity": "publication", "iuid": "9a66e1ee51af4d9dacf0840a88138663", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a66e1ee51af4d9dacf0840a88138663"}}, "title": "A pathology atlas of the human cancer transcriptome.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G", "orcid": "0000-0001-5232-6094", "researcher": {"href": "https://publications.scilifelab.se/researcher/c76df55999a74ebfaada13e0cc775de8.json"}}, {"family": "Benfeitas", "given": "Rui", "initials": "R", "orcid": "0000-0001-7972-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca09f57bdc44e7fa33a472f04859a4d.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Liu", "given": "Zhengtao", "initials": "Z", "orcid": "0000-0001-7803-6044", "researcher": {"href": "https://publications.scilifelab.se/researcher/53a62a58b12f4f4c87ebe4135826c91a.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Sanli", "given": "Kemal", "initials": "K"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B", "orcid": "0000-0002-5440-791X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e79e661083f49bf90cbbfc19670f404.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH", "orcid": "0000-0002-8330-0134", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd5ff31463cd4345a1fc8351e797ac7f.json"}}, {"family": "Djureinovic", "given": "Dijana", "initials": "D", "orcid": "0000-0002-1852-5409", "researcher": {"href": "https://publications.scilifelab.se/researcher/17058abc202c4da794e35722c1f234df.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2017-08-18", "journal": {"volume": "357", "issn": "1095-9203", "issue": "6352", "title": "Science", "pages": "eaan2507", "issn-l": "0036-8075"}, "abstract": "Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.", "doi": "10.1126/science.aan2507", "pmid": "28818916", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "357/6352/eaan2507"}], "notes": [], "created": "2017-11-03T16:19:27.334Z", "modified": "2024-01-16T13:48:47.600Z"}, {"entity": "publication", "iuid": "b85241f44e074517a87e335217e446e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b85241f44e074517a87e335217e446e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b85241f44e074517a87e335217e446e7"}}, "title": "Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-08-09", "journal": {"volume": "5", "issn": "2049-2618", "issue": "1", "pages": "96", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.\n\nCompared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.\n\nThese novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.", "doi": "10.1186/s40168-017-0311-5", "pmid": "28793929", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0311-5"}, {"db": "pmc", "key": "PMC5549381"}], "notes": [], "created": "2017-11-03T16:21:35.164Z", "modified": "2024-01-16T13:48:47.631Z"}, {"entity": "publication", "iuid": "b95838961321464bbddc6e42c65bc466", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b95838961321464bbddc6e42c65bc466.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b95838961321464bbddc6e42c65bc466"}}, "title": "Rho-associated kinase is a therapeutic target in neuroblastoma.", "authors": [{"family": "Dyberg", "given": "Cecilia", "initials": "C"}, {"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "Andonova", "given": "Teodora", "initials": "T"}, {"family": "Sveinbj\u00f6rnsson", "given": "Baldur", "initials": "B"}, {"family": "L\u00e4nnerholm-Palm", "given": "Jessika", "initials": "J"}, {"family": "Olsen", "given": "Thale K", "initials": "TK"}, {"family": "Forsberg", "given": "David", "initials": "D"}, {"family": "Herlenius", "given": "Eric", "initials": "E"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}, {"family": "Brodin", "given": "Bertha", "initials": "B"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Johnsen", "given": "John Inge", "initials": "JI"}, {"family": "Wickstr\u00f6m", "given": "Malin", "initials": "M"}], "type": "journal article", "published": "2017-08-08", "journal": {"volume": "114", "issn": "1091-6490", "issue": "32", "pages": "E6603-E6612", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Neuroblastoma is a peripheral neural system tumor that originates from the neural crest and is the most common and deadly tumor of infancy. Here we show that neuroblastoma harbors frequent mutations of genes controlling the Rac/Rho signaling cascade important for proper migration and differentiation of neural crest cells during neuritogenesis. RhoA is activated in tumors from neuroblastoma patients, and elevated expression of Rho-associated kinase (ROCK)2 is associated with poor patient survival. Pharmacological or genetic inhibition of ROCK1 and 2, key molecules in Rho signaling, resulted in neuroblastoma cell differentiation and inhibition of neuroblastoma cell growth, migration, and invasion. Molecularly, ROCK inhibition induced glycogen synthase kinase 3\u03b2-dependent phosphorylation and degradation of MYCN protein. Small-molecule inhibition of ROCK suppressed MYCN-driven neuroblastoma growth in TH-MYCN homozygous transgenic mice and MYCN gene-amplified neuroblastoma xenograft growth in nude mice. Interference with Rho/Rac signaling might offer therapeutic perspectives for high-risk neuroblastoma.", "doi": "10.1073/pnas.1706011114", "pmid": "28739902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1706011114"}, {"db": "pmc", "key": "PMC5559038"}], "notes": [], "created": "2017-11-03T16:22:26.931Z", "modified": "2024-01-16T13:48:47.638Z"}, {"entity": "publication", "iuid": "d24174e71c854ddfb3f607e66dfac13e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d24174e71c854ddfb3f607e66dfac13e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d24174e71c854ddfb3f607e66dfac13e"}}, "title": "PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.", "authors": [{"family": "K\u00e4mpe", "given": "Anders J", "initials": "AJ"}, {"family": "Costantini", "given": "Alice", "initials": "A"}, {"family": "Levy-Shraga", "given": "Yael", "initials": "Y"}, {"family": "Zeitlin", "given": "Leonid", "initials": "L"}, {"family": "Roschger", "given": "Paul", "initials": "P"}, {"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Paschalis", "given": "Eleftherios P", "initials": "EP"}, {"family": "Gamsjaeger", "given": "Sonja", "initials": "S"}, {"family": "Raas-Rothschild", "given": "Annick", "initials": "A"}, {"family": "H\u00f6vel", "given": "Matthias", "initials": "M"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Klaushofer", "given": "Klaus", "initials": "K"}, {"family": "Grasemann", "given": "Corinna", "initials": "C"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}], "type": "journal article", "published": "2017-08-04", "journal": {"volume": null, "issn": "1523-4681", "issue": null, "title": "J. Bone Miner. Res.", "issn-l": "0884-0431"}, "abstract": "Mutations in the PLS3 gene, encoding Plastin 3, were described in 2013 as a cause for X-linked primary bone fragility in children. The specific role of PLS3 in bone metabolism remains inadequately understood. Here we describe for the first time PLS3 deletions as the underlying cause for childhood-onset primary osteoporosis in 3 boys from 2 families. We carried out thorough clinical, radiological, and bone tissue analyses to explore the consequences of these deletions and to further elucidate the role of PLS3 in bone homeostasis. In family 1, the 2 affected brothers had a deletion of exons 4-16 (NM_005032) in PLS3, inherited from their healthy mother. In family 2, the index patient had a deletion involving the entire PLS3 gene (exons 1-16), inherited from his mother who had osteoporosis. The 3 patients presented in early childhood with severe spinal compression fractures involving all vertebral bodies. The 2 brothers in family 1 also displayed subtle dysmorphic facial features and both had developed a myopathic gait. Extensive analyses of a transiliac bone biopsy from 1 patient showed a prominent increase in osteoid volume, osteoid thickness, and in mineralizing lag time. Results from quantitative backscattered electron imaging and Raman microspectroscopy showed a significant hypomineralization of the bone. Together our results indicate that PLS3 deletions lead to severe childhood-onset osteoporosis resulting from defective bone matrix mineralization, suggesting a specific role for PLS3 in the mineralization process. \u00a9 2017 American Society for Bone and Mineral Research.", "doi": "10.1002/jbmr.3233", "pmid": "28777485", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:19:23.777Z", "modified": "2024-01-16T13:48:47.646Z"}, {"entity": "publication", "iuid": "b8df50988dd14ad9808582b7400559b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8df50988dd14ad9808582b7400559b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8df50988dd14ad9808582b7400559b1"}}, "title": "Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.", "authors": [{"family": "Broman", "given": "Elias", "initials": "E"}, {"family": "Jawad", "given": "Abbtesaim", "initials": "A"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Ni", "given": "Gaofeng", "initials": "G"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Sundkvist", "given": "Jan-Eric", "initials": "JE"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "28", "issn": "1572-9729", "issue": "4", "pages": "287-301", "title": "Biodegradation", "issn-l": "0923-9820"}, "abstract": "Wastewaters generated during mining and processing of metal sulfide ores are often acidic (pH\u00a0<\u00a03) and can contain significant concentrations of nitrate, nitrite, and ammonium from nitrogen based explosives. In addition, wastewaters from sulfide ore treatment plants and tailings ponds typically contain large amounts of inorganic sulfur compounds, such as thiosulfate and tetrathionate. Release of these wastewaters can lead to environmental acidification as well as an increase in nutrients (eutrophication) and compounds that are potentially toxic to humans and animals. Waters from cyanidation plants for gold extraction will often conjointly include toxic, sulfur containing thiocyanate. More stringent regulatory limits on the release of mining wastes containing compounds such as inorganic sulfur compounds, nitrate, and thiocyanate, along the need to increase production from sulfide mineral mining calls for low cost techniques to remove these pollutants under ambient temperatures (approximately 8\u00a0\u00b0C). In this study, we used both aerobic and anaerobic continuous cultures to successfully couple inorganic sulfur compound (i.e. thiosulfate and thiocyanate) oxidation for the removal of nitrogenous compounds under neutral to acidic pH at the low temperatures typical for boreal climates. Furthermore, the development of the respective microbial communities was identified over time by DNA sequencing, and found to contain a consortium including populations aligning within Flavobacterium, Thiobacillus, and Comamonadaceae lineages. This is the first study to remediate mining waste waters by coupling autotrophic thiocyanate oxidation to nitrate reduction at low temperatures and acidic pH by means of an identified microbial community.", "doi": "10.1007/s10532-017-9796-7", "pmid": "28577026", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10532-017-9796-7"}, {"db": "pmc", "key": "PMC5500686"}], "notes": [], "created": "2017-11-03T16:21:55.117Z", "modified": "2024-01-16T13:48:47.674Z"}, {"entity": "publication", "iuid": "e1513cc970f64beb9b07fcd904d17c04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1513cc970f64beb9b07fcd904d17c04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1513cc970f64beb9b07fcd904d17c04"}}, "title": "Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks", "authors": [{"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Liedvogel", "given": "Miriam", "initials": "M"}, {"family": "Larson", "given": "Keith", "initials": "K"}, {"family": "Sigeman", "given": "Hanna", "initials": "H"}, {"family": "Grahn", "given": "Mats", "initials": "M"}, {"family": "Wright", "given": "Anthony", "initials": "A"}, {"family": "\u00c5kesson", "given": "Susanne", "initials": "S"}, {"family": "Bensch", "given": "Staffan", "initials": "S"}], "type": "journal-article", "published": "2017-08-00", "journal": {"volume": "1", "issn": "2056-3744", "issue": "3", "pages": "155-168", "title": "Evolution Letters", "issn-l": "2056-3744"}, "abstract": null, "doi": "10.1002/evl3.15", "pmid": "30283646", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:41.042Z", "modified": "2024-01-16T13:48:47.681Z"}, {"entity": "publication", "iuid": "5ef10a01a35845139e73fd3393b8b2a7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ef10a01a35845139e73fd3393b8b2a7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ef10a01a35845139e73fd3393b8b2a7"}}, "title": "Data on haplotype-supported immunoglobulin germline gene inference.", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "13", "issn": "2352-3409", "issue": null, "pages": "620-640", "title": "Data Brief", "issn-l": "2352-3409"}, "abstract": "Data that defines IGHV (immunoglobulin heavy chain variable) germline gene inference using sequences of IgM-encoding transcriptomes obtained by Illumina MiSeq sequencing technology are described. Such inference is used to establish personalized germline gene sets for in-depth antibody repertoire studies and to detect new antibody germline genes from widely available immunoglobulin-encoding transcriptome data sets. Specifically, the data has been used to validate (Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery (DOI: 10.1016/j.molimm.2017.03.012) (Kirik et al., 2017) [1]) the inference process. This was accomplished based on analysis of the inferred germline genes' association to the donors' different haplotypes as defined by their different, expressed IGHJ alleles and/or IGHD genes/alleles. The data is important for development of validated germline gene databases containing entries inferred from immunoglobulin-encoding transcriptome sequencing data sets, and for generation of valid, personalized antibody germline gene repertoires.", "doi": "10.1016/j.dib.2017.06.031", "pmid": "28725665", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S2352-3409(17)30275-5"}, {"db": "pmc", "key": "PMC5502703"}], "notes": [], "created": "2017-11-03T16:22:11.988Z", "modified": "2024-01-16T13:48:47.688Z"}, {"entity": "publication", "iuid": "00efcc10c8fe4acdb9bdc477e661536f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/00efcc10c8fe4acdb9bdc477e661536f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/00efcc10c8fe4acdb9bdc477e661536f"}}, "title": "A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.", "authors": [{"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Rasi", "given": "Chiara", "initials": "C"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Ali", "given": "Abir S", "initials": "AS"}, {"family": "Gr\u00f6nberg", "given": "Malin", "initials": "M"}, {"family": "Welin", "given": "Staffan", "initials": "S"}, {"family": "Sorbye", "given": "Halfdan", "initials": "H"}, {"family": "Gr\u00f8nb\u00e6k", "given": "Henning", "initials": "H"}, {"family": "Cunningham", "given": "Janet L", "initials": "JL"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Tiensuu Janson", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "24", "issn": "1479-6821", "issue": "8", "pages": "427-443", "title": "Endocr. Relat. Cancer", "issn-l": "1351-0088"}, "abstract": "The genetics behind predisposition to small intestinal neuroendocrine tumors (SI-NETs) is largely unknown, but there is growing awareness of a familial form of the disease. We aimed to identify germline mutations involved in the carcinogenesis of SI-NETs. The strategy included next-generation sequencing of exome- and/or whole-genome of blood DNA, and in selected cases, tumor DNA, from 24 patients from 15 families with the history of SI-NETs. We identified seven candidate mutations in six genes that were further studied using 215 sporadic SI-NET patients. The result was compared with the frequency of the candidate mutations in three control cohorts with a total of 35,688 subjects. A heterozygous variant causing an amino acid substitution p.(Gly396Asp) in the MutY DNA glycosylase gene (MUTYH) was significantly enriched in SI-NET patients (minor allele frequencies 0.013 and 0.003 for patients and controls respectively) and resulted in odds ratio of 5.09 (95% confidence interval 1.56-14.74; P value\u2009=\u20090.0038). We also found a statistically significant difference in age at diagnosis between familial and sporadic SI-NETs. MUTYH is involved in the protection of DNA from mutations caused by oxidative stress. The inactivation of this gene leads to specific increase of G:C-\u2009>\u2009T:A transversions in DNA sequence and has been shown to cause various cancers in humans and experimental animals. Our results suggest that p.(Gly396Asp) in MUTYH, and potentially other mutations in additional members of the same DNA excision-repair pathway (such as the OGG1 gene) might be involved in driving the tumorigenesis leading to familial and sporadic SI-NETs.", "doi": "10.1530/ERC-17-0196", "pmid": "28634180", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ERC-17-0196"}, {"db": "pmc", "key": "PMC5527373"}], "notes": [], "created": "2017-10-17T09:23:36.141Z", "modified": "2024-01-16T13:48:47.705Z"}, {"entity": "publication", "iuid": "4bce9e4e56a24b87b1fc941557a2ade8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4bce9e4e56a24b87b1fc941557a2ade8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4bce9e4e56a24b87b1fc941557a2ade8"}}, "title": "Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "He", "given": "Mengxiao", "initials": "M"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2017-07-27", "journal": {"volume": "45", "issn": "1362-4962", "issue": "13", "pages": "e125", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable exploration of other forms of genetic variation; beyond studies of just nucleotide polymorphisms, such as compound heterozygosity and structural variations. Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices. Barcode generation and template amplification is performed simultaneously in a single enzymatic reaction, greatly simplifying the workflow and minimizing assay costs compared to alternative approaches. The method has been applied to phase multiple loci targeting all exons of the highly variable Human Leukocyte Antigen A (HLA-A) gene, with DNA from eight individuals present in the same assay. Barcode-based clustering of sequencing reads confirmed analysis of over 2000 independently assayed template molecules, with an average of 753 reads in support of called polymorphisms. Our results show unequivocal characterization of all alleles present, validated by correspondence against confirmed HLA database entries and haplotyping results from previous studies.", "doi": "10.1093/nar/gkx436", "pmid": "28525570", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3835310"}, {"db": "pmc", "key": "PMC5569991"}], "notes": [], "created": "2017-11-03T16:11:37.322Z", "modified": "2024-01-16T13:48:47.712Z"}, {"entity": "publication", "iuid": "fd87172e6f1e446c876e6805eeb45307", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd87172e6f1e446c876e6805eeb45307.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd87172e6f1e446c876e6805eeb45307"}}, "title": "PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.", "authors": [{"family": "K\u00e4mpe", "given": "A J", "initials": "AJ"}, {"family": "Costantini", "given": "A", "initials": "A"}, {"family": "M\u00e4kitie", "given": "R E", "initials": "RE"}, {"family": "J\u00e4ntti", "given": "N", "initials": "N"}, {"family": "Valta", "given": "H", "initials": "H"}, {"family": "M\u00e4yr\u00e4np\u00e4\u00e4", "given": "M", "initials": "M"}, {"family": "Kr\u00f6ger", "given": "H", "initials": "H"}, {"family": "Pekkinen", "given": "M", "initials": "M"}, {"family": "Taylan", "given": "F", "initials": "F"}, {"family": "Jiao", "given": "H", "initials": "H"}, {"family": "M\u00e4kitie", "given": "O", "initials": "O"}], "type": "journal article", "published": "2017-07-26", "journal": {"volume": null, "issn": "1433-2965", "issue": null, "title": "Osteoporos Int", "issn-l": "0937-941X"}, "abstract": "Altogether 95 children with primary bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Two children with multiple peripheral and spinal fractures and low BMD had novel disease-causing PLS3 variants. Children with milder phenotypes had no pathogenic variants. PLS3 screening is indicated in childhood-onset primary osteoporosis.\n\nThe study aimed to determine the role of pathogenic PLS3 variants in children's bone fragility and to elucidate the associated phenotypic features.\n\nTwo cohorts of children with bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Cohort I comprised 31 patients with childhood-onset primary osteoporosis of unknown etiology. Cohort II comprised 64 children who had sustained multiple fractures but were otherwise healthy. Clinical and radiological data were reviewed. Peripheral blood DNA was Sanger sequenced for coding exons and flanking intronic regions of PLS3.\n\nIn two patients of cohort I, where other common genetic causes had been excluded, we identified two novel disease-causing PLS3 variants. Patient 1 was a male with bilateral femoral fractures at 10\u00a0years, low BMD (Z-score -4.1; 18\u00a0years), and multiple vertebral compression fractures. He had a novel nonsense variant in PLS3. Patient 2 was a girl with multiple long bone and vertebral fractures and low BMD (Z-score -6.6 at 6\u00a0years). She had a de novo missense variant in PLS3; whole exome sequencing and array-CGH identified no other genetic causes. Iliac crest bone biopsies confirmed low-turnover osteoporosis in both patients. In cohort II, no pathogenic PLS3 variants were identified in any of the subjects.\n\nTwo novel disease-causing variants in PLS3 were identified in a boy and a girl with multiple peripheral and spinal fractures and very low BMD while no pathogenic variants were identified in children with less severe skeletal fragility. PLS3 screening is warranted in male and female patients with childhood-onset primary osteoporosis.", "doi": "10.1007/s00198-017-4150-9", "pmid": "28748388", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00198-017-4150-9"}, {"db": "pmc", "key": "PMC5624974"}], "notes": [], "created": "2017-11-03T16:21:20.042Z", "modified": "2024-01-16T13:48:47.719Z"}, {"entity": "publication", "iuid": "3da58343c0134a8797edd61438e049be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3da58343c0134a8797edd61438e049be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3da58343c0134a8797edd61438e049be"}}, "title": "Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.", "authors": [{"family": "Neogi", "given": "Ujjwal", "initials": "U"}, {"family": "Siddik", "given": "Abu Bakar", "initials": "AB"}, {"family": "Kalaghatgi", "given": "Prabhav", "initials": "P"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Marrone", "given": "Gaetano", "initials": "G"}, {"family": "S\u00f6nnerborg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "7", "issn": "2045-2322", "issue": "1", "pages": "6371", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A temporal increase in non-B subtypes has earlier been described in Sweden by us and we hypothesized that this increased viral heterogeneity may become a hotspot for the development of more complex and unique recombinant forms (URFs) if the epidemics converge. In the present study, we performed subtyping using four automated tools and phylogenetic analysis by RAxML of pol gene sequences (n\u2009=\u20095246) and HIV-1 near full-length genome (HIV-NFLG) sequences (n\u2009=\u2009104). A CD4+ T-cell decline trajectory algorithm was used to estimate time of HIV infection. Transmission clusters were identified using the family-joining method. The analysis of HIV-NFLG and pol gene described 10.6% (11/104) and 2.6% (137/5246) of the strains as URFs, respectively. An increasing trend of URFs was observed in recent years by both approaches (p\u2009=\u20090\u00b70082; p\u2009<\u20090\u00b70001). Transmission cluster analysis using the pol gene of all URFs identified 14 clusters with two to eight sequences. Larger transmission clusters of URFs (BF1 and 01B) were observed among MSM who mostly were sero-diagnosed in recent time. Understanding the increased appearance and transmission of URFs in recent years could have importance for public health interventions and the use of HIV-NFLG would provide better statistical support for such assessments.", "doi": "10.1038/s41598-017-06860-2", "pmid": "28744024", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-017-06860-2"}, {"db": "pmc", "key": "PMC5527090"}], "notes": [], "created": "2018-01-10T09:44:11.655Z", "modified": "2020-01-21T13:56:10.864Z"}, {"entity": "publication", "iuid": "4d52df4d173f48a3bb793b23674dbb2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d52df4d173f48a3bb793b23674dbb2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d52df4d173f48a3bb793b23674dbb2a"}}, "title": "Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2\u03b1 to tumor suppression.", "authors": [{"family": "Westerlund", "given": "Isabelle", "initials": "I"}, {"family": "Shi", "given": "Yao", "initials": "Y"}, {"family": "Toskas", "given": "Konstantinos", "initials": "K"}, {"family": "Fell", "given": "Stuart M", "initials": "SM"}, {"family": "Li", "given": "Shuijie", "initials": "S"}, {"family": "Surova", "given": "Olga", "initials": "O"}, {"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Nyman", "given": "Ulrika", "initials": "U"}, {"family": "Schlisio", "given": "Susanne", "initials": "S"}, {"family": "Holmberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2017-07-25", "journal": {"volume": "114", "issn": "1091-6490", "issue": "30", "pages": "E6137-E6146", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Neuroblastoma is a pediatric cancer characterized by variable outcomes ranging from spontaneous regression to life-threatening progression. High-risk neuroblastoma patients receive myeloablative chemotherapy with hematopoietic stem-cell transplant followed by adjuvant retinoid differentiation treatment. However, the overall survival remains low; hence, there is an urgent need for alternative therapeutic approaches. One feature of high-risk neuroblastoma is the high level of DNA methylation of putative tumor suppressors. Combining the reversibility of DNA methylation with the differentiation-promoting activity of retinoic acid (RA) could provide an alternative strategy to treat high-risk neuroblastoma. Here we show that treatment with the DNA-demethylating drug 5-Aza-deoxycytidine (AZA) restores high-risk neuroblastoma sensitivity to RA. Combined systemic distribution of AZA and RA impedes tumor growth and prolongs survival. Genome-wide analysis of treated tumors reveals that this combined treatment rapidly induces a HIF2\u03b1-associated hypoxia-like transcriptional response followed by an increase in neuronal gene expression and a decrease in cell-cycle gene expression. A small-molecule inhibitor of HIF2\u03b1 activity diminishes the tumor response to AZA+RA treatment, indicating that the increase in HIF2\u03b1 levels is a key component in tumor response to AZA+RA. The link between increased HIF2\u03b1 levels and inhibited tumor growth is reflected in large neuroblastoma patient datasets. Therein, high levels of HIF2\u03b1, but not HIF1\u03b1, significantly correlate with expression of neuronal differentiation genes and better prognosis but negatively correlate with key features of high-risk tumors, such as MYCN amplification. Thus, contrary to previous studies, our findings indicate an unanticipated tumor-suppressive role for HIF2\u03b1 in neuroblastoma.", "doi": "10.1073/pnas.1700655114", "pmid": "28696319", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1700655114"}, {"db": "pmc", "key": "PMC5544284"}], "notes": [], "created": "2018-01-10T09:44:13.665Z", "modified": "2020-01-21T13:56:10.878Z"}, {"entity": "publication", "iuid": "7783b21966b7491599b406ca7b2ba22a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7783b21966b7491599b406ca7b2ba22a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7783b21966b7491599b406ca7b2ba22a"}}, "title": "Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.", "authors": [{"family": "Morud", "given": "Julia", "initials": "J"}, {"family": "Ashouri", "given": "Arghavan", "initials": "A"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Ericson", "given": "Mia", "initials": "M"}, {"family": "S\u00f6derpalm", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181084", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Alcohol use disorder is a chronic relapsing brain disorder and a global health issue. Prolonged high alcohol consumption increases the risk for dependence development, a complex state that includes progressive alterations in brain function. The molecular mechanisms behind these changes remain to be fully disclosed, but several genes show altered expression in various regions of the rat brain even after modest alcohol exposure. The present study utilizes whole-transcriptome sequencing (RNA-seq) to investigate expression changes in the brain nucleus accumbens (NAc), an area of particular interest in addictive disorders, of alcohol consuming rats. The impact on gene expression after eight weeks of moderate voluntary alcohol consumption or voluntary consumption combined with forced excessive exposure was explored in two separate experiments. The results point to a lack of strong and consistent expression alterations in the NAc after alcohol exposure, suggesting that transcriptional effects of alcohol are weak or transient, or occur primarily in brain regions other than NAc.", "doi": "10.1371/journal.pone.0181084", "pmid": "28715440", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-11371"}, {"db": "pmc", "key": "PMC5513432"}, {"db": "GEO", "description": "Genome-wide analysis of nucleus accumbens gene expression after ethanol consumption in rat", "key": "GSE73627"}], "notes": [], "created": "2017-11-03T16:20:57.403Z", "modified": "2024-01-16T13:48:47.727Z"}, {"entity": "publication", "iuid": "a3a741c3582e433b9c7ff312acb3c831", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3a741c3582e433b9c7ff312acb3c831.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3a741c3582e433b9c7ff312acb3c831"}}, "title": "Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.", "authors": [{"family": "Lind", "given": "Ulrika", "initials": "U"}, {"family": "J\u00e4rv\u00e5", "given": "Michael", "initials": "M"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pingitore", "given": "Piero", "initials": "P"}, {"family": "Karlsson", "given": "Emil", "initials": "E"}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL"}, {"family": "Kamdal", "given": "Emelie", "initials": "E"}, {"family": "Sundell", "given": "Kristina", "initials": "K"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Havenhand", "given": "Jon", "initials": "J"}, {"family": "Eriksson", "given": "Leif A", "initials": "LA"}, {"family": "Hedfalk", "given": "Kristina", "initials": "K"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2017-07-17", "journal": {"volume": "12", "issn": "1932-6203", "issue": "7", "pages": "e0181192", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation.", "doi": "10.1371/journal.pone.0181192", "pmid": "28715506", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-17-05123"}, {"db": "pmc", "key": "PMC5513457"}, {"db": "GENBANK", "description": "sequence", "key": "KY508284"}, {"db": "GENBANK", "description": "sequence", "key": "KY508285"}, {"db": "GENBANK", "description": "sequence", "key": "KY508286"}, {"db": "GENBANK", "description": "sequence", "key": "KY508287"}, {"db": "GENBANK", "description": "sequence", "key": "KY508289"}, {"db": "GENBANK", "description": "sequence", "key": "KY508290"}, {"db": "GENBANK", "description": "sequence", "key": "KY508291"}, {"db": "GENBANK", "description": "sequence", "key": "KY508292"}, {"db": "GENBANK", "description": "sequence", "key": "KY508288"}, {"db": "GENBANK", "description": "sequence", "key": "KY508293"}, {"db": "GENBANK", "description": "sequence", "key": "KY508294"}, {"db": "GENBANK", "description": "sequence", "key": "KY508295"}, {"db": "GENBANK", "description": "sequence", "key": "KY508296"}, {"db": "GENBANK", "description": "sequence", "key": "KY508297"}, {"db": "GENBANK", "description": "sequence", "key": "KY508298"}], "notes": [], "created": "2017-10-17T09:32:54.872Z", "modified": "2024-01-16T13:48:47.750Z"}, {"entity": "publication", "iuid": "358a7e145b1147069d52e3cd9b925630", "links": {"self": {"href": "https://publications.scilifelab.se/publication/358a7e145b1147069d52e3cd9b925630.json"}, "display": {"href": "https://publications.scilifelab.se/publication/358a7e145b1147069d52e3cd9b925630"}}, "title": "Does antifouling paint select for antibiotic resistance?", "authors": [{"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Svensson", "given": "Carl Johan", "initials": "CJ"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2017-07-15", "journal": {"volume": "590-591", "issn": "1879-1026", "issue": null, "pages": "461-468", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis. Plastic panels with one side painted with copper and zinc-containing antifouling paint were submerged in a Swedish marina and biofilms from both sides of the panels were harvested after 2.5-4weeks. DNA was isolated from the biofilms and subjected to metagenomic sequencing. Biofilm bacteria were cultured on marine agar supplemented with tetracycline, gentamicin, copper sulfate or zinc sulfate. Biofilm communities from painted surfaces displayed lower taxonomic diversity and enrichment of Gammaproteobacteria. Bacteria from these communities showed increased resistance to both heavy metals and tetracycline but not to gentamicin. Significantly higher abundance of metal and biocide resistance genes was observed, whereas mobile antibiotic resistance genes were not enriched in these communities. In contrast, we found an enrichment of chromosomal RND efflux system genes, including such with documented ability to confer decreased susceptibility to both antibiotics and biocides/heavy metals. This was paralleled by increased abundances of integron-associated integrase and ISCR transposase genes. The results show that the heavy metal-based antifouling paint exerts a strong selection pressure on marine bacterial communities and can co-select for certain antibiotic-resistant bacteria, likely by favoring species and strains carrying genes that provide cross-resistance. Although this does not indicate an immediate risk for promotion of mobile antibiotic resistance, the clear increase of genes involved in mobilizing DNA provides a foundation for increased opportunities for gene transfer in such communities, which might also involve yet unknown resistance mechanisms.", "doi": "10.1016/j.scitotenv.2017.01.213", "pmid": "28284638", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(17)30230-9"}], "notes": [], "created": "2017-11-03T16:21:00.820Z", "modified": "2024-01-16T13:48:47.758Z"}, {"entity": "publication", "iuid": "c39c34f5c43d412487543502873a6519", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c39c34f5c43d412487543502873a6519.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c39c34f5c43d412487543502873a6519"}}, "title": "Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.", "authors": [{"family": "Mead", "given": "Adam J", "initials": "AJ"}, {"family": "Neo", "given": "Wen Hao", "initials": "WH"}, {"family": "Barkas", "given": "Nikolaos", "initials": "N"}, {"family": "Matsuoka", "given": "Sahoko", "initials": "S"}, {"family": "Giustacchini", "given": "Alice", "initials": "A"}, {"family": "Facchini", "given": "Raffaella", "initials": "R"}, {"family": "Thongjuea", "given": "Supat", "initials": "S"}, {"family": "Jamieson", "given": "Lauren", "initials": "L"}, {"family": "Booth", "given": "Christopher A G", "initials": "CAG"}, {"family": "Fordham", "given": "Nicholas", "initials": "N"}, {"family": "Di Genua", "given": "Cristina", "initials": "C"}, {"family": "Atkinson", "given": "Deborah", "initials": "D"}, {"family": "Chowdhury", "given": "Onima", "initials": "O"}, {"family": "Repapi", "given": "Emmanouela", "initials": "E"}, {"family": "Gray", "given": "Nicki", "initials": "N"}, {"family": "Kharazi", "given": "Shabnam", "initials": "S"}, {"family": "Clark", "given": "Sally-Ann", "initials": "SA"}, {"family": "Bouriez", "given": "Tiphaine", "initials": "T"}, {"family": "Woll", "given": "Petter", "initials": "P"}, {"family": "Suda", "given": "Toshio", "initials": "T"}, {"family": "Nerlov", "given": "Claus", "initials": "C"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW"}], "type": "journal article", "published": "2017-07-03", "journal": {"volume": "214", "issn": "1540-9538", "issue": "7", "pages": "2005-2021", "title": "J. Exp. Med.", "issn-l": "0022-1007"}, "abstract": "Although previous studies suggested that the expression of FMS-like tyrosine kinase 3 (Flt3) initiates downstream of mouse hematopoietic stem cells (HSCs), FLT3 internal tandem duplications (FLT3 ITDs) have recently been suggested to intrinsically suppress HSCs. Herein, single-cell interrogation found Flt3 mRNA expression to be absent in the large majority of phenotypic HSCs, with a strong negative correlation between Flt3 and HSC-associated gene expression. Flt3-ITD knock-in mice showed reduced numbers of phenotypic HSCs, with an even more severe loss of long-term repopulating HSCs, likely reflecting the presence of non-HSCs within the phenotypic HSC compartment. Competitive transplantation experiments established that Flt3-ITD compromises HSCs through an extrinsically mediated mechanism of disrupting HSC-supporting bone marrow stromal cells, with reduced numbers of endothelial and mesenchymal stromal cells showing increased inflammation-associated gene expression. Tumor necrosis factor (TNF), a cell-extrinsic potent negative regulator of HSCs, was overexpressed in bone marrow niche cells from FLT3-ITD mice, and anti-TNF treatment partially rescued the HSC phenotype. These findings, which establish that Flt3-ITD-driven myeloproliferation results in cell-extrinsic suppression of the normal HSC reservoir, are of relevance for several aspects of acute myeloid leukemia biology.", "doi": "10.1084/jem.20161418", "pmid": "28637883", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "jem.20161418"}, {"db": "pmc", "key": "PMC5502426"}], "notes": [], "created": "2018-01-10T09:44:12.302Z", "modified": "2020-01-21T13:56:10.871Z"}, {"entity": "publication", "iuid": "1fe52c77fec94407939714b233d44d7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fe52c77fec94407939714b233d44d7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fe52c77fec94407939714b233d44d7b"}}, "title": "Mineral Type Structures Soil Microbial Communities", "authors": [{"family": "Ahmed", "given": "Engy", "initials": "E"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Logue", "given": "J\u00fcrg B", "initials": "JB"}, {"family": "Br\u00fcchert", "given": "Volker", "initials": "V"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Holmstr\u00f6m", "given": "Sara J M", "initials": "SJM"}], "type": "journal-article", "published": "2017-07-03", "journal": {"volume": "34", "issn": "0149-0451", "issue": "6", "pages": "538-545", "title": "Geomicrobiology Journal", "issn-l": null}, "abstract": null, "doi": "10.1080/01490451.2016.1225868", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:57:48.638Z", "modified": "2024-01-16T13:48:47.765Z"}, {"entity": "publication", "iuid": "e81cd30a07184c74adb303274bd88923", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e81cd30a07184c74adb303274bd88923.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e81cd30a07184c74adb303274bd88923"}}, "title": "Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).", "authors": [{"family": "Sullivan", "given": "Alexis R", "initials": "AR"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Thompson", "given": "Stacey Lee", "initials": "SL"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Wang", "given": "Xiao-Ru", "initials": "XR"}], "type": "journal article", "published": "2017-07-01", "journal": {"volume": "34", "issn": "1537-1719", "issue": "7", "pages": "1689-1701", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of \u223c35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.", "doi": "10.1093/molbev/msx111", "pmid": "28383641", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3104592"}, {"db": "pmc", "key": "PMC5455968"}], "notes": [], "created": "2017-11-03T16:22:17.119Z", "modified": "2024-01-16T13:48:47.773Z"}, {"entity": "publication", "iuid": "6eaf552089d04408868b0adaa7a16350", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6eaf552089d04408868b0adaa7a16350.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6eaf552089d04408868b0adaa7a16350"}}, "title": "Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.", "authors": [{"family": "Andersson", "given": "Kristina E", "initials": "KE"}, {"family": "Chawade", "given": "Aakash", "initials": "A"}, {"family": "Thuresson", "given": "Narda", "initials": "N"}, {"family": "Rascon", "given": "Ana", "initials": "A"}, {"family": "\u00d6ste", "given": "Rickard", "initials": "R"}, {"family": "Sterner", "given": "Olov", "initials": "O"}, {"family": "Olsson", "given": "Olof", "initials": "O"}, {"family": "Hellstrand", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "61", "issn": "1613-4133", "issue": "7", "title": "Mol Nutr Food Res", "issn-l": "1613-4125"}, "abstract": "The molecular mechanisms underlying the cholesterol-lowering properties of oats are only partly known. To study possible pathways involved, we investigated gene expressions in the liver and small intestine of mice fed oats.\n\nCholesterol and bile acids were analyzed in plasma and feces from LDL-receptor deficient (LDLr(-/-) ) mice fed Western diet with wholegrain oats. A transcriptome analysis of mRNA from liver and jejunum was performed together with quantitative RT-PCR. Oat-fed mice had lower levels of plasma lipids and increased levels of bile acids and cholesterol in feces compared with controls. Two hundred thirty nine genes in jejunum and 25 genes in liver were differentially expressed (FDR corrected p < 0.05). The most affected biological process in jejunum was lipid biosynthesis and regulation. The apical sodium-dependent bile acid transporter (ASBT, Slc10a) and the intracellular bile acid binding protein (Fabp6) were both upregulated, whereas small heterodimer partner-1 (Shp-1) and apolipoprotein CII (Apoc2) were downregulated.\n\nWhole oats attenuated responses typically induced by high-fat diet. Increased expression of genes for intestinal bile acid uptake following oat consumption suggests retention in the gut lumen rather than decreased uptake capacity as cause for the increased bile acid excretion and the concomitant reduction of plasma cholesterol.", "doi": "10.1002/mnfr.201600874", "pmid": "28205325", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:18:36.937Z", "modified": "2024-01-16T13:48:47.781Z"}, {"entity": "publication", "iuid": "fed9a0e44bda4fa89406ae38f21e2413", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fed9a0e44bda4fa89406ae38f21e2413.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fed9a0e44bda4fa89406ae38f21e2413"}}, "title": "Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2.", "authors": [{"family": "Pasanen", "given": "P", "initials": "P"}, {"family": "M\u00e4kinen", "given": "J", "initials": "J"}, {"family": "Myllykangas", "given": "L", "initials": "L"}, {"family": "Guerreiro", "given": "R", "initials": "R"}, {"family": "Bras", "given": "J", "initials": "J"}, {"family": "Valori", "given": "M", "initials": "M"}, {"family": "Viitanen", "given": "M", "initials": "M"}, {"family": "Baumann", "given": "M", "initials": "M"}, {"family": "Tienari", "given": "P J", "initials": "PJ"}, {"family": "P\u00f6yh\u00f6nen", "given": "M", "initials": "M"}, {"family": "Baumann", "given": "P", "initials": "P"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "136", "issn": "1600-0404", "issue": "1", "pages": "59-63", "title": "Acta Neurol. Scand.", "issn-l": "0001-6314"}, "abstract": "Primary familial brain calcification (PFBC) is a rare neurological disease often inherited as a dominant trait. Mutations in four genes (SLC20A2, PDGFB, PDGFRB, and XPR1) have been reported in patients with PFBC. Of these, point mutations or small deletions in SLC20A2 are most common. Thus far, only one large deletion covering entire SLC20A2 and several smaller, exonic deletions of SLC20A2 have been reported. The aim of this study was to identify the causative gene defect in a Finnish PFBC family with three affected patients.\n\nA Finnish family with three PFBC patients and five unaffected subjects was studied. Sanger sequencing was used to exclude mutations in the coding and splice site regions of SLC20A2, PDGFRB, and PDGFB. Whole-exome (WES) and whole-genome sequencing (WGS) were performed to identify the causative mutation. A SNP array was used in segregation analysis.\n\nCopy number analysis of the WGS data revealed a heterozygous deletion of ~578\u00a0kb on chromosome 8. The deletion removes the 5' UTR region, the noncoding exon 1 and the putative promoter region of SLC20A2 as well as the coding regions of six other genes.\n\nOur results support haploinsufficiency of SLC20A2 as a pathogenetic mechanism in PFBC. Analysis of copy number variations (CNVs) is emerging as a crucial step in the molecular genetic diagnostics of PFBC, and it should not be limited to coding regions, as causative variants may reside in the noncoding parts of known disease-associated genes.", "doi": "10.1111/ane.12697", "pmid": "27726124", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:01:04.288Z", "modified": "2020-01-21T13:56:09.131Z"}, {"entity": "publication", "iuid": "c821e88dea2e412b8fe53454a68c5fb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c821e88dea2e412b8fe53454a68c5fb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c821e88dea2e412b8fe53454a68c5fb0"}}, "title": "Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.", "authors": [{"family": "Kirik", "given": "Ufuk", "initials": "U"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Ohlin", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "87", "issn": "1872-9142", "issue": null, "pages": "12-22", "title": "Mol. Immunol.", "issn-l": "0161-5890"}, "abstract": "Analysis of antibody repertoire development and specific antibody responses important for e.g. autoimmune conditions, allergy, and protection against disease is supported by high throughput sequencing and associated bioinformatics pipelines that describe the diversity of the encoded antibody variable domains. Proper assignment of sequences to germline genes are important for many such processes, for instance in the analysis of somatic hypermutation. Germline gene inference from antibody-encoding transcriptomes, by using tools such as TIgGER or IgDiscover, has a potential to enhance the quality of such analyses. These tools may also be used to identify germline genes not previously known. In this study, we exploited such software for germline gene inference and define aspects of analysis settings and pre-existing knowledge of germline genes that affect the outcome of gene inference. Furthermore, we demonstrate the capacity of IGHJ and IGHD haplotype inference, whenever subjects are heterozygous with respect to such genes, to lend support to IGHV gene inference in general, and to the identification of novel alleles presently not recognized by germline gene reference directories. We propose that such haplotype analysis shall, whenever possible, be used in future best practice to support the outcome of germline gene inference. IGHJ-directed haplotype inference was also used to identify haplotypes not expressing some IGHV germline genes. In particular, we identified a haplotype that did not express several major germline genes such as IGHV1-8, IGHV3-9, IGHV3-15, IGHV1-18, IGHV3-21, and IGHV3-23. We envisage that haplotype analysis will provide an efficient approach to identify subjects for further studies of the link between the available immunoglobulin repertoire and outcomes of immune responses.", "doi": "10.1016/j.molimm.2017.03.012", "pmid": "28388445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0161-5890(17)30081-0"}], "notes": [], "created": "2017-11-03T16:22:12.638Z", "modified": "2024-01-16T13:48:47.788Z"}, {"entity": "publication", "iuid": "e1ee87b50807452bbdaa71bc517f10ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1ee87b50807452bbdaa71bc517f10ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1ee87b50807452bbdaa71bc517f10ca"}}, "title": "Genomewide analysis of admixture and adaptation in the Africanized honeybee.", "authors": [{"family": "Nelson", "given": "Ronald M", "initials": "RM"}, {"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Sim\u00f5es", "given": "Zil\u00e1 Luz Paulino", "initials": "ZLP"}, {"family": "Lawson", "given": "Daniel J", "initials": "DJ"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}], "type": "journal article", "published": "2017-07-00", "journal": {"volume": "26", "issn": "1365-294X", "issue": "14", "pages": "3603-3617", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60\u00a0years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole-genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0\u00a0years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.", "doi": "10.1111/mec.14122", "pmid": "28378497", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "BioProject", "description": "Population-scale sequencing of Apis mellifera and Apis cerana", "key": "PRJNA236426"}, {"db": "BioProject", "description": "Africanized honeybee (Apis mellifera) sequencing", "key": "PRJNA350769"}], "notes": [], "created": "2017-11-02T13:51:52.946Z", "modified": "2024-01-16T13:48:47.796Z"}, {"entity": "publication", "iuid": "b81d4cdfd4e04cea8794379691537941", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b81d4cdfd4e04cea8794379691537941.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b81d4cdfd4e04cea8794379691537941"}}, "title": "2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.", "authors": [{"family": "Hernandez-Castro", "given": "Luis E", "initials": "LE"}, {"family": "Paterno", "given": "Marta", "initials": "M"}, {"family": "Villac\u00eds", "given": "Anita G", "initials": "AG"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Costales", "given": "Jaime A", "initials": "JA"}, {"family": "De Noia", "given": "Michele", "initials": "M"}, {"family": "Oca\u00f1a-Mayorga", "given": "Sof\u00eda", "initials": "S"}, {"family": "Yumiseva", "given": "Cesar A", "initials": "CA"}, {"family": "Grijalva", "given": "Mario J", "initials": "MJ"}, {"family": "Llewellyn", "given": "Martin S", "initials": "MS"}], "type": "evaluation studies", "published": "2017-07-00", "journal": {"volume": "11", "issn": "1935-2735", "issue": "7", "pages": "e0005710", "title": "PLoS Negl Trop Dis", "issn-l": "1935-2727"}, "abstract": "Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses.\n\nThe 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area.\n\nOur findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment.", "doi": "10.1371/journal.pntd.0005710", "pmid": "28723901", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PNTD-D-16-01890"}, {"db": "pmc", "key": "PMC5536387"}], "notes": [], "created": "2017-11-03T16:19:49.882Z", "modified": "2024-01-16T13:48:47.833Z"}, {"entity": "publication", "iuid": "7c8cc7a768524b84be600507b658f4b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c8cc7a768524b84be600507b658f4b9"}}, "title": "The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.", "authors": [{"family": "Gopalakrishnan", "given": "Shyam", "initials": "S"}, {"family": "Samaniego Castruita", "given": "Jose A", "initials": "JA"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Kuderna", "given": "Lukas F K", "initials": "LFK"}, {"family": "R\u00e4ikk\u00f6nen", "given": "Jannikke", "initials": "J"}, {"family": "Petersen", "given": "Bent", "initials": "B"}, {"family": "Sicheritz-Ponten", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}, {"family": "Larson", "given": "Greger", "initials": "G"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Hansen", "given": "Anders J", "initials": "AJ"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}], "type": "journal article", "published": "2017-06-29", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "495", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference.\n\nReassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples.\n\nIn conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.", "doi": "10.1186/s12864-017-3883-3", "pmid": "28662691", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3883-3"}, {"db": "pmc", "key": "PMC5492679"}], "notes": [], "created": "2017-11-03T16:21:39.181Z", "modified": "2021-07-07T20:31:10.838Z"}, {"entity": "publication", "iuid": "5f80f81f0f7c4ae7ab8b10c643e0c47c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f80f81f0f7c4ae7ab8b10c643e0c47c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f80f81f0f7c4ae7ab8b10c643e0c47c"}}, "title": "Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.", "authors": [{"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ"}, {"family": "Kim", "given": "Young-Mo", "initials": "YM"}, {"family": "Wei", "given": "Siwei", "initials": "S"}, {"family": "Nicora", "given": "Carrie D", "initials": "CD"}, {"family": "Fillmore", "given": "Thomas L", "initials": "TL"}, {"family": "Purvine", "given": "Samuel O", "initials": "SO"}, {"family": "Webb-Robertson", "given": "Bobbie-Jo", "initials": "BJ"}, {"family": "Smith", "given": "Richard D", "initials": "RD"}, {"family": "Baker", "given": "Scott E", "initials": "SE"}, {"family": "Metz", "given": "Thomas O", "initials": "TO"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-06-20", "journal": {"volume": "8", "issn": "2150-7511", "issue": "3", "title": "MBio", "issn-l": null}, "abstract": "The yeast Yarrowia lipolytica is a potent accumulator of lipids, and lipogenesis in this organism can be influenced by a variety of factors, such as genetics and environmental conditions. Using a multifactorial study, we elucidated the effects of both genetic and environmental factors on regulation of lipogenesis in Y.\u00a0lipolytica and identified how two opposite regulatory states both result in lipid accumulation. This study involved comparison of a strain overexpressing diacylglycerol acyltransferase (DGA1) with a control strain grown under either nitrogen or carbon limitation conditions. A strong correlation was observed between the responses on the transcript and protein levels. Combination of DGA1 overexpression with nitrogen limitation resulted in a high level of lipid accumulation accompanied by downregulation of several amino acid biosynthetic pathways, including that of leucine in particular, and these changes were further correlated with a decrease in metabolic fluxes. This downregulation was supported by the measured decrease in the level of 2-isopropylmalate, an intermediate of leucine biosynthesis. Combining the multi-omics data with putative transcription factor binding motifs uncovered a contradictory role for TORC1 in controlling lipid accumulation, likely mediated through 2-isopropylmalate and a Leu3-like transcription factor.IMPORTANCE The ubiquitous metabolism of lipids involves refined regulation, and an enriched understanding of this regulation would have wide implications. Various factors can influence lipid metabolism, including the environment and genetics. We demonstrated, using a multi-omics and multifactorial experimental setup, that multiple factors affect lipid accumulation in the yeast Yarrowia lipolytica Using integrative analysis, we identified novel interactions between nutrient restriction and genetic factors involving regulators that are highly conserved among eukaryotes. Given that lipid metabolism is involved in many diseases but is also vital to the development of microbial cell factories that can provide us with sustainable fuels and oleochemicals, we envision that our report introduces foundational work to further unravel the regulation of lipid accumulation in eukaryal cells.", "doi": "10.1128/mBio.00857-17", "pmid": "28634240", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mBio.00857-17"}, {"db": "pmc", "key": "PMC5478895"}], "notes": [], "created": "2017-11-03T16:22:28.954Z", "modified": "2024-01-16T13:48:47.862Z"}, {"entity": "publication", "iuid": "420b235c51914d58af7a8184175a8059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/420b235c51914d58af7a8184175a8059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/420b235c51914d58af7a8184175a8059"}}, "title": "Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.", "authors": [{"family": "Neubeck", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Ivarsson", "given": "Magnus", "initials": "M"}, {"family": "Hosg\u00f6rmez", "given": "Hakan", "initials": "H"}, {"family": "\u00d6zcan", "given": "Dogacan", "initials": "D"}, {"family": "Broman", "given": "Curt", "initials": "C"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-06-15", "journal": {"volume": "83", "issn": "1098-5336", "issue": "12", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "The surface waters at the ultramafic ophiolitic outcrop in Chimaera, Turkey, are characterized by high pH values and high metal levels due to the percolation of fluids through areas of active serpentinization. We describe the influence of the liquid chemistry, mineralogy, and H2 and CH4 levels on the bacterial community structure in a semidry, exposed, ultramafic environment. The bacterial and archaeal community structures were monitored using Illumina sequencing targeting the 16S rRNA gene. At all sampling points, four phyla, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, accounted for the majority of taxa. Members of the Chloroflexi phylum dominated low-diversity sites, whereas Proteobacteria dominated high-diversity sites. Methane, nitrogen, iron, and hydrogen oxidizers were detected as well as archaea and metal-resistant bacteria.IMPORTANCE Our study is a comprehensive microbial investigation of the Chimaera ophiolite. DNA has been extracted from 16 sites in the area and has been studied from microbial and geochemical points of view. We describe a microbial community structure that is dependent on terrestrial, serpentinization-driven abiotic H2, which is poorly studied due to the rarity of these environments on Earth.", "doi": "10.1128/AEM.03430-16", "pmid": "28389534", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "AEM.03430-16"}, {"db": "pmc", "key": "PMC5452829"}], "notes": [], "created": "2017-11-03T16:19:53.338Z", "modified": "2020-01-21T13:56:09.096Z"}, {"entity": "publication", "iuid": "3a3c6631eadb4decbde40c86edda9348", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a3c6631eadb4decbde40c86edda9348.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a3c6631eadb4decbde40c86edda9348"}}, "title": "Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.", "authors": [{"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Pinder", "given": "Matthew I M", "initials": "MIM"}, {"family": "Johansson", "given": "Oskar N", "initials": "ON"}, {"family": "Kourtchenko", "given": "Olga", "initials": "O"}, {"family": "Godhe", "given": "Anna", "initials": "A"}, {"family": "Clarke", "given": "Adrian K", "initials": "AK"}], "type": "journal article", "published": "2017-06-01", "journal": {"volume": "5", "issn": "2169-8287", "issue": "22", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "We present the genome of Roseovarius mucosus strain SMR3, a marine bacterium isolated from the diatom Skeletonema marinoi strain RO5AC sampled from top layer sediments at 14\u00a0m depth. Its 4,381,426\u00a0bp genome consists of a circular chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).", "doi": "10.1128/genomeA.00394-17", "pmid": "28572309", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5/22/e00394-17"}, {"db": "pmc", "key": "PMC5454192"}], "notes": [], "created": "2017-10-30T13:56:28.143Z", "modified": "2024-01-16T13:48:47.888Z"}, {"entity": "publication", "iuid": "d704cde438624d95bc290a353f9f47c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d704cde438624d95bc290a353f9f47c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d704cde438624d95bc290a353f9f47c4"}}, "title": "Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability", "authors": [{"family": "Mogodiniyai Kasmaei", "given": "K", "initials": "K"}, {"family": "Dicksved", "given": "J", "initials": "J"}, {"family": "Sp\u00f6rndly", "given": "R", "initials": "R"}, {"family": "Ud\u00e9n", "given": "P", "initials": "P"}], "type": "journal-article", "published": "2017-06-00", "journal": {"volume": "72", "issn": "0142-5242", "issue": "2", "pages": "281-289", "title": "Grass Forage Sci", "issn-l": null}, "abstract": null, "doi": "10.1111/gfs.12238", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:58:06.074Z", "modified": "2024-01-16T13:48:47.898Z"}, {"entity": "publication", "iuid": "9ffdf7a669174f9b940bb01c93fab8a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ffdf7a669174f9b940bb01c93fab8a9"}}, "title": "A subcellular map of the human proteome.", "authors": [{"family": "Thul", "given": "Peter J", "initials": "PJ", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1441c2fca5d4946987ec975986fcfa2.json"}}, {"family": "\u00c5kesson", "given": "Lovisa", "initials": "L", "orcid": "0000-0002-2387-3491", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b0ca6c2a8f64be89222a6029885b08c.json"}}, {"family": "Wiking", "given": "Mikaela", "initials": "M", "orcid": "0000-0002-6368-6690", "researcher": {"href": "https://publications.scilifelab.se/researcher/b69baef540a14859a7b4fd966c3b9245.json"}}, {"family": "Mahdessian", "given": "Diana", "initials": "D", "orcid": "0000-0003-0750-1070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc22f13eb21a4c75a6e7cad7686bcc8a.json"}}, {"family": "Geladaki", "given": "Aikaterini", "initials": "A", "orcid": "0000-0002-0530-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/28081295132343c5bfc4b1e9bcfb8201.json"}}, {"family": "Ait Blal", "given": "Hammou", "initials": "H"}, {"family": "Alm", "given": "Tove", "initials": "T", "orcid": "0000-0002-2643-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0b5ee89148475581faf42ea53d61bd.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Bj\u00f6rk", "given": "Lars", "initials": "L", "orcid": "0000-0002-8116-882X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1092280955d44d1f99258f4f812fb6c7.json"}}, {"family": "Breckels", "given": "Lisa M", "initials": "LM", "orcid": "0000-0001-8918-7171", "researcher": {"href": "https://publications.scilifelab.se/researcher/3efbca65f39d4f7aa8df049a39e0c8a9.json"}}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Fall", "given": "Jenny", "initials": "J"}, {"family": "Gatto", "given": "Laurent", "initials": "L", "orcid": "0000-0002-1520-2268", "researcher": {"href": "https://publications.scilifelab.se/researcher/242f5219a40547439c0cc4b07e26e71d.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Hjelmare", "given": "Martin", "initials": "M", "orcid": "0000-0001-7375-9681", "researcher": {"href": "https://publications.scilifelab.se/researcher/80019f26676347d5b6c4124d63eeaf86.json"}}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S", "orcid": "0000-0002-6428-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb2e42e0ef0247ba9365148ab2c164c0.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Mulvey", "given": "Claire M", "initials": "CM", "orcid": "0000-0002-2989-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc08b919bd8a423f8a6df8b880979045.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "Rockberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-9977-5724", "researcher": {"href": "https://publications.scilifelab.se/researcher/34ad1d3b1313460583a16329a0143a1d.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R", "orcid": "0000-0001-8787-8868", "researcher": {"href": "https://publications.scilifelab.se/researcher/83314cf7a93543bf9cd6f68f9657e99e.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-8800-8469", "researcher": {"href": "https://publications.scilifelab.se/researcher/9046f902d0624af0969c4409351f22ba.json"}}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP", "orcid": "0000-0001-6176-108X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2a96138841741f9acff4a50100c2a25.json"}}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Winsnes", "given": "Casper", "initials": "C", "orcid": "0000-0002-0028-5865", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a64c707c8b54b6bbd31dae6485a1392.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2017-05-26", "journal": {"volume": "356", "issn": "1095-9203", "issue": "6340", "pages": null, "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.", "doi": "10.1126/science.aal3321", "pmid": "28495876", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Spatial Proteomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aal3321"}], "notes": [], "created": "2017-10-31T15:27:28.787Z", "modified": "2024-01-16T13:48:47.941Z"}, {"entity": "publication", "iuid": "914e667e695641e7827adaf9b0dcf69b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/914e667e695641e7827adaf9b0dcf69b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/914e667e695641e7827adaf9b0dcf69b"}}, "title": "Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.", "authors": [{"family": "V\u00e4remo", "given": "Leif", "initials": "L"}, {"family": "Henriksen", "given": "Tora Ida", "initials": "TI"}, {"family": "Scheele", "given": "Camilla", "initials": "C"}, {"family": "Broholm", "given": "Christa", "initials": "C"}, {"family": "Pedersen", "given": "Maria", "initials": "M"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pedersen", "given": "Bente Klarlund", "initials": "BK"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "9", "issn": "1756-994X", "issue": "1", "pages": "47", "title": "Genome Med", "issn-l": "1756-994X"}, "abstract": "Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity.\n\nWe generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription. This setup enabled us to identify intrinsic properties, originating from muscle precursor cells and retained in the corresponding myocytes. Bioinformatic and statistical methods, including differential expression analysis, gene-set analysis, and metabolic network analysis, were used to characterize the different myocytes.\n\nWe found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional signatures. T2D and obesity were independently associated with dysregulated myogenesis, down-regulated muscle function, and up-regulation of inflammation and extracellular matrix components. Metabolic network analysis identified that in T2D but not obesity a specific metabolite subnetwork involved in sphingolipid metabolism was transcriptionally regulated.\n\nOur findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D.", "doi": "10.1186/s13073-017-0432-2", "pmid": "28545587", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13073-017-0432-2"}, {"db": "pmc", "key": "PMC5444103"}], "notes": [], "created": "2017-11-03T15:53:40.517Z", "modified": "2024-01-16T13:48:47.954Z"}, {"entity": "publication", "iuid": "1b262db9b2e649d3b068b24a164ca06f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b262db9b2e649d3b068b24a164ca06f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b262db9b2e649d3b068b24a164ca06f"}}, "title": "Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2017-05-25", "journal": {"volume": "5", "issn": "2169-8287", "issue": "21", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "The oomycete Pythium oligandrum is a mycoparasite and licenced biological control agent. Here, we report the draft genome sequence of P.\u00a0oligandrum strain CBS 530.74, which is 36.80\u00a0Mb. It contains 341 scaffolds and 11,647 predicted protein-coding genes. As reported for plant-pathogenic Pythium species, RXLR-type effector sequences are absent.", "doi": "10.1128/genomeA.00346-17", "pmid": "28546478", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5/21/e00346-17"}, {"db": "pmc", "key": "PMC5477391"}], "notes": [], "created": "2017-11-03T16:21:52.480Z", "modified": "2020-01-21T13:56:17.422Z"}, {"entity": "publication", "iuid": "cb72c2b5a1184d3591fc1e7dc95f3813", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb72c2b5a1184d3591fc1e7dc95f3813.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb72c2b5a1184d3591fc1e7dc95f3813"}}, "title": "TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-05-10", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "664", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.", "doi": "10.12688/f1000research.11168.2", "pmid": "28781756", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5521161"}], "notes": [], "created": "2017-10-04T15:14:48.609Z", "modified": "2024-01-16T13:48:47.976Z"}, {"entity": "publication", "iuid": "788bcedf458c46bca3f4b731190d6c65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/788bcedf458c46bca3f4b731190d6c65"}}, "title": "Spatially resolved transcriptome profiling in model plant species.", "authors": [{"family": "Giacomello", "given": "Stefania", "initials": "S", "orcid": "0000-0003-0738-1574", "researcher": {"href": "https://publications.scilifelab.se/researcher/8499e792cc394c42b4240ef5fb3fd06c.json"}}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Vickovic", "given": "Sanja", "initials": "S", "orcid": "0000-0003-0985-9885", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fc02717a5784908b583ef5bbf09a910.json"}}, {"family": "Navarro", "given": "Jos\u00e9 Fernandez", "initials": "JF"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "McKee", "given": "Lauren S", "initials": "LS"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Bulone", "given": "Vincent", "initials": "V"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2017-05-08", "journal": {"volume": "3", "issn": "2055-0278", "issue": null, "pages": "17061", "title": "NPLANTS", "issn-l": "2055-0278"}, "abstract": "Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.", "doi": "10.1038/nplants.2017.61", "pmid": "28481330", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nplants201761"}], "notes": [], "created": "2017-08-23T14:09:59.506Z", "modified": "2024-01-16T13:48:47.983Z"}, {"entity": "publication", "iuid": "8447b66fc57d40adb9dc7b36a4840536", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8447b66fc57d40adb9dc7b36a4840536.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8447b66fc57d40adb9dc7b36a4840536"}}, "title": "Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.", "authors": [{"family": "Chan", "given": "Sherwin", "initials": "S"}, {"family": "Frasch", "given": "Alejandra", "initials": "A"}, {"family": "Mandava", "given": "Chandra Sekhar", "initials": "CS"}, {"family": "Ch'ng", "given": "Jun-Hong", "initials": "JH"}, {"family": "Quintana", "given": "Maria Del Pilar", "initials": "MDP"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}, {"family": "Ghorbal", "given": "Mehdi", "initials": "M"}, {"family": "Joannin", "given": "Nicolas", "initials": "N"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Lopez-Rubio", "given": "Jose-Juan", "initials": "JJ"}, {"family": "Barbieri", "given": "Sonia", "initials": "S"}, {"family": "Lanzavecchia", "given": "Antonio", "initials": "A"}, {"family": "Sanyal", "given": "Suparna", "initials": "S"}, {"family": "Wahlgren", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2017-05-08", "journal": {"volume": "2", "issn": "2058-5276", "issue": null, "pages": "17068", "title": "Nat Microbiol", "issn-l": "2058-5276"}, "abstract": "Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain. Cleavage generates a C-terminal domain that contains a sterile-alpha-motif-like domain. The C-terminal domain is permissive to cytoplasmic shuttling and interacts with ribosomes to facilitate translational derepression of the var2csa coding sequence. It also enhances translation in a heterologous translation system and thus represents the first non-canonical translation enhancing factor to be found in a protozoan. Our results implicate PTEF in regulating placental CSA binding of infected erythrocytes.", "doi": "10.1038/nmicrobiol.2017.68", "pmid": "28481333", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nmicrobiol201768"}], "notes": [], "created": "2017-11-03T16:22:14.766Z", "modified": "2024-01-16T13:48:47.993Z"}, {"entity": "publication", "iuid": "181c30fb74a842d1b820ac8da5faf40c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/181c30fb74a842d1b820ac8da5faf40c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/181c30fb74a842d1b820ac8da5faf40c"}}, "title": "Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.", "authors": [{"family": "Wallberg", "given": "Andreas", "initials": "A"}, {"family": "Sch\u00f6ning", "given": "Caspar", "initials": "C"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Hasselmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "5", "pages": "e1006792", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Understanding the genetic basis of adaption is a central task in biology. Populations of the honey bee Apis mellifera that inhabit the mountain forests of East Africa differ in behavior and morphology from those inhabiting the surrounding lowland savannahs, which likely reflects adaptation to these habitats. We performed whole genome sequencing on 39 samples of highland and lowland bees from two pairs of populations to determine their evolutionary affinities and identify the genetic basis of these putative adaptations. We find that in general, levels of genetic differentiation between highland and lowland populations are very low, consistent with them being a single panmictic population. However, we identify two loci on chromosomes 7 and 9, each several hundred kilobases in length, which exhibit near fixation for different haplotypes between highland and lowland populations. The highland haplotypes at these loci are extremely rare in samples from the rest of the world. Patterns of segregation of genetic variants suggest that recombination between haplotypes at each locus is suppressed, indicating that they comprise independent structural variants. The haplotype on chromosome 7 harbors nearly all octopamine receptor genes in the honey bee genome. These have a role in learning and foraging behavior in honey bees and are strong candidates for adaptation to highland habitats. Molecular analysis of a putative breakpoint indicates that it may disrupt the coding sequence of one of these genes. Divergence between the highland and lowland haplotypes at both loci is extremely high suggesting that they are ancient balanced polymorphisms that greatly predate divergence between the extant honey bee subspecies.", "doi": "10.1371/journal.pgen.1006792", "pmid": "28542163", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00165"}, {"db": "pmc", "key": "PMC5444601"}, {"db": "BioProject", "description": "Population-scale sequencing of Apis mellifera monticola and scutellata from Kenya", "key": "PRJNA357367"}, {"db": "Dryad", "description": "Data from: Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees", "key": "https://doi.org/10.5061/dryad.jn630"}], "notes": [], "created": "2017-10-27T06:59:44.233Z", "modified": "2024-01-16T13:48:48.005Z"}, {"entity": "publication", "iuid": "3932c9f238004aaa8daf5320158c70ff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3932c9f238004aaa8daf5320158c70ff"}}, "title": "Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.", "authors": [{"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Wojdacz", "given": "Tomasz K", "initials": "TK"}, {"family": "Marabita", "given": "Francesco", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Prezza", "given": "Nicola", "initials": "N"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "91", "issn": "1432-0738", "issue": "5", "pages": "2067-2078", "title": "Arch. Toxicol.", "issn-l": "0340-5761"}, "abstract": "Arsenic, a carcinogen with immunotoxic effects, is a common contaminant of drinking water and certain food worldwide. We hypothesized that chronic arsenic exposure alters gene expression, potentially by altering DNA methylation of genes encoding central components of the immune system. We therefore analyzed the transcriptomes (by RNA sequencing) and methylomes (by target-enrichment next-generation sequencing) of primary CD4-positive T cells from matched groups of four women each in the Argentinean Andes, with fivefold differences in urinary arsenic concentrations (median concentrations of urinary arsenic in the lower- and high-arsenic groups: 65 and 276 \u03bcg/l, respectively). Arsenic exposure was associated with genome-wide alterations of gene expression; principal component analysis indicated that the exposure explained 53% of the variance in gene expression among the top variable genes and 19% of 28,351 genes were differentially expressed (false discovery rate <0.05) between the exposure groups. Key genes regulating the immune system, such as tumor necrosis factor alpha and interferon gamma, as well as genes related to the NF-kappa-beta complex, were significantly downregulated in the high-arsenic group. Arsenic exposure was associated with genome-wide DNA methylation; the high-arsenic group had 3% points higher genome-wide full methylation (>80% methylation) than the lower-arsenic group. Differentially methylated regions that were hyper-methylated in the high-arsenic group showed enrichment for immune-related gene ontologies that constitute the basic functions of CD4-positive T cells, such as isotype switching and lymphocyte activation and differentiation. In conclusion, chronic arsenic exposure from drinking water was related to changes in the transcriptome and methylome of CD4-positive T cells, both genome wide and in specific genes, supporting the hypothesis that arsenic causes immunotoxicity by interfering with gene expression and regulation.", "doi": "10.1007/s00204-016-1879-4", "pmid": "27838757", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s00204-016-1879-4"}, {"db": "pmc", "key": "PMC5399044"}], "notes": [], "created": "2017-05-03T12:59:46.128Z", "modified": "2024-01-16T13:48:48.019Z"}, {"entity": "publication", "iuid": "a03bd7f66d9048c8b0bc3e8e576bd31e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a03bd7f66d9048c8b0bc3e8e576bd31e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a03bd7f66d9048c8b0bc3e8e576bd31e"}}, "title": "The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.", "authors": [{"family": "Hou", "given": "Chen", "initials": "C"}, {"family": "Wikstr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Rydin", "given": "Catarina", "initials": "C"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "28", "issn": "2470-1408", "issue": "3", "pages": "330-331", "title": "Mitochondrial DNA A DNA Mapp Seq Anal", "issn-l": "2470-1394"}, "abstract": "This study presents the chloroplast genome of Ephedra foeminea, an entomophilous gymnosperm, sister to the remaining (wind-pollinated) species of Ephedra (Ephedraceae, Gnetales). Based on the reference-guided assembly, the length of the chloroplast genome was estimated to be 109\u00a0584\u2009bp, comprising a large single copy region of 60\u2009027\u2009bp, a small single copy 8079\u2009bp, and inverted repeat regions of 20\u00a0739\u2009bp. In total, 118 genes were detected, including 73 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene density is 1.076 (genes/kb) and the GC content is 36.7%. The genomic sequence of the entomophilous, Mediterranean species E. foeminea, differs from that of the anemophilous, Asian species E. equisetina by 1018 point mutations and 1334 indels. The detected variation is useful for future development of new plastid markers for phylogenetic purposes. Our phylogenetic analysis based on 55 protein-coding chloroplast genes resolve Ephedra as monophyletic and sister to a Gnetum-Welwitschia clade. The Gnetales are sister to Cupressophytes.", "doi": "10.3109/19401736.2015.1122768", "pmid": "26713841", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:18.729Z", "modified": "2024-01-16T13:48:48.033Z"}, {"entity": "publication", "iuid": "9fa1f34c27fa45719956c93209b8bf51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fa1f34c27fa45719956c93209b8bf51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fa1f34c27fa45719956c93209b8bf51"}}, "title": "Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model.", "authors": [{"family": "Rivetti di Val Cervo", "given": "Pia", "initials": "P"}, {"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Spigolon", "given": "Giada", "initials": "G"}, {"family": "Masini", "given": "D\u00e9bora", "initials": "D"}, {"family": "Mart\u00edn-Monta\u00f1ez", "given": "Elisa", "initials": "E"}, {"family": "Toledo", "given": "Enrique M", "initials": "EM"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Feyder", "given": "Michael", "initials": "M"}, {"family": "Pifl", "given": "Christian", "initials": "C"}, {"family": "Ng", "given": "Yi-Han", "initials": "YH"}, {"family": "S\u00e1nchez", "given": "Sara Padrell", "initials": "SP"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Wernig", "given": "Marius", "initials": "M"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "Fisone", "given": "Gilberto", "initials": "G"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "35", "issn": "1546-1696", "issue": "5", "pages": "444-452", "title": "Nat. Biotechnol.", "issn-l": "1087-0156"}, "abstract": "Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here we describe an alternative strategy for Parkinson's disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, we reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs). Reprogramming efficiency in vitro is improved by small molecules that promote chromatin remodeling and activate the TGF\u03b2, Shh and Wnt signaling pathways. The reprogramming efficiency of human astrocytes reaches up to 16%, resulting in iDANs with appropriate midbrain markers and excitability. In a mouse model of Parkinson's disease, NeAL218 alone reprograms adult striatal astrocytes into iDANs that are excitable and correct some aspects of motor behavior in vivo, including gait impairments. With further optimization, this approach may enable clinical therapies for Parkinson's disease by delivery of genes rather than cells.", "doi": "10.1038/nbt.3835", "pmid": "28398344", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nbt.3835"}], "notes": [], "created": "2017-11-03T16:21:17.986Z", "modified": "2024-01-16T13:48:48.046Z"}, {"entity": "publication", "iuid": "4eab694bf7e14ca5a71b01cb978a023a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4eab694bf7e14ca5a71b01cb978a023a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4eab694bf7e14ca5a71b01cb978a023a"}}, "title": "Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity.", "authors": [{"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Bergendal", "given": "Birgitta", "initials": "B"}, {"family": "Norderyd", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "173", "issn": "1552-4833", "issue": "5", "pages": "1396-1399", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Singleton-Merten syndrome (MIM 182250) is an autosomal dominant inherited disorder characterized by early onset periodontitis, root resorption, osteopenia, osteoporosis, and aortic valve or thoracic aorta calcification. The disorder can have significant intrafamilial phenotypic variability. Here, we present a mother and daughter with Singleton-Merten syndrome harboring a previously described pathogenic missense mutation, c.2465G>A p.(Arg822Gln), in IFIH1 (interferon induced with helicase C domain 1), encoding MDA5 (Melanoma Differentiation-Associated protein 5). These data confirm the pathogenicity of IFIH1 c.2465G>A p.(Arg822Gln) for Singleton-Merten syndrome and affirm the striking phenotypic heterogeneity of this disorder. In addition, we expand the Singleton-Merten phenotype by adding severe systemic lupus erythematosus (SLE) to the clinical picture. Investigations of known SLE genes as well as a single nucleotide polymorphism suggested to be involved in development of SLE were normal.", "doi": "10.1002/ajmg.a.38214", "pmid": "28319323", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:19:24.520Z", "modified": "2024-01-16T13:48:48.059Z"}, {"entity": "publication", "iuid": "8fdeb5a6200148f7b6db35cc74332911", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fdeb5a6200148f7b6db35cc74332911.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fdeb5a6200148f7b6db35cc74332911"}}, "title": "Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.", "authors": [{"family": "Weissensteiner", "given": "Matthias H", "initials": "MH"}, {"family": "Pang", "given": "Andy W C", "initials": "AWC"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Vinnere-Petterson", "given": "Olga", "initials": "O"}, {"family": "Suh", "given": "Alexander", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2017-05-00", "journal": {"volume": "27", "issn": "1549-5469", "issue": "5", "pages": "697-708", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Accurate and contiguous genome assembly is key to a comprehensive understanding of the processes shaping genomic diversity and evolution. Yet, it is frequently constrained by constitutive heterochromatin, usually characterized by highly repetitive DNA. As a key feature of genome architecture associated with centromeric and subtelomeric regions, it locally influences meiotic recombination. In this study, we assess the impact of large tandem repeat arrays on the recombination rate landscape in an avian speciation model, the Eurasian crow. We assembled two high-quality genome references using single-molecule real-time sequencing (long-read assembly [LR]) and single-molecule optical maps (optical map assembly [OM]). A three-way comparison including the published short-read assembly (SR) constructed for the same individual allowed assessing assembly properties and pinpointing misassemblies. By combining information from all three assemblies, we characterized 36 previously unidentified large repetitive regions in the proximity of sequence assembly breakpoints, the majority of which contained complex arrays of a 14-kb satellite repeat or its 1.2-kb subunit. Using whole-genome population resequencing data, we estimated the population-scaled recombination rate (\u03c1) and found it to be significantly reduced in these regions. These findings are consistent with an effect of low recombination in regions adjacent to centromeric or subtelomeric heterochromatin and add to our understanding of the processes generating widespread heterogeneity in genetic diversity and differentiation along the genome. By combining three different technologies, our results highlight the importance of adding a layer of information on genome structure that is inaccessible to each approach independently.", "doi": "10.1101/gr.215095.116", "pmid": "28360231", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gr.215095.116"}, {"db": "pmc", "key": "PMC5411765"}], "notes": [], "created": "2017-10-17T09:42:42.055Z", "modified": "2024-01-16T13:48:48.069Z"}, {"entity": "publication", "iuid": "9c9d3150115a4c5fafc029f1f5279164", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c9d3150115a4c5fafc029f1f5279164.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c9d3150115a4c5fafc029f1f5279164"}}, "title": "Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk.", "authors": [{"family": "Skovrind", "given": "Mikkel", "initials": "M", "orcid": "0000-0002-5430-5884", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d66c99ebd514dc98230f3e636100050.json"}}, {"family": "Samaniego Castruita", "given": "Jose Alfredo", "initials": "JA", "orcid": "0000-0001-5904-1198", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c719c4a3e3d4c2fa886d0837dc353df.json"}}, {"family": "Heide-J\u00f8rgensen", "given": "Mads Peter", "initials": "MP", "orcid": "0000-0003-4846-7622", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9e5faf23cc44a0cb5d1c122a4e30ce1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Lorenzen", "given": "Eline", "initials": "E", "orcid": "0000-0002-6353-2819", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2671a526ba54081889f378be5efba1e.json"}}], "type": "journal article", "published": "2017-04-28", "journal": {"volume": "2", "issn": "2380-2359", "issue": "1", "pages": "257-258", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "The beluga whale is one of three endemic Arctic whales. The species is philopatric, and its migration patterns are passed from mother to calf. Management of the species is informed by the levels of genetic structuring among summer aggregation sites based on mitochondrial D-Loop data. To assess the levels of differentiation across the entire mitochondrial genome within belugas, we present a comparison between the first two complete mitochondrial genomes from opposite sides of their distribution range: Baffin Bay and the Russian Far East. Our analyses reveal that additional phylogenetic insights can be gained from expanding the genetic region analyzed. Further, we estimate the divergence time between the two mitochondrial genomes to be 0.469 MYA.", "doi": "10.1080/23802359.2017.1318686", "pmid": "33473790", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1318686"}, {"db": "pmc", "key": "PMC7800697"}], "notes": [], "created": "2017-11-03T15:53:38.584Z", "modified": "2021-06-21T15:47:55.199Z"}, {"entity": "publication", "iuid": "28528687ee0e4b6baf2aa786d22d9983", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28528687ee0e4b6baf2aa786d22d9983.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28528687ee0e4b6baf2aa786d22d9983"}}, "title": "Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Gonzales-Sil\u00e8s", "given": "Lucia", "initials": "L"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ER"}], "type": "journal article", "published": "2017-04-06", "journal": {"volume": "5", "issn": "2169-8287", "issue": "14", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Streptococcus pneumoniae is a pathogenic bacterium found most commonly in the respiratory tract of humans and is a common cause of pneumonia and bacterial meningitis. Here, we report the draft genome sequences of six S.\u00a0pneumoniae strains: CCUG 1350, CCUG 7206, CCUG 11780, CCUG 33774, CCUG 35180, and CCUG 35272.", "doi": "10.1128/genomeA.00125-17", "pmid": "28385844", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5/14/e00125-17"}, {"db": "pmc", "key": "PMC5383892"}], "notes": [], "created": "2017-11-03T16:21:51.107Z", "modified": "2024-01-16T13:48:48.105Z"}, {"entity": "publication", "iuid": "5c60d95ec1144a3f84f4f35dbac8f469", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c60d95ec1144a3f84f4f35dbac8f469.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c60d95ec1144a3f84f4f35dbac8f469"}}, "title": "Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.", "authors": [{"family": "Zangenah", "given": "S", "initials": "S"}, {"family": "Andersson", "given": "A F", "initials": "AF"}, {"family": "\u00d6zenci", "given": "V", "initials": "V"}, {"family": "Bergman", "given": "P", "initials": "P"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "36", "issn": "1435-4373", "issue": "4", "pages": "657-662", "title": "Eur. J. Clin. Microbiol. Infect. Dis.", "issn-l": "0934-9723"}, "abstract": "Capnocytophga canimorsus and Capnocytophga cynodegmi can be transmitted from cats and dogs to humans, and can cause a wide range of infections including wound infections, sepsis, or endocarditis. We and others recently discovered two new Capnocytophaga species, C. canis and C. stomatis, mainly associated with wound infections. The first-line treatment of animal bite related infections is penicillin, and in case of allergy, doxycycline and trimethoprim/sulfamethoxazole. However, there is a lack of antibiotic susceptibility patterns for animal bite associated Capnocytophaga species. Thus, we \ufeffset out to study the antibiotic profiles against animal bite associated Capnocytophaga species isolated from wound and blood cultures after cat and dog bites and coupled the findings to whole genome sequencing data. A total of 24 strains were included in the study. Phenotypic analysis of antibiotic resistance was performed with E-tests. The web-based tool 'Resfinder' was used to identify resistance genes in the whole genome dataset. Two strains of C. cynodegmi and two strains of the recently discovered C. stomatis were resistant to penicillin (MIC\u2009> 24 mg\ufeff/L) and cephalosporins (MIC\u2009>\u200924 mg/\ufeffL), and three out of these strains also exhibited resistance to imipenem (MIC\u2009=\u200932 mg/\ufeffL). Genomic analysis revealed that these strains carried a class D beta-lactamase gene, which has not previously been found in Capnocytophaga spp. A class D beta lactamase with broad substrate specificity was found in animal bite associated Capnocytophaga species, which could have important implications when treating wound infections after cat and dog bites. It also suggests that pet animal bacteria can harbour resistance genes with relevance for human infections.", "doi": "10.1007/s10096-016-2842-2", "pmid": "27909820", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s10096-016-2842-2"}, {"db": "pmc", "key": "PMC5366173"}], "notes": [], "created": "2017-05-03T12:58:58.451Z", "modified": "2024-01-16T13:48:48.169Z"}, {"entity": "publication", "iuid": "9861fe84e8714daba4df313b6aa9fe1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9861fe84e8714daba4df313b6aa9fe1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9861fe84e8714daba4df313b6aa9fe1b"}}, "title": "Gene co-expression network connectivity is an important determinant of selective constraint.", "authors": [{"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Terebieniec", "given": "Barbara K", "initials": "BK"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "4", "pages": "e1006402", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure. Here we utilised RNA-Sequencing to assay gene expression in winter buds undergoing bud flush in a natural population of Populus tremula, an outbreeding forest tree species. We performed expression Quantitative Trait Locus (eQTL) mapping and identified 164,290 significant eQTLs associating 6,241 unique genes (eGenes) with 147,419 unique SNPs (eSNPs). We found approximately four times as many local as distant eQTLs, with local eQTLs having significantly higher effect sizes. eQTLs were primarily located in regulatory regions of genes (UTRs or flanking regions), regardless of whether they were local or distant. We used the gene expression data to infer a co-expression network and investigated the relationship between network topology, the genetic architecture of gene expression and signatures of selection. Within the co-expression network, eGenes were underrepresented in network module cores (hubs) and overrepresented in the periphery of the network, with a negative correlation between eQTL effect size and network connectivity. We additionally found that module core genes have experienced stronger selective constraint on coding and non-coding sequence, with connectivity associated with signatures of selection. Our integrated genetics and genomics results suggest that purifying selection is the primary mechanism underlying the genetic architecture of natural variation in gene expression assayed in flushing leaf buds of P. tremula and that connectivity within the co-expression network is linked to the strength of purifying selection.", "doi": "10.1371/journal.pgen.1006402", "pmid": "28406900", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-16-02227"}, {"db": "pmc", "key": "PMC5407845"}], "notes": [], "created": "2017-11-03T16:22:16.369Z", "modified": "2024-01-16T13:48:48.178Z"}, {"entity": "publication", "iuid": "582a1ec0dba34f4f83e8c24ff80a6284", "links": {"self": {"href": "https://publications.scilifelab.se/publication/582a1ec0dba34f4f83e8c24ff80a6284.json"}, "display": {"href": "https://publications.scilifelab.se/publication/582a1ec0dba34f4f83e8c24ff80a6284"}}, "title": "Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout", "authors": [{"family": "Huyben", "given": "David", "initials": "D", "orcid": "0000-0001-7913-851X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e03b5f5591824373a7eb756f21a93001.json"}}, {"family": "Nyman", "given": "Andreas", "initials": "A"}, {"family": "Vidakovi\u0107", "given": "Aleksandar", "initials": "A"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}, {"family": "Moccia", "given": "Richard", "initials": "R"}, {"family": "Kiessling", "given": "Anders", "initials": "A"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Lundh", "given": "Torbj\u00f6rn", "initials": "T"}], "type": "journal-article", "published": "2017-04-00", "journal": {"volume": "473", "issn": "0044-8486", "issue": null, "pages": "528-537", "title": "Aquaculture", "issn-l": null}, "abstract": null, "doi": "10.1016/j.aquaculture.2017.03.024", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:41.442Z", "modified": "2024-01-16T13:48:48.198Z"}, {"entity": "publication", "iuid": "3a1cc06125b84310aade5d4e82d2ae12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a1cc06125b84310aade5d4e82d2ae12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a1cc06125b84310aade5d4e82d2ae12"}}, "title": "A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gs\u03b1 Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).", "authors": [{"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Nevalainen", "given": "Pasi I", "initials": "PI"}, {"family": "Reyes", "given": "Monica", "initials": "M"}, {"family": "Thiele", "given": "Susanne", "initials": "S"}, {"family": "Tafaj", "given": "Olta", "initials": "O"}, {"family": "Molinaro", "given": "Angelo", "initials": "A"}, {"family": "Takatani", "given": "Rieko", "initials": "R"}, {"family": "Ala-Houhala", "given": "Marja", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Kottler", "given": "Marie-Laure", "initials": "ML"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "J\u00fcppner", "given": "Harald", "initials": "H"}], "type": "case reports", "published": "2017-04-00", "journal": {"volume": "32", "issn": "1523-4681", "issue": "4", "pages": "776-783", "title": "J. Bone Miner. Res.", "issn-l": "0884-0431"}, "abstract": "Pseudohypoparathyroidism type Ib (PHP1B) is characterized primarily by resistance to parathyroid hormone (PTH) and thus hypocalcemia and hyperphosphatemia, in most cases without evidence for Albright hereditary osteodystrophy (AHO). PHP1B is associated with epigenetic changes at one or several differentially-methylated regions (DMRs) within GNAS, which encodes the \u03b1-subunit of the stimulatory G protein (Gs\u03b1) and splice variants thereof. Heterozygous, maternally inherited STX16 or GNAS deletions leading to isolated loss-of-methylation (LOM) at exon A/B alone or at all maternal DMRs are the cause of autosomal dominant PHP1B (AD-PHP1B). In this study, we analyzed three affected individuals, the female proband and her two sons. All three revealed isolated LOM at GNAS exon A/B, whereas the proband's healthy maternal grandmother and uncle showed normal methylation at this locus. Haplotype analysis was consistent with linkage to the STX16/GNAS region, yet no deletion could be identified. Whole-genome sequencing of one of the patients revealed a large heterozygous inversion (1,882,433 bp). The centromeric breakpoint of the inversion is located 7,225 bp downstream of GNAS exon XL, but its DMR showed no methylation abnormality, raising the possibility that the inversion disrupts a regulatory element required only for establishing or maintaining exon A/B methylation. Because our three patients presented phenotypes consistent with PHP1B, and not with PHP1A, the Gs\u03b1 promoter is probably unaffected by the inversion. Our findings expand the spectrum of genetic mutations that lead to LOM at exon A/B alone and thus biallelic expression of the transcript derived from this alternative first GNAS exon. \u00a9 2017 American Society for Bone and Mineral Research.", "doi": "10.1002/jbmr.3083", "pmid": "28084650", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5395346"}, {"db": "mid", "key": "NIHMS843464"}], "notes": [], "created": "2017-11-03T12:53:35.193Z", "modified": "2024-01-16T13:48:48.221Z"}, {"entity": "publication", "iuid": "4329e9402acb48b795c634b93c76be4b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4329e9402acb48b795c634b93c76be4b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4329e9402acb48b795c634b93c76be4b"}}, "title": "Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches.", "authors": [{"family": "Lamei", "given": "Sepideh", "initials": "S"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Olofsson", "given": "Tobias C", "initials": "TC"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Forsgren", "given": "Eva", "initials": "E"}, {"family": "V\u00e1squez", "given": "Alejandra", "initials": "A"}], "type": "journal article", "published": "2017-03-27", "journal": {"volume": "12", "issn": "1932-6203", "issue": "3", "pages": "e0174614", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Honeybees face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. The crop microbiota of Apis mellifera, composed of 13 Lactic Acid Bacterial (LAB) species within the genera Lactobacillus and Bifidobacterium, form a beneficial symbiotic relationship with each other and the honeybee to protect their niche and their host. Possibly playing a vital role in honeybee health, it is important that these honeybee specific Lactic Acid Bacterial (hbs-LAB) symbionts can be correctly identified, isolated and cultured, to further investigate their health promoting properties. We have previously reported successful identification to the strain level by culture-dependent methods and we recently sequenced and annotated the genomes of the 13 hbs-LAB. However, the hitherto applied techniques are unfortunately very time consuming, expensive and not ideal when analyzing a vast quantity of samples. In addition, other researchers have constantly failed to identify the 13 hbs-LAB from honeybee samples by using inadequate media and/or molecular techniques based on 16S rRNA gene sequencing with insufficient discriminatory power. The aim of this study was to develop better and more suitable methods for the identification and cultivation of hbs-LAB. We compared currently used bacterial cultivation media and could for the first time demonstrate a significant variation in the hbs-LAB basic requirements for optimal growth. We also present a new bacterial identification approach based on amplicon sequencing of a region of the 16S rRNA gene using the Illumina platform and an error correction software that can be used to successfully differentiate and rapidly identify the 13 hbs-LAB to the strain level.", "doi": "10.1371/journal.pone.0174614", "pmid": "28346815", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-47026"}, {"db": "pmc", "key": "PMC5367889"}], "notes": [], "created": "2017-11-03T16:11:40.176Z", "modified": "2024-01-16T13:48:48.244Z"}, {"entity": "publication", "iuid": "a9f6d02505334fa7bdeddc62f4a05039", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9f6d02505334fa7bdeddc62f4a05039.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9f6d02505334fa7bdeddc62f4a05039"}}, "title": "Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.", "authors": [{"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Pedersen", "given": "Karsten", "initials": "K"}, {"family": "Edlund", "given": "Johanna", "initials": "J"}, {"family": "Eriksson", "given": "Lena", "initials": "L"}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "5", "issn": "2049-2618", "issue": "1", "pages": "37", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere.\n\nIn this study, flow cells were attached to boreholes containing either \"modern marine\" or \"old saline\" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide- and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria.\n\nPopulations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.", "doi": "10.1186/s40168-017-0253-y", "pmid": "28335808", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-017-0253-y"}, {"db": "pmc", "key": "PMC5364579"}], "notes": [], "created": "2017-11-03T16:11:41.099Z", "modified": "2024-01-16T13:48:48.253Z"}, {"entity": "publication", "iuid": "9199b6ea51d04aa2b2f5f831a3d4e154", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9199b6ea51d04aa2b2f5f831a3d4e154.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9199b6ea51d04aa2b2f5f831a3d4e154"}}, "title": "Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.", "authors": [{"family": "Kushwaha", "given": "Sandeep K", "initials": "SK"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}], "type": "journal article", "published": "2017-03-23", "journal": {"volume": "5", "issn": "2169-8287", "issue": "12", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "The oomycete Pythium periplocum is an aggressive mycoparasite of a number of plant pathogenic fungi and oomycetes and therefore has potential as a biological control agent. Here, we report the first draft genome sequence of P. periplocum, which comprises 35.89\u00a0Mb. It contains 1,043 scaffolds and 14,399 predicted protein-coding genes.", "doi": "10.1128/genomeA.00057-17", "pmid": "28336598", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "5/12/e00057-17"}, {"db": "pmc", "key": "PMC5364223"}], "notes": [], "created": "2017-11-03T16:21:53.141Z", "modified": "2020-01-21T13:56:17.350Z"}, {"entity": "publication", "iuid": "0990de43373146d69c60334dffbe0590", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0990de43373146d69c60334dffbe0590.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0990de43373146d69c60334dffbe0590"}}, "title": "The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.", "authors": [{"family": "Chang", "given": "Dan", "initials": "D"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Enk", "given": "Jacob", "initials": "J"}, {"family": "Lippold", "given": "Sebastian", "initials": "S"}, {"family": "Kircher", "given": "Martin", "initials": "M"}, {"family": "Lister", "given": "Adrian", "initials": "A"}, {"family": "MacPhee", "given": "Ross D E", "initials": "RD"}, {"family": "Widga", "given": "Christopher", "initials": "C"}, {"family": "Czechowski", "given": "Paul", "initials": "P"}, {"family": "Sommer", "given": "Robert", "initials": "R"}, {"family": "Hodges", "given": "Emily", "initials": "E"}, {"family": "St\u00fcmpel", "given": "Nikolaus", "initials": "N"}, {"family": "Barnes", "given": "Ian", "initials": "I"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Derevianko", "given": "Anatoly", "initials": "A"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Hillebrand-Voiculescu", "given": "Alexandra", "initials": "A"}, {"family": "Constantin", "given": "Silviu", "initials": "S"}, {"family": "Kuznetsova", "given": "Tatyana", "initials": "T"}, {"family": "Mol", "given": "Dick", "initials": "D"}, {"family": "Rathgeber", "given": "Thomas", "initials": "T"}, {"family": "Rosendahl", "given": "Wilfried", "initials": "W"}, {"family": "Tikhonov", "given": "Alexey N", "initials": "AN"}, {"family": "Willerslev", "given": "Eske", "initials": "E"}, {"family": "Hannon", "given": "Greg", "initials": "G"}, {"family": "Lalueza-Fox", "given": "Carles", "initials": "C"}, {"family": "Joger", "given": "Ulrich", "initials": "U"}, {"family": "Poinar", "given": "Hendrik", "initials": "H"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}], "type": "journal article", "published": "2017-03-22", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "44585", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0-2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.", "doi": "10.1038/srep44585", "pmid": "28327635", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep44585"}, {"db": "pmc", "key": "PMC5361112"}], "notes": [], "created": "2017-11-03T16:21:50.396Z", "modified": "2021-07-07T20:31:10.689Z"}, {"entity": "publication", "iuid": "233b062d1f5d47e5ac0971cd9ea0a47f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f"}}, "title": "Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Sinika", "given": "Vitaly", "initials": "V"}, {"family": "Piontek", "given": "Janusz", "initials": "J"}, {"family": "Ivanova", "given": "Svetlana", "initials": "S"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2017-03-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43950", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.", "doi": "10.1038/srep43950", "pmid": "28266657", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep43950"}, {"db": "pmc", "key": "PMC5339713"}], "notes": [], "created": "2017-11-03T16:18:39.704Z", "modified": "2021-07-07T10:48:05.331Z"}, {"entity": "publication", "iuid": "d76c5dadcc0f4b3a8c4a2839d6667beb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d76c5dadcc0f4b3a8c4a2839d6667beb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d76c5dadcc0f4b3a8c4a2839d6667beb"}}, "title": "Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).", "authors": [{"family": "Haddad", "given": "Nizar Jamal", "initials": "NJ", "orcid": "0000-0003-0250-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ff610b5673c4050a4e4377c48b2a372.json"}}, {"family": "Al-Nakeeb", "given": "Kosai", "initials": "K", "orcid": "0000-0003-3432-3628", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d87f93200b4f0ba3480a0f975e9cd9.json"}}, {"family": "Petersen", "given": "Bent", "initials": "B", "orcid": "0000-0002-2472-8317", "researcher": {"href": "https://publications.scilifelab.se/researcher/62045d9b6dc443be936d3346daa4e1b1.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Blom", "given": "Nikolaj", "initials": "N", "orcid": "0000-0001-8012-6380", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd245cd9d02443f4814e6fb1e949265d.json"}}, {"family": "Sicheritz-Pont\u00e9n", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6615-1141", "researcher": {"href": "https://publications.scilifelab.se/researcher/0da5029f417945a790fbb57b5120dceb.json"}}], "type": "journal article", "published": "2017-03-01", "journal": {"volume": "2", "issn": "2380-2359", "issue": "1", "pages": "139-140", "title": "Mitochondrial DNA Part B", "issn-l": "2380-2359"}, "abstract": "The Oriental Hornet ( Vespa orientalis) is a social insect belonging to the Vespiade family (Wasps, Hornets, Yellowjackets), genus Vespa (true Hornets). The oriental hornet is a scavenger and an agricultural pest, especially to bee farmers, but is also recently described as a harvester of solar energy. Here, we report the mitochondrial genome sequence of the Oriental Hornet, Vespa orientalis F., which may play a vital role in understanding this wasp biology, light trapping and generation of electricity. The mitochondrial genome of this hornet is 16,099 bp in length, containing 13 protein-coding genes, 21 transfer RNA genes, and 2 ribosomal RNA genes. The overall base composition of the heavy-strand is 40.3% A, 5.9% C, 13.2% G, and 40.6% T, the percentages of A and T being higher than that of G and C. The mitochondrial genome of the Oriental Hornet, Vespa orientalis F. represents the first mitogenome of a solar energy harvesting insect.", "doi": "10.1080/23802359.2017.1292480", "pmid": "33473744", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1292480"}, {"db": "pmc", "key": "PMC7800523"}], "notes": [], "created": "2017-11-03T15:53:38.192Z", "modified": "2021-06-21T15:47:32.461Z"}, {"entity": "publication", "iuid": "8b4b362f5f4b417c937c972e94b1ace8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b4b362f5f4b417c937c972e94b1ace8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b4b362f5f4b417c937c972e94b1ace8"}}, "title": "Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Ekstam", "given": "B\u00f6rje", "initials": "B"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2017-03-00", "journal": {"volume": "19", "issn": "1462-2920", "issue": "3", "pages": "1222-1236", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.", "doi": "10.1111/1462-2920.13650", "pmid": "28028880", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:11:41.751Z", "modified": "2024-01-16T13:48:48.333Z"}, {"entity": "publication", "iuid": "3e47041311a44189b48417dec4292e33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e47041311a44189b48417dec4292e33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e47041311a44189b48417dec4292e33"}}, "title": "Antibody-encoding repertoires of bone marrow and peripheral blood\u2014a focus on IgE", "authors": [{"family": "Levin", "given": "Mattias", "initials": "M"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Greiff", "given": "Lennart", "initials": "L"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}], "type": "journal-article", "published": "2017-03-00", "journal": {"volume": "139", "issn": "1085-8725", "issue": "3", "pages": "1026-1030", "title": "Journal of Allergy and Clinical Immunology", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2016.06.040", "pmid": "27521279", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0091-6749(16)30779-5"}], "notes": [], "created": "2017-05-03T12:59:52.904Z", "modified": "2024-01-16T13:48:48.371Z"}, {"entity": "publication", "iuid": "bd94aea05d1b4f7da7b5165ed48d553a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd94aea05d1b4f7da7b5165ed48d553a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd94aea05d1b4f7da7b5165ed48d553a"}}, "title": "Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.", "authors": [{"family": "Sandmann", "given": "Sarah", "initials": "S"}, {"family": "de Graaf", "given": "Aniek O", "initials": "AO"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "van der Reijden", "given": "Bert A", "initials": "BA"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Jansen", "given": "Joop H", "initials": "JH"}, {"family": "Dugas", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2017-02-24", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43169", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322\u2009bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.", "doi": "10.1038/srep43169", "pmid": "28233799", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "srep43169"}, {"db": "pmc", "key": "PMC5324109"}], "notes": [], "created": "2018-01-10T09:44:12.939Z", "modified": "2020-01-21T13:56:10.961Z"}, {"entity": "publication", "iuid": "7168b95dce2a405386fcbade449d4999", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7168b95dce2a405386fcbade449d4999.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7168b95dce2a405386fcbade449d4999"}}, "title": "Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.", "authors": [{"family": "Danielsson", "given": "Rebecca", "initials": "R"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Gonda", "given": "Horacio", "initials": "H"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Bertilsson", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2017-02-17", "journal": {"volume": "8", "issn": "1664-302X", "issue": null, "pages": "226", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Methane (CH4) is produced as an end product from feed fermentation in the rumen. Yield of CH4 varies between individuals despite identical feeding conditions. To get a better understanding of factors behind the individual variation, 73 dairy cows given the same feed but differing in CH4 emissions were investigated with focus on fiber digestion, fermentation end products and bacterial and archaeal composition. In total 21 cows (12 Holstein, 9 Swedish Red) identified as persistent low, medium or high CH4 emitters over a 3 month period were furthermore chosen for analysis of microbial community structure in rumen fluid. This was assessed by sequencing the V4 region of 16S rRNA gene and by quantitative qPCR of targeted Methanobrevibacter groups. The results showed a positive correlation between low CH4 emitters and higher abundance of Methanobrevibacter ruminantium clade. Principal coordinate analysis (PCoA) on operational taxonomic unit (OTU) level of bacteria showed two distinct clusters (P < 0.01) that were related to CH4 production. One cluster was associated with low CH4 production (referred to as cluster L) whereas the other cluster was associated with high CH4 production (cluster H) and the medium emitters occurred in both clusters. The differences between clusters were primarily linked to differential abundances of certain OTUs belonging to Prevotella. Moreover, several OTUs belonging to the family Succinivibrionaceae were dominant in samples belonging to cluster L. Fermentation pattern of volatile fatty acids showed that proportion of propionate was higher in cluster L, while proportion of butyrate was higher in cluster H. No difference was found in milk production or organic matter digestibility between cows. Cows in cluster L had lower CH4/kg energy corrected milk (ECM) compared to cows in cluster H, 8.3 compared to 9.7 g CH4/kg ECM, showing that low CH4 cows utilized the feed more efficient for milk production which might indicate a more efficient microbial population or host genetic differences that is reflected in bacterial and archaeal (or methanogens) populations.", "doi": "10.3389/fmicb.2017.00226", "pmid": "28261182", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5313486"}], "notes": [], "created": "2017-11-03T16:20:56.020Z", "modified": "2024-01-16T13:48:48.405Z"}, {"entity": "publication", "iuid": "f35c109acf9743b79cb359d6a7b17c91", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f35c109acf9743b79cb359d6a7b17c91"}}, "title": "The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.", "authors": [{"family": "Adrian-Kalchhauser", "given": "Irene", "initials": "I"}, {"family": "Svensson", "given": "Ola", "initials": "O"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Alm Rosenblad", "given": "Magnus", "initials": "M"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Schloissnig", "given": "Siegfried", "initials": "S"}, {"family": "Blomberg", "given": "Anders", "initials": "A"}, {"family": "Burkhardt-Holm", "given": "Patricia", "initials": "P"}], "type": "journal article", "published": "2017-02-16", "journal": {"volume": "18", "issn": "1471-2164", "issue": "1", "pages": "177", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb).\n\nDuring genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4\u00a0kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19\u00a0kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies.\n\nOur results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence.", "doi": "10.1186/s12864-017-3550-8", "pmid": "28209125", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-017-3550-8"}, {"db": "pmc", "key": "PMC5314710"}], "notes": [], "created": "2017-11-01T12:54:58.955Z", "modified": "2024-01-16T13:48:48.415Z"}, {"entity": "publication", "iuid": "171899c09f704f0499506bbae6f97a8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/171899c09f704f0499506bbae6f97a8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/171899c09f704f0499506bbae6f97a8e"}}, "title": "Comparison of whole genome amplification techniques for human single cell exome sequencing.", "authors": [{"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Paterlini", "given": "Marta", "initials": "M"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Frisen", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "comparative study", "published": "2017-02-16", "journal": {"volume": "12", "issn": "1932-6203", "issue": "2", "pages": "e0171566", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly.\n\nThe largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells.\n\nIn this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.", "doi": "10.1371/journal.pone.0171566", "pmid": "28207771", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-34697"}, {"db": "pmc", "key": "PMC5313163"}], "notes": [], "created": "2017-11-03T16:21:22.034Z", "modified": "2024-01-16T13:48:48.426Z"}, {"entity": "publication", "iuid": "209932748e35452f8c3277616f4a166f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/209932748e35452f8c3277616f4a166f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/209932748e35452f8c3277616f4a166f"}}, "title": "The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.", "authors": [{"family": "Zeigler Allen", "given": "Lisa", "initials": "L"}, {"family": "McCrow", "given": "John P", "initials": "JP"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Badger", "given": "Jonathan H", "initials": "JH"}, {"family": "Hoffman", "given": "Jeffery M", "initials": "JM"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Venter", "given": "J Craig", "initials": "JC"}], "type": "journal article", "published": "2017-02-14", "journal": {"volume": "2", "issn": "2379-5077", "issue": "1", "title": "mSystems", "issn-l": "2379-5077"}, "abstract": "Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Tornetr\u00e4sk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Tornetr\u00e4sk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.", "doi": "10.1128/mSystems.00125-16", "pmid": "28217745", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mSystems00125-16"}, {"db": "pmc", "key": "PMC5309335"}], "notes": [], "created": "2017-11-03T16:19:51.205Z", "modified": "2024-01-16T13:48:48.463Z"}, {"entity": "publication", "iuid": "74fcedf830fe4da28feaf59862e5d126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74fcedf830fe4da28feaf59862e5d126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74fcedf830fe4da28feaf59862e5d126"}}, "title": "A novel RNA sequencing data analysis method for cell line authentication.", "authors": [{"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Raso", "given": "Cinzia", "initials": "C"}, {"family": "Kennedy", "given": "Susan", "initials": "S"}, {"family": "Rauch", "given": "Nora", "initials": "N"}, {"family": "Lundin", "given": "P\u00e4r", "initials": "P"}, {"family": "Kolch", "given": "Walter", "initials": "W"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Al-Khalili Szigyarto", "given": "Cristina", "initials": "C", "orcid": "0000-0001-6990-1905", "researcher": {"href": "https://publications.scilifelab.se/researcher/cff94d8d749248d38f5da13c1f636c9d.json"}}], "type": "journal article", "published": "2017-02-13", "journal": {"volume": "12", "issn": "1932-6203", "issue": "2", "pages": "e0171435", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.", "doi": "10.1371/journal.pone.0171435", "pmid": "28192450", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-35145"}, {"db": "pmc", "key": "PMC5305277"}], "notes": [], "created": "2017-11-03T16:20:58.076Z", "modified": "2021-07-08T13:44:33.358Z"}, {"entity": "publication", "iuid": "1ca13a5dbc2c44329bbbefec4d917ee0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1ca13a5dbc2c44329bbbefec4d917ee0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1ca13a5dbc2c44329bbbefec4d917ee0"}}, "title": "microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.", "authors": [{"family": "Zhou", "given": "Y", "initials": "Y"}, {"family": "Frings", "given": "O", "initials": "O"}, {"family": "Branca", "given": "R M", "initials": "RM"}, {"family": "Boekel", "given": "J", "initials": "J"}, {"family": "le Sage", "given": "C", "initials": "C"}, {"family": "Fredlund", "given": "E", "initials": "E"}, {"family": "Agami", "given": "R", "initials": "R"}, {"family": "Orre", "given": "L M", "initials": "LM"}], "type": "journal article", "published": "2017-02-09", "journal": {"volume": "36", "issn": "1476-5594", "issue": "6", "pages": "731-745", "title": "Oncogene", "issn-l": "0950-9232"}, "abstract": "microRNA (miRNA) dysregulation is a common feature of cancer cells, but the complex roles of miRNAs in cancer are not fully elucidated. Here, we used functional genomics to identify oncogenic miRNAs in non-small cell lung cancer and evaluate their impact on response to epidermal growth factor (EGFR)-targeting therapy. Our data demonstrate that miRNAs with an AAGUGC motif in their seed sequence increase both cancer cell proliferation and sensitivity to EGFR inhibitors. Global transcriptomics, proteomics and target prediction resulted in the identification of several tumor suppressors involved in the G1/S transition as AAGUGC-miRNA targets. The clinical implications of our findings were evaluated by analysis of AAGUGC-miRNA expression in multiple cancer types, supporting the link between this miRNA seed family, their tumor suppressor targets and cancer cell proliferation. In conclusion, we propose the AAGUGC seed motif as an oncomotif and that oncomotif-miRNAs promote cancer cell proliferation. These findings have potential therapeutic implications, especially in selecting patients for EGFR-targeting therapy.", "doi": "10.1038/onc.2016.242", "pmid": "27477696", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "onc2016242"}, {"db": "pmc", "key": "PMC5311252"}], "notes": [], "created": "2017-05-03T13:00:40.536Z", "modified": "2020-01-21T13:56:16.909Z"}, {"entity": "publication", "iuid": "8e9f2942aae54865a9b27b0869aeffb0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e9f2942aae54865a9b27b0869aeffb0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e9f2942aae54865a9b27b0869aeffb0"}}, "title": "The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2017-02-01", "journal": {"volume": "158", "issn": "1945-7170", "issue": "2", "pages": "239-251", "title": "Endocrinology", "issn-l": "0013-7227"}, "abstract": "The adrenal gland is a composite endocrine organ with vital functions that include the synthesis and release of glucocorticoids and catecholamines. To define the molecular landscape that underlies the specific functions of the adrenal gland, we combined a genome-wide transcriptomics approach using messenger RNA sequencing of human tissues with immunohistochemistry-based protein profiling on tissue microarrays. Approximately two-thirds of all putative protein coding genes were expressed in the adrenal gland, and the analysis identified 253 genes with an elevated pattern of expression in the adrenal gland, with only 37 genes showing a markedly greater expression level (more than fivefold) in the adrenal gland compared with 31 other normal human tissue types analyzed. The analyses allowed for an assessment of the relative expression levels for well-known proteins involved in adrenal gland function but also identified previously poorly characterized proteins in the adrenal cortex, such as the FERM (4.1 protein, ezrin, radixin, moesin) domain containing 5 and the nephroblastoma overexpressed (NOV) protein homolog. We have provided a global analysis of the adrenal gland transcriptome and proteome, with a comprehensive list of genes with elevated expression in the adrenal gland and spatial information with examples of protein expression patterns for corresponding proteins. These genes and proteins constitute important starting points for an improved understanding of the normal function and pathophysiology of the adrenal glands.", "doi": "10.1210/en.2016-1758", "pmid": "27901589", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:56:06.552Z", "modified": "2024-01-16T13:48:48.500Z"}, {"entity": "publication", "iuid": "7de7ae9e75fe4fa281ab300f10a19c69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7de7ae9e75fe4fa281ab300f10a19c69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7de7ae9e75fe4fa281ab300f10a19c69"}}, "title": "Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.", "authors": [{"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "Gustavsson", "given": "Peter", "initials": "P"}, {"family": "F\u00f6rster", "given": "Alisa", "initials": "A"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Lupski", "given": "James R", "initials": "JR"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "38", "issn": "1098-1004", "issue": "2", "pages": "180-192", "title": "Hum. Mutat.", "issn-l": "1059-7794"}, "abstract": "Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.", "doi": "10.1002/humu.23146", "pmid": "27862604", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5225243"}, {"db": "mid", "key": "NIHMS830031"}], "notes": [], "created": "2017-05-03T12:59:45.241Z", "modified": "2024-01-16T13:48:48.524Z"}, {"entity": "publication", "iuid": "f501789b43404e2bab18536f512912c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f501789b43404e2bab18536f512912c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f501789b43404e2bab18536f512912c3"}}, "title": "Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.", "authors": [{"family": "Celepli", "given": "Narin", "initials": "N"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Dupont", "given": "Chris L", "initials": "CL"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "19", "issn": "1462-2920", "issue": "2", "pages": "673-686", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradients in salinity and nutrient concentrations. Here, we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa. Cyanobacteria in the Baltic Sea differed genetically from those in adjacent limnic and marine waters as well as from cultivated and sequenced picocyanobacterial strains. Diversity peaked at brackish salinities 3.5-16\u00a0psu, with low N:P ratios. A shift in community composition from brackish to marine strains was accompanied by a change in the repertoire and expression of genes involved in salt acclimation. Overall, the pre-bloom cyanobacterial population was more genetically diverse, widespread and abundant than previously documented, with unicellular picocyanobacteria being the most abundant clade along the entire Baltic Sea salinity gradient.", "doi": "10.1111/1462-2920.13592", "pmid": "27871145", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:10.996Z", "modified": "2024-01-16T13:48:48.558Z"}, {"entity": "publication", "iuid": "52e6b8f5adc249aaac10a6fd81033e5b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52e6b8f5adc249aaac10a6fd81033e5b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52e6b8f5adc249aaac10a6fd81033e5b"}}, "title": "Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy", "authors": [{"family": "Dalin", "given": "Martin G", "initials": "MG"}, {"family": "Engstr\u00f6m", "given": "P\u00e4r G", "initials": "PG", "orcid": "0000-0001-5265-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce330ec225f4a8595932d092ab8c8d1.json"}}, {"family": "Ivarsson", "given": "Emil G", "initials": "EG"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Light", "given": "Sara", "initials": "S"}, {"family": "Schaufelberger", "given": "Maria", "initials": "M"}, {"family": "Gilljam", "given": "Thomas", "initials": "T"}, {"family": "Andersson", "given": "Bert", "initials": "B", "orcid": "0000-0001-7957-2463", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf5a4c61accb4c7b93bca8e713be3694.json"}}, {"family": "Bergo", "given": "Martin O", "initials": "MO"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "228", "issn": "0167-5273", "issue": null, "pages": "742-748", "title": "International Journal of Cardiology", "issn-l": "0167-5273"}, "abstract": "Germline genetic variants are an important cause of dilated cardiomyopathy (DCM). However, recent sequencing studies have revealed rare variants in DCM-associated genes also in individuals without known heart disease. In this study, we investigate variant prevalence and genotype-phenotype correlations in Swedish DCM patients, and compare their genetic variants to those detected in reference cohorts.\n\nWe sequenced the coding regions of 41 DCM-associated genes in 176 unrelated patients with idiopathic DCM and found 102 protein-altering variants with an allele frequency of <0.04% in reference cohorts; the majority were missense variants not previously described in DCM. Fifty-five (31%) patients had one variant, and 24 (14%) patients had two or more variants in the analysed genes. Detection of genetic variants in any gene, and in LMNA, MYH7 or TTN alone, was associated with early onset disease and reduced transplant-free survival. As expected, nonsense and frameshift variants were more common in DCM patients than in healthy individuals of the reference cohort 1000 Genomes Europeans. Surprisingly however, the prevalence, conservation and pathogenicity scores, and localization of missense variants were similar in DCM patients and healthy reference individuals.\n\nTo our knowledge, this is the first study to identify correlations between genotype and prognosis when sequencing a large number of genes in unselected DCM patients. The similar distribution of missense variants in DCM patients and healthy reference individuals questions the pathogenic role of many variants, and suggests that results from genetic testing of DCM patients should be interpreted with caution.", "doi": "10.1016/j.ijcard.2016.11.066", "pmid": "27886618", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0167-5273(16)33512-4"}], "notes": [], "created": "2017-05-03T12:58:56.344Z", "modified": "2024-01-16T13:48:48.570Z"}, {"entity": "publication", "iuid": "b555f13298ec4a75b25a26825eb7af97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b555f13298ec4a75b25a26825eb7af97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b555f13298ec4a75b25a26825eb7af97"}}, "title": "Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism.", "authors": [{"family": "Bramswig", "given": "Nuria C", "initials": "NC"}, {"family": "L\u00fcdecke", "given": "H-J", "initials": "HJ"}, {"family": "Pettersson", "given": "M", "initials": "M"}, {"family": "Albrecht", "given": "B", "initials": "B"}, {"family": "Bernier", "given": "R A", "initials": "RA"}, {"family": "Cremer", "given": "K", "initials": "K"}, {"family": "Eichler", "given": "E E", "initials": "EE"}, {"family": "Falkenstein", "given": "D", "initials": "D"}, {"family": "Gerdts", "given": "J", "initials": "J"}, {"family": "Jansen", "given": "S", "initials": "S"}, {"family": "Kuechler", "given": "A", "initials": "A"}, {"family": "Kvarnung", "given": "M", "initials": "M"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Nilsson", "given": "D", "initials": "D"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Pfundt", "given": "R", "initials": "R"}, {"family": "Spruijt", "given": "L", "initials": "L"}, {"family": "Surowy", "given": "H M", "initials": "HM"}, {"family": "de Vries", "given": "B B A", "initials": "BB"}, {"family": "Wieland", "given": "T", "initials": "T"}, {"family": "Engels", "given": "H", "initials": "H"}, {"family": "Strom", "given": "T M", "initials": "TM"}, {"family": "Kleefstra", "given": "T", "initials": "T"}, {"family": "Wieczorek", "given": "D", "initials": "D"}], "type": "journal article", "published": "2017-02-00", "journal": {"volume": "136", "issn": "1432-1203", "issue": "2", "pages": "179-192", "title": "Hum. Genet.", "issn-l": "0340-6717"}, "abstract": "The ubiquitin pathway is an enzymatic cascade including activating E1, conjugating E2, and ligating E3 enzymes, which governs protein degradation and sorting. It is crucial for many physiological processes. Compromised function of members of the ubiquitin pathway leads to a wide range of human diseases, such as cancer, neurodegenerative diseases, and neurodevelopmental disorders. Mutations in the thyroid hormone receptor interactor 12 (TRIP12) gene (OMIM 604506), which encodes an E3 ligase in the ubiquitin pathway, have been associated with autism spectrum disorder (ASD). In addition to autistic features, TRIP12 mutation carriers showed intellectual disability (ID). More recently, TRIP12 was postulated as a novel candidate gene for intellectual disability in a meta-analysis of published ID cohorts. However, detailed clinical information characterizing the phenotype of these individuals was not provided. In this study, we present seven novel individuals with private TRIP12 mutations including two splice site mutations, one nonsense mutation, three missense mutations, and one translocation case with a breakpoint in intron 1 of the TRIP12 gene and clinically review four previously published cases. The TRIP12 mutation-positive individuals presented with mild to moderate ID (10/11) or learning disability [intelligence quotient (IQ) 76 in one individual], ASD (8/11) and some of them with unspecific craniofacial dysmorphism and other anomalies. In this study, we provide detailed clinical information of 11 TRIP12 mutation-positive individuals and thereby expand the clinical spectrum of the TRIP12 gene in non-syndromic intellectual disability with or without ASD.", "doi": "10.1007/s00439-016-1743-x", "pmid": "27848077", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00439-016-1743-x"}], "notes": [], "created": "2017-05-03T12:59:46.726Z", "modified": "2024-01-16T13:48:48.579Z"}, {"entity": "publication", "iuid": "571f5407c7cb4f8499d389e458b520d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/571f5407c7cb4f8499d389e458b520d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/571f5407c7cb4f8499d389e458b520d5"}}, "title": "Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr ( Salvelinus alpinus )", "authors": [{"family": "Nyman", "given": "Andreas", "initials": "A"}, {"family": "Huyben", "given": "David", "initials": "D"}, {"family": "Lundh", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-02-00", "journal": {"volume": "5", "issn": "2352-5134", "issue": null, "pages": "34-40", "title": "Aquaculture Reports", "issn-l": "2352-5134"}, "abstract": null, "doi": "10.1016/j.aqrep.2016.12.003", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T16:10:04.160Z", "modified": "2024-01-16T13:48:48.611Z"}, {"entity": "publication", "iuid": "0b27d073b90240b18860ecc4d243d200", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b27d073b90240b18860ecc4d243d200.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b27d073b90240b18860ecc4d243d200"}}, "title": "Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.", "authors": [{"family": "Cimdins", "given": "Annika", "initials": "A"}, {"family": "L\u00fcthje", "given": "Petra", "initials": "P"}, {"family": "Li", "given": "Fengyang", "initials": "F"}, {"family": "Ahmad", "given": "Irfan", "initials": "I"}, {"family": "Brauner", "given": "Annelie", "initials": "A"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}], "type": "journal article", "published": "2017-01-26", "journal": {"volume": "5", "issn": "2169-8287", "issue": "4", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Strains of Escherichia coli exhibit diverse biofilm formation capabilities. E.\u00a0coli K-12 expresses the red, dry, and rough (rdar) morphotype below 30\u00b0C, whereas clinical isolates frequently display the rdar morphotype semiconstitutively. We sequenced the genomes of eight E.\u00a0coli strains to subsequently investigate the molecular basis of semiconstitutive rdar morphotype expression.", "doi": "10.1128/genomeA.01249-16", "pmid": "28126929", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "5/4/e01249-16"}, {"db": "pmc", "key": "PMC5270688"}], "notes": [], "created": "2017-10-17T07:55:03.116Z", "modified": "2020-01-21T13:56:17.431Z"}, {"entity": "publication", "iuid": "982fd0bf85684fa2b08e09e4171d860a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/982fd0bf85684fa2b08e09e4171d860a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/982fd0bf85684fa2b08e09e4171d860a"}}, "title": "Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.", "authors": [{"family": "Sigurgeirsson", "given": "Benjamin", "initials": "B"}, {"family": "\u00c5mark", "given": "Hanna", "initials": "H"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Ujvari", "given": "Dorina", "initials": "D"}, {"family": "Westgren", "given": "Magnus", "initials": "M"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gidl\u00f6f", "given": "Sebastian", "initials": "S"}], "type": "comparative study", "published": "2017-01-01", "journal": {"volume": "96", "issn": "1529-7268", "issue": "1", "pages": "24-33", "title": "Biol. Reprod.", "issn-l": "0006-3363"}, "abstract": "Endometrial receptivity is crucial for implantation and establishment of a normal pregnancy. The shift from proliferative to receptive endometrium is still far from being understood. In this paper, we comprehensively present the transcriptome of the human endometrium by comparing endometrial biopsies from proliferative phase with consecutive biopsies 7-9 days after ovulation. The results show a clear difference in expression between the two time points using both total and small RNA sequencing. A total of 3,297 messenger RNAs (mRNAs), 516 long noncoding RNAs (lncRNAs), and 102 small noncoding RNAs were identified as statistically differentially expressed between the two time points. We show a thorough description of the change in mRNA between the two time points and display lncRNAs, small nucleolar RNAs, and small nuclear RNAs not previously reported in the healthy human endometrium. In conclusion, this paper reports in detail the shift in RNA expression from the proliferative to receptive endometrium.", "doi": "10.1095/biolreprod.116.142547", "pmid": "28395321", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2725477"}, {"db": "GEO", "key": "GSE86491"}], "notes": [], "created": "2017-11-03T16:21:34.477Z", "modified": "2024-01-16T13:48:48.703Z"}, {"entity": "publication", "iuid": "79209a0da0ed46bfac15fb20ace04226", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79209a0da0ed46bfac15fb20ace04226.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79209a0da0ed46bfac15fb20ace04226"}}, "title": "P1.02-063 Mutation Profiling by Targeted Next-Generation Sequencing of an Unselected NSCLC Cohort", "authors": [{"family": "La Fleur", "given": "Linnea", "initials": "L"}, {"family": "Falk-Sorqvist", "given": "Elin", "initials": "E"}, {"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Sundstrom", "given": "Magnus", "initials": "M"}, {"family": "Mattsson", "given": "Johanna", "initials": "J"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Isaksson", "given": "Johan", "initials": "J"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Sandelin", "given": "Martin", "initials": "M"}, {"family": "Lamberg", "given": "Kristina", "initials": "K"}, {"family": "Landelius", "given": "Per", "initials": "P"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Moens", "given": "Lotte", "initials": "L"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "journal-article", "published": "2017-01-00", "journal": {"volume": "12", "issn": "1556-0864", "issue": "1", "pages": "S526-S527", "title": "Journal of Thoracic Oncology", "issn-l": "1556-0864"}, "abstract": null, "doi": "10.1016/j.jtho.2016.11.647", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-11-03T15:53:40.001Z", "modified": "2024-01-16T13:48:48.725Z"}, {"entity": "publication", "iuid": "15650b102c574ba3b445c90eef4e6c11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15650b102c574ba3b445c90eef4e6c11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15650b102c574ba3b445c90eef4e6c11"}}, "title": "Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.", "authors": [{"family": "Fletcher", "given": "Eugene", "initials": "E"}, {"family": "Feizi", "given": "Amir", "initials": "A"}, {"family": "Bisschops", "given": "Markus M M", "initials": "MMM"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Khoomrung", "given": "Sakda", "initials": "S"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2017-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "39", "issue": null, "pages": "19-28"}, "abstract": "Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest.", "doi": "10.1016/j.ymben.2016.10.010", "pmid": "27815194", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1096-7176(16)30175-6"}], "notes": [], "created": "2017-11-03T16:22:27.564Z", "modified": "2024-01-16T13:48:48.775Z"}, {"entity": "publication", "iuid": "a965f00cd08e43a19a3edd336da2cc19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a965f00cd08e43a19a3edd336da2cc19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a965f00cd08e43a19a3edd336da2cc19"}}, "title": "Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1.", "authors": [{"family": "Acevedo", "given": "Nathalie", "initials": "N"}, {"family": "Bornacelly", "given": "Adriana", "initials": "A"}, {"family": "Mercado", "given": "Dilia", "initials": "D"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Mittermann", "given": "Irene", "initials": "I"}, {"family": "Valenta", "given": "Rudolf", "initials": "R"}, {"family": "Kennedy", "given": "Malcolm", "initials": "M"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Caraballo", "given": "Luis", "initials": "L"}], "type": "journal article", "published": "2016-12-15", "journal": {"volume": "11", "issn": "1932-6203", "issue": "12", "pages": "e0167453", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Helminth infections and allergic diseases are associated with IgE hyperresponsiveness but the genetics of this phenotype remain to be defined. Susceptibility to Ascaris lumbricoides infection and antibody levels to this helminth are associated with polymorphisms in locus 13q33-34. We aimed to explore this and other genomic regions to identify genetic variants associated with the IgE responsiveness in humans. Forty-eight subjects from Cartagena, Colombia, with extreme values of specific IgE to Ascaris and ABA-1, a resistance marker of this nematode, were selected for targeted resequencing. Burden analyses were done comparing extreme groups for IgE values. One-hundred one SNPs were genotyped in 1258 individuals of two well-characterized populations from Colombia and Sweden. Two low-frequency coding variants in the gene encoding the Acidic Mammalian Chitinase (CHIA rs79500525, rs139812869, tagged by rs10494133) were found enriched in high IgE responders to ABA-1 and confirmed by genetic association analyses. The SNP rs4950928 in the Chitinase 3 Like 1 gene (CHI3L1) was associated with high IgE to ABA-1 in Colombians and with high IgE to Bet v 1 in the Swedish population. CHIA rs10494133 and ABDH13 rs3783118 were associated with IgE responses to Ascaris. SNPs in the Tumor Necrosis Factor Superfamily Member 13b gene (TNFSF13B) encoding the cytokine B cell activating Factor were associated with high levels of total IgE in both populations. This is the first report on the association between low-frequency and common variants in the chitinases-related genes CHIA and CHI3L1 with the intensity of specific IgE to ABA-1 in a population naturally exposed to Ascaris and with Bet v 1 in a Swedish population. Our results add new information about the genetic influences of human IgE responsiveness; since the genes encode for enzymes involved in the immune response to parasitic infections, they could be helpful for understanding helminth immunity and allergic responses. We also confirmed that TNFSF13B has an important and conserved role in the regulation of total IgE levels, which supports potential evolutionary links between helminth immunity and allergic response.", "doi": "10.1371/journal.pone.0167453", "pmid": "27977724", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-33646"}, {"db": "pmc", "key": "PMC5157985"}], "notes": [], "created": "2017-05-03T12:58:57.854Z", "modified": "2020-01-21T13:56:04.443Z"}, {"entity": "publication", "iuid": "5722f97ece754a98b422ac1b7114ae1d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5722f97ece754a98b422ac1b7114ae1d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5722f97ece754a98b422ac1b7114ae1d"}}, "title": "Disentangling genetic and epigenetic determinants of ultrafast adaptation.", "authors": [{"family": "Gjuvsland", "given": "Arne B", "initials": "AB"}, {"family": "Z\u00f6rg\u00f6", "given": "Enik\u00f6", "initials": "E"}, {"family": "Samy", "given": "Jeevan Ka", "initials": "JK"}, {"family": "Stenberg", "given": "Simon", "initials": "S"}, {"family": "Demirsoy", "given": "Ibrahim H", "initials": "IH"}, {"family": "Roque", "given": "Francisco", "initials": "F"}, {"family": "Maciaszczyk-Dziubinska", "given": "Ewa", "initials": "E"}, {"family": "Migocka", "given": "Magdalena", "initials": "M"}, {"family": "Alonso-Perez", "given": "Elisa", "initials": "E"}, {"family": "Zackrisson", "given": "Martin", "initials": "M"}, {"family": "Wysocki", "given": "Robert", "initials": "R"}, {"family": "Tam\u00e1s", "given": "Markus J", "initials": "MJ"}, {"family": "Jonassen", "given": "Inge", "initials": "I"}, {"family": "Omholt", "given": "Stig W", "initials": "SW"}, {"family": "Warringer", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2016-12-15", "journal": {"volume": "12", "issn": "1744-4292", "issue": "12", "pages": "892", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical-experimental framework for disclosing the presence of such adaptation-speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation-accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic-adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data-driven individual-based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation-speeding mechanisms in general.", "doi": "10.15252/msb.20166951", "pmid": "27979908", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5199126"}], "notes": [], "created": "2017-05-03T12:58:58.747Z", "modified": "2020-01-21T13:56:02.383Z"}, {"entity": "publication", "iuid": "af84b9a196824a34bd3fa45aa9f41ce5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af84b9a196824a34bd3fa45aa9f41ce5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af84b9a196824a34bd3fa45aa9f41ce5"}}, "title": "The In Vitro Stability of Circulating Tumour DNA.", "authors": [{"family": "Henao Diaz", "given": "Emanuela", "initials": "E"}, {"family": "Yachnin", "given": "Jeffrey", "initials": "J"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2016-12-13", "journal": {"volume": "11", "issn": "1932-6203", "issue": "12", "pages": "e0168153", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "DNA from apoptotic cancer cells, present in the circulation, has the potential to facilitate genomic profiling and disease monitoring. However, only low fractions of total cell-free DNA originates from cancer cells, limiting the applicability of circulating tumour DNA (ctDNA). Optimal sample processing is consequently of uttermost importance. Therefore, we evaluated the in vitro stability of ctDNA.\n\nBlood was collected in 10 ml EDTA or Streck tubes. Three conditions (EDTA and Streck tubes in room temperature, EDTA tubes at five degrees) and four time points (plasma harvested from blood aliquots of each 10 ml tube in a time series up to 24 h) were investigated. Each condition was evaluated in five metastatic prostate cancer patients. Subsequently, three additional patients were collected enabling investigation of the in vitro stability in EDTA tubes up to 48 h.\n\nThe in vitro stability of ctDNA was interrogated by low-pass whole genome sequencing which allows for the identification of somatic copy-number alterations (CNAs). In silico simulations demonstrated that non-parametric testing could detect a 1% contamination by white blood cell DNA. Mutational profiling was performed by targeted, in-solution based hybridization capture and subsequent sequencing. The allelic fraction of individual mutations was used as an estimate of the in vitro stability.\n\nSomatic CNAs were detected in all patients. Surprisingly, the ctDNA levels at zero hours were not significantly different to 24 or 48 hour in vitro incubation in any investigated condition. Subsequently, mutational profiling corroborated the conclusions from the CNA analysis.\n\nThe stability of ctDNA simplifies logistics without the requirement of immediate processing or applying fixatives to prevent white blood cell lysis.", "doi": "10.1371/journal.pone.0168153", "pmid": "27959945", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-23413"}, {"db": "pmc", "key": "PMC5154581"}], "notes": [], "created": "2017-05-03T12:58:59.341Z", "modified": "2020-01-21T13:56:04.618Z"}, {"entity": "publication", "iuid": "8a8e6eb7f7f94c1fb129b51ef32d3405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a8e6eb7f7f94c1fb129b51ef32d3405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a8e6eb7f7f94c1fb129b51ef32d3405"}}, "title": "Cluster Flow: A user-friendly bioinformatics workflow tool.", "authors": [{"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Krueger", "given": "Felix", "initials": "F"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Andrews", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2016-12-06", "journal": {"volume": "5", "issn": "2046-1402", "issue": null, "pages": "2824", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.", "doi": "10.12688/f1000research.10335.2", "pmid": "28299179", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5310375"}], "notes": [], "created": "2020-06-30T12:52:40.081Z", "modified": "2021-07-07T15:22:42.766Z"}, {"entity": "publication", "iuid": "a7f8cdcb464249c6878b51041d271c74", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7f8cdcb464249c6878b51041d271c74.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7f8cdcb464249c6878b51041d271c74"}}, "title": "Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.", "authors": [{"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R"}, {"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bj\u00f6rlenius", "given": "Berndt", "initials": "B"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Fick", "given": "Jerker", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2016-12-01", "journal": {"volume": "572", "issn": "1879-1026", "issue": null, "pages": "697-712", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "Sewage treatment plants (STPs) have repeatedly been suggested as \"hotspots\" for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.", "doi": "10.1016/j.scitotenv.2016.06.228", "pmid": "27542633", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(16)31417-6"}], "notes": [], "created": "2017-05-03T13:00:57.273Z", "modified": "2020-01-21T13:56:04.335Z"}, {"entity": "publication", "iuid": "d9586420d4b34537a01e2dbad1282dba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9586420d4b34537a01e2dbad1282dba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9586420d4b34537a01e2dbad1282dba"}}, "title": "Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family.", "authors": [{"family": "Brace", "given": "Selina", "initials": "S"}, {"family": "Thomas", "given": "Jessica A", "initials": "JA"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Burger", "given": "Joachim", "initials": "J"}, {"family": "MacPhee", "given": "Ross D E", "initials": "RD"}, {"family": "Barnes", "given": "Ian", "initials": "I"}, {"family": "Turvey", "given": "Samuel T", "initials": "ST"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "33", "issn": "1537-1719", "issue": "12", "pages": "3095-3103", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a \u223c750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as \"museums\" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.", "doi": "10.1093/molbev/msw186", "pmid": "27624716", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "msw186"}], "notes": [], "created": "2017-05-03T13:01:02.888Z", "modified": "2021-07-07T20:31:10.923Z"}, {"entity": "publication", "iuid": "a24e7ebb50c9439b8b7038899c4d1657", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a24e7ebb50c9439b8b7038899c4d1657.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a24e7ebb50c9439b8b7038899c4d1657"}}, "title": "Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.", "authors": [{"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "18", "issn": "1462-2920", "issue": "12", "pages": "4442-4455", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from \u223c0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 \u03bcm), relative to the medium (0.8-3.0 \u03bcm) and large (>3.0 \u03bcm) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.", "doi": "10.1111/1462-2920.13407", "pmid": "27306515", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:10.704Z", "modified": "2024-01-16T13:48:48.907Z"}, {"entity": "publication", "iuid": "d196fec9fa804725a0ee47d0c435b243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d196fec9fa804725a0ee47d0c435b243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d196fec9fa804725a0ee47d0c435b243"}}, "title": "Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea.", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DP"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}], "type": "journal article", "published": "2016-11-24", "journal": {"volume": "7", "issn": "1664-302X", "issue": null, "pages": "1883", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity.", "doi": "10.3389/fmicb.2016.01883", "pmid": "27933046", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5121245"}], "notes": [], "created": "2017-05-08T07:56:08.506Z", "modified": "2020-01-21T13:56:05.363Z"}, {"entity": "publication", "iuid": "ea3c7640be344f078a374d4ffec835f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ea3c7640be344f078a374d4ffec835f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ea3c7640be344f078a374d4ffec835f2"}}, "title": "A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.", "authors": [{"family": "Hefzi", "given": "Hooman", "initials": "H"}, {"family": "Ang", "given": "Kok Siong", "initials": "KS"}, {"family": "Hanscho", "given": "Michael", "initials": "M"}, {"family": "Bordbar", "given": "Aarash", "initials": "A"}, {"family": "Ruckerbauer", "given": "David", "initials": "D"}, {"family": "Lakshmanan", "given": "Meiyappan", "initials": "M"}, {"family": "Orellana", "given": "Camila A", "initials": "CA"}, {"family": "Baycin-Hizal", "given": "Deniz", "initials": "D"}, {"family": "Huang", "given": "Yingxiang", "initials": "Y"}, {"family": "Ley", "given": "Daniel", "initials": "D"}, {"family": "Martinez", "given": "Veronica S", "initials": "VS"}, {"family": "Kyriakopoulos", "given": "Sarantos", "initials": "S"}, {"family": "Jim\u00e9nez", "given": "Natalia E", "initials": "NE"}, {"family": "Zielinski", "given": "Daniel C", "initials": "DC"}, {"family": "Quek", "given": "Lake-Ee", "initials": "LE"}, {"family": "Wulff", "given": "Tune", "initials": "T"}, {"family": "Arnsdorf", "given": "Johnny", "initials": "J"}, {"family": "Li", "given": "Shangzhong", "initials": "S"}, {"family": "Lee", "given": "Jae Seong", "initials": "JS"}, {"family": "Paglia", "given": "Giuseppe", "initials": "G"}, {"family": "Loira", "given": "Nicolas", "initials": "N"}, {"family": "Spahn", "given": "Philipp N", "initials": "PN"}, {"family": "Pedersen", "given": "Lasse E", "initials": "LE"}, {"family": "Gutierrez", "given": "Jahir M", "initials": "JM"}, {"family": "King", "given": "Zachary A", "initials": "ZA"}, {"family": "Lund", "given": "Anne Mathilde", "initials": "AM"}, {"family": "Nagarajan", "given": "Harish", "initials": "H"}, {"family": "Thomas", "given": "Alex", "initials": "A"}, {"family": "Abdel-Haleem", "given": "Alyaa M", "initials": "AM"}, {"family": "Zanghellini", "given": "Juergen", "initials": "J"}, {"family": "Kildegaard", "given": "Helene F", "initials": "HF"}, {"family": "Voldborg", "given": "Bj\u00f8rn G", "initials": "BG"}, {"family": "Gerdtzen", "given": "Ziomara P", "initials": "ZP"}, {"family": "Betenbaugh", "given": "Michael J", "initials": "MJ"}, {"family": "Palsson", "given": "Bernhard O", "initials": "BO"}, {"family": "Andersen", "given": "Mikael R", "initials": "MR"}, {"family": "Nielsen", "given": "Lars K", "initials": "LK"}, {"family": "Borth", "given": "Nicole", "initials": "N"}, {"family": "Lee", "given": "Dong-Yup", "initials": "DY"}, {"family": "Lewis", "given": "Nathan E", "initials": "NE"}], "type": "journal article", "published": "2016-11-23", "journal": {"volume": "3", "issn": "2405-4712", "issue": "5", "pages": "434-443.e8", "title": "Cell Syst", "issn-l": null}, "abstract": "Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.", "doi": "10.1016/j.cels.2016.10.020", "pmid": "27883890", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S2405-4712(16)30363-5"}, {"db": "pmc", "key": "PMC5132346"}, {"db": "mid", "key": "NIHMS827636"}], "notes": [], "created": "2017-05-03T12:58:59.045Z", "modified": "2020-01-21T13:56:05.966Z"}, {"entity": "publication", "iuid": "9851dccf90c74df7b967de69cb54985c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9851dccf90c74df7b967de69cb54985c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9851dccf90c74df7b967de69cb54985c"}}, "title": "An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.", "authors": [{"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Fern\u00e1ndez Navarro", "given": "Jos\u00e9", "initials": "J"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2016-11-16", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "37137", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Furthermore, an increased understanding of tissue heterogeneity has lead to the development of several unique sequencing protocols that aim to retain or infer spatial context. In this study, a protocol for retaining spatial information of transcripts has been adapted to run on a robotic workstation. The method spatial transcriptomics is evaluated in terms of robustness and variability through the preparation of reference RNA, as well as through preparation and sequencing of six replicate sections of a gingival tissue biopsy from a patient with periodontitis. The results are reduced technical variability between replicates and a higher throughput, processing four times more samples with less than a third of the hands on time, compared to the standard protocol.", "doi": "10.1038/srep37137", "pmid": "27849009", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep37137"}, {"db": "pmc", "key": "PMC5111054"}], "notes": [], "created": "2017-05-03T13:00:03.893Z", "modified": "2024-01-16T13:48:48.988Z"}, {"entity": "publication", "iuid": "a2b8945b364b4f2696cc5cab53335002", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b8945b364b4f2696cc5cab53335002.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b8945b364b4f2696cc5cab53335002"}}, "title": "Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8\u00a0\u00b0C suggesting it is a eurypsychrophile.", "authors": [{"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Fridlund", "given": "Jimmy", "initials": "J"}, {"family": "Watkin", "given": "Elizabeth L", "initials": "EL"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-11-00", "journal": {"volume": "20", "issn": "1433-4909", "issue": "6", "pages": "903-913", "title": "Extremophiles", "issn-l": "1431-0651"}, "abstract": "Acidithiobacillus ferrivorans is an acidophilic bacterium that represents a substantial proportion of the microbial community in a low temperature mining waste stream. Due to its ability to grow at temperatures below 15\u00a0\u00b0C, it has previously been classified as 'psychrotolerant'. Low temperature-adapted microorganisms have strategies to grow at cold temperatures such as the production of cold acclimation proteins, DEAD/DEAH box helicases, and compatible solutes plus increasing their cellular membrane fluidity. However, little is known about At. ferrivorans adaptation strategies employed during culture at its temperature extremes. In this study, we report the transcriptomic response of At. ferrivorans SS3 to culture at 8\u00a0\u00b0C compared to 20\u00a0\u00b0C. Analysis revealed 373 differentially expressed genes of which, the majority were of unknown function. Only few changes in transcript counts of genes previously described to be cold adaptation genes were detected. Instead, cells cultured at cold (8\u00a0\u00b0C) altered the expression of a wide range of genes ascribed to functions in transcription, translation, and energy production. It is, therefore, suggested that a temperature of 8\u00a0\u00b0C imposed little cold stress on At. ferrivorans, underlining its adaptation to growth in the cold as well as suggesting it should be classified as a 'eurypsychrophile'.", "doi": "10.1007/s00792-016-0882-2", "pmid": "27783177", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00792-016-0882-2"}, {"db": "pmc", "key": "PMC5085989"}], "notes": [], "created": "2017-05-08T07:57:09.272Z", "modified": "2024-01-16T13:48:49.070Z"}, {"entity": "publication", "iuid": "953d1846d44d44799b45f228c942e31b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/953d1846d44d44799b45f228c942e31b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/953d1846d44d44799b45f228c942e31b"}}, "title": "Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells.", "authors": [{"family": "Ma", "given": "Yuanjun", "initials": "Y"}, {"family": "Miao", "given": "Yali", "initials": "Y"}, {"family": "Peng", "given": "Zhuochun", "initials": "Z"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "De St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Lennartsson", "given": "Lena", "initials": "L"}, {"family": "Liu", "given": "Yanling", "initials": "Y"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M"}, {"family": "Nilsson", "given": "Sten", "initials": "S"}, {"family": "Li", "given": "Chunde", "initials": "C"}], "type": "journal article", "published": "2016-10-24", "journal": {"volume": "5", "issn": "2193-1801", "issue": "1", "pages": "1861", "title": "Springerplus", "issn-l": "2193-1801"}, "abstract": "Docetaxel has been the standard first-line therapy in metastatic castration resistant prostate cancer. The survival benefit is, however, limited by either primary or acquired resistance. In this study, Du145 prostate cancer cells were converted to docetaxel-resistant cells Du145-R and Du145-RB by in vitro culturing. Next generation RNAseq was employed to analyze these cell lines. Forty-two genes were identified to have acquired mutations after the resistance development, of which thirty-four were found to have mutations in published sequencing studies using prostate cancer samples from patients. Fourteen novel and 2 previously known fusion genes were inferred from the RNA-seq data, and 13 of these were validated by RT-PCR and/or re-sequencing. Four in-frame fusion transcripts could be transcribed into fusion proteins in stably transfected HEK293 cells, including MYH9-EIF3D and LDLR-RPL31P11, which were specific identified or up-regulated in the docetaxel resistant DU145 cells. A panel of 615 gene transcripts was identified to have significantly changed expression profile in the docetaxel resistant cells. These transcriptional changes have potential for further study as predictive biomarkers and as targets of docetaxel treatment.", "doi": "10.1186/s40064-016-3543-0", "pmid": "27822437", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "3543"}, {"db": "pmc", "key": "PMC5078122"}], "notes": [], "created": "2017-05-08T07:58:23.221Z", "modified": "2024-01-16T13:48:49.104Z"}, {"entity": "publication", "iuid": "265ee528c68645a284f784e988878c51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/265ee528c68645a284f784e988878c51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/265ee528c68645a284f784e988878c51"}}, "title": "Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic.", "authors": [{"family": "Baltar", "given": "Federico", "initials": "F"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Palovaara", "given": "Joakim", "initials": "J"}, {"family": "Lekunberri", "given": "Itziar", "initials": "I"}, {"family": "Reinthaler", "given": "Thomas", "initials": "T"}, {"family": "Herndl", "given": "Gerhard J", "initials": "GJ"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2016-10-21", "journal": {"volume": "7", "issn": "1664-302X", "issue": null, "pages": "1670", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.", "doi": "10.3389/fmicb.2016.01670", "pmid": "27818655", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5073097"}], "notes": [], "created": "2017-05-03T13:00:31.010Z", "modified": "2024-01-16T13:48:49.113Z"}, {"entity": "publication", "iuid": "bf8d55f934a541faa1c01e2be78c1376", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf8d55f934a541faa1c01e2be78c1376.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf8d55f934a541faa1c01e2be78c1376"}}, "title": "Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells.", "authors": [{"family": "Panula", "given": "Sarita", "initials": "S"}, {"family": "Reda", "given": "Ahmed", "initials": "A"}, {"family": "Stukenborg", "given": "Jan-Bernd", "initials": "JB"}, {"family": "Ramathal", "given": "Cyril", "initials": "C"}, {"family": "Sukhwani", "given": "Meena", "initials": "M"}, {"family": "Albalushi", "given": "Halima", "initials": "H"}, {"family": "Edsg\u00e4rd", "given": "Daniel", "initials": "D"}, {"family": "Nakamura", "given": "Michiko", "initials": "M"}, {"family": "S\u00f6der", "given": "Olle", "initials": "O"}, {"family": "Orwig", "given": "Kyle E", "initials": "KE"}, {"family": "Yamanaka", "given": "Shinya", "initials": "S"}, {"family": "Reijo Pera", "given": "Renee A", "initials": "RA"}, {"family": "Hovatta", "given": "Outi", "initials": "O"}], "type": "journal article", "published": "2016-10-21", "journal": {"volume": "11", "issn": "1932-6203", "issue": "10", "pages": "e0165268", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The mechanisms underlying human germ cell development are largely unknown, partly due to the scarcity of primordial germ cells and the inaccessibility of the human germline to genetic analysis. Human embryonic stem cells can differentiate to germ cells in vitro and can be genetically modified to study the genetic requirements for germ cell development. Here, we studied NANOS3 and DAZL, which have critical roles in germ cell development in several species, via their over expression in human embryonic stem cells using global transcriptional analysis, in vitro germ cell differentiation, and in vivo germ cell formation assay by xenotransplantation. We found that NANOS3 over expression prolonged pluripotency and delayed differentiation. In addition, we observed a possible connection of NANOS3 with inhibition of apoptosis. For DAZL, our results suggest a post-transcriptional regulation mechanism in hES cells. In addition, we found that DAZL suppressed the translation of OCT4, and affected the transcription of several genes associated with germ cells, cell cycle arrest, and cell migration. Furthermore, DAZL over expressed cells formed spermatogonia-like colonies in a rare instance upon xenotransplantation. These data can be used to further elucidate the role of NANOS3 and DAZL in germ cell development both in vitro and in vivo.", "doi": "10.1371/journal.pone.0165268", "pmid": "27768780", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-35619"}, {"db": "pmc", "key": "PMC5074499"}], "notes": [], "created": "2017-05-03T13:00:26.654Z", "modified": "2024-01-16T13:48:49.123Z"}, {"entity": "publication", "iuid": "07c67e69fc3948739042d9185b0062de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07c67e69fc3948739042d9185b0062de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07c67e69fc3948739042d9185b0062de"}}, "title": "Gene-specific correlation of RNA and protein levels in human cells and tissues.", "authors": [{"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "comparative study", "published": "2016-10-20", "journal": {"volume": "12", "issn": "1744-4292", "issue": "10", "pages": "883", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.", "doi": "10.15252/msb.20167144", "pmid": "27951527", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5081484"}], "notes": [], "created": "2017-05-03T12:58:57.561Z", "modified": "2021-07-05T16:33:38.545Z"}, {"entity": "publication", "iuid": "e8dfff1926bb43dab23eea6f7b9e061b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e8dfff1926bb43dab23eea6f7b9e061b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e8dfff1926bb43dab23eea6f7b9e061b"}}, "title": "The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1.", "authors": [{"family": "S\u00e4vneby", "given": "Anna", "initials": "A"}, {"family": "Luthman", "given": "Johannes", "initials": "J"}, {"family": "Nordenskj\u00f6ld", "given": "Fabian", "initials": "F"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lindberg", "given": "A Michael", "initials": "AM"}], "type": "journal article", "published": "2016-10-19", "journal": {"volume": "11", "issn": "1932-6203", "issue": "10", "pages": "e0164548", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The transcriptomes of cells infected with lytic and non-lytic variants of coxsackievirus B2 Ohio-1 (CVB2O) were analyzed using next generation sequencing. This approach was selected with the purpose of elucidating the effects of lytic and non-lytic viruses on host cell transcription. Total RNA was extracted from infected cells and sequenced. The resulting reads were subsequently mapped against the human and CVB2O genomes. The amount of intracellular RNA was measured, indicating lower proportions of human RNA in the cells infected with the lytic virus compared to the non-lytic virus after 48 hours. This may be explained by reduced activity of the cellular transcription/translation machinery in lytic enteroviral replication due to activities of the enteroviral proteases 2A and/or 3C. Furthermore, differential expression in the cells infected with the two virus variants was identified and a number of transcripts were singled out as possible answers to the question of how the viruses interact with the host cells, resulting in lytic or non-lytic infections.", "doi": "10.1371/journal.pone.0164548", "pmid": "27760161", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-16-25162"}, {"db": "pmc", "key": "PMC5070843"}], "notes": [], "created": "2017-05-03T13:00:26.361Z", "modified": "2024-01-16T13:48:49.134Z"}, {"entity": "publication", "iuid": "f1cce8e886ef43968171b6032e2d342c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1cce8e886ef43968171b6032e2d342c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1cce8e886ef43968171b6032e2d342c"}}, "title": "Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites.", "authors": [{"family": "Grijseels", "given": "Sietske", "initials": "S"}, {"family": "Nielsen", "given": "Jens Christian", "initials": "JC", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Randelovic", "given": "Milica", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Nielsen", "given": "Kristian Fog", "initials": "KF"}, {"family": "Workman", "given": "Mhairi", "initials": "M"}, {"family": "Frisvad", "given": "Jens Christian", "initials": "JC"}], "type": "journal article", "published": "2016-10-14", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "35112", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311(T)\u2009=\u2009IBT 12289(T)). The genome was sequenced and assembled into 33.7\u2009Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species.", "doi": "10.1038/srep35112", "pmid": "27739446", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep35112"}, {"db": "pmc", "key": "PMC5064400"}], "notes": [], "created": "2017-05-03T13:00:03.295Z", "modified": "2024-01-16T13:48:49.145Z"}, {"entity": "publication", "iuid": "2e8f1d544b044178a9a6ac0e5f49534c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e8f1d544b044178a9a6ac0e5f49534c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e8f1d544b044178a9a6ac0e5f49534c"}}, "title": "Massive and parallel expression profiling using microarrayed single-cell sequencing.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Giatrellis", "given": "Sarantis", "initials": "S"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Navarro", "given": "Jos\u00e9 Fern\u00e1ndez", "initials": "JF"}, {"family": "Custodio", "given": "Joaquin", "initials": "J"}, {"family": "Bienko", "given": "Magda", "initials": "M"}, {"family": "Sutton", "given": "Lesley-Ann", "initials": "L"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2016-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "7", "issue": null, "pages": "13182"}, "abstract": "Single-cell transcriptome analysis overcomes problems inherently associated with averaging gene expression measurements in bulk analysis. However, single-cell analysis is currently challenging in terms of cost, throughput and robustness. Here, we present a method enabling massive microarray-based barcoding of expression patterns in single cells, termed MASC-seq. This technology enables both imaging and high-throughput single-cell analysis, characterizing thousands of single-cell transcriptomes per day at a low cost (0.13 USD/cell), which is two orders of magnitude less than commercially available systems. Our novel approach provides data in a rapid and simple way. Therefore, MASC-seq has the potential to accelerate the study of subtle clonal dynamics and help provide critical insights into disease development and other biological processes.", "doi": "10.1038/ncomms13182", "pmid": "27739429", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Advanced FISH Technologies": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "ncomms13182"}, {"db": "pmc", "key": "PMC5067491"}], "notes": [], "created": "2017-05-03T12:59:57.922Z", "modified": "2024-01-16T13:48:49.157Z"}, {"entity": "publication", "iuid": "37da054057334f7491acea69ccac08ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37da054057334f7491acea69ccac08ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37da054057334f7491acea69ccac08ca"}}, "title": "Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia.", "authors": [{"family": "Bogdanovic", "given": "G", "initials": "G"}, {"family": "Pou", "given": "C", "initials": "C"}, {"family": "Barrientos-Somarribas", "given": "M", "initials": "M"}, {"family": "Bjerkner", "given": "A", "initials": "A"}, {"family": "Honkaniemi", "given": "E", "initials": "E"}, {"family": "Allander", "given": "T", "initials": "T"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "Gustafsson", "given": "B", "initials": "B"}], "type": "journal article", "published": "2016-10-11", "journal": {"volume": "115", "issn": "1532-1827", "issue": "8", "pages": "1008-1014", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "Some childhood acute lymphoblastic leukaemias (ALL) can be traced back to a prenatal origin, where a virus infection could be involved in the first pre-leukaemic clone development. The DNA virome of 95 children who later developed ALL was characterised from neonatal blood spots (NBS) using unbiased next-generation sequencing (NGS) and compared with the virome of 95 non-ALL controls.\n\nDNA was individually extracted from the ALL-patients and controls, pooled, randomly amplified and sequenced using the Illumina MiSeq Sequencing System.\n\nVirus-like sequences identified in both groups mapped to human endogenous retroviruses and propionibacterium phage, considered a part of the normal microbial flora. Potential pathogens human herpesvirus type 6 (HHV-6) and parvovirus B19 were also identified, but only few samples in both ALL and controls tested positive by PCR follow-up.\n\nUnbiased NGS was employed to search for DNA from potential infectious agents in neonatal samples of children who later developed ALL. Although several viral candidates were identified in the NBS samples, further investigation by PCR suggested that these viruses did not have a major role in ALL development.", "doi": "10.1038/bjc.2016.261", "pmid": "27552439", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "bjc2016261"}, {"db": "pmc", "key": "PMC5061901"}], "notes": [], "created": "2017-05-03T12:59:54.986Z", "modified": "2024-01-16T13:48:49.189Z"}, {"entity": "publication", "iuid": "dc9edc5a5dc24559b72aaed9c365389f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc9edc5a5dc24559b72aaed9c365389f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc9edc5a5dc24559b72aaed9c365389f"}}, "title": "The structure and diversity of human, animal and environmental resistomes.", "authors": [{"family": "Pal", "given": "Chandan", "initials": "C"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2016-10-07", "journal": {"volume": "4", "issn": "2049-2618", "issue": "1", "pages": "54", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals. This paucity prevents efficient identification of risk environments.\n\nWe provide a comprehensive characterization of resistance genes, mobile genetic elements (MGEs) and bacterial taxonomic compositions for 864 metagenomes from humans (n\u2009=\u2009350), animals (n\u2009=\u2009145) and external environments (n\u2009=\u2009369), all deeply sequenced using Illumina technology. Environment types showed clear differences in both resistance profiles and bacterial community compositions. Human and animal microbial communities were characterized by limited taxonomic diversity and low abundance and diversity of biocide/metal resistance genes and MGEs but a relatively high abundance of ARGs. In contrast, external environments showed consistently high taxonomic diversity which in turn was linked to high diversity of both biocide/metal resistance genes and MGEs. Water, sediment and soil generally carried low relative abundance and few varieties of known ARGs, whereas wastewater/sludge was on par with the human gut. The environments with the largest relative abundance and/or diversity of ARGs, including genes encoding resistance to last resort antibiotics, were those subjected to industrial antibiotic pollution and a limited set of deeply sequenced air samples from a Beijing smog event.\n\nOur study identifies air and antibiotic-polluted environments as under-investigated transmission routes and reservoirs for antibiotic resistance. The high taxonomic and genetic diversity of external environments supports the hypothesis that these also form vast sources of unknown resistance genes, with potential to be transferred to pathogens in the future.", "doi": "10.1186/s40168-016-0199-5", "pmid": "27717408", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s40168-016-0199-5"}, {"db": "pmc", "key": "PMC5055678"}], "notes": [], "created": "2017-05-03T13:01:07.888Z", "modified": "2020-01-21T13:56:05.643Z"}, {"entity": "publication", "iuid": "ffdd5d444f57461cbd582c672f725ad8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffdd5d444f57461cbd582c672f725ad8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffdd5d444f57461cbd582c672f725ad8"}}, "title": "Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.", "authors": [{"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Codeluppi", "given": "Simone", "initials": "S"}, {"family": "Nishimura", "given": "Kaneyasu", "initials": "K"}, {"family": "Salto", "given": "Carmen", "initials": "C"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Borm", "given": "Lars E", "initials": "LE"}, {"family": "Stott", "given": "Simon R W", "initials": "SR"}, {"family": "Toledo", "given": "Enrique M", "initials": "EM"}, {"family": "Villaescusa", "given": "J Carlos", "initials": "JC"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Ryge", "given": "Jesper", "initials": "J"}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "comparative study", "published": "2016-10-06", "journal": {"volume": "167", "issn": "1097-4172", "issue": "2", "pages": "566-580.e19", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "Understanding human embryonic ventral midbrain is\u00a0of major interest for Parkinson's disease. However, the cell types, their gene expression dynamics, and\u00a0their relationship to commonly used rodent models remain to be defined. We performed single-cell RNA sequencing to examine ventral midbrain development in human and mouse. We found 25\u00a0molecularly defined human cell types, including five subtypes of radial glia-like cells and four progenitors. In the mouse, two mature fetal dopaminergic neuron subtypes diversified into five adult classes during postnatal development. Cell types and gene expression were generally conserved across species, but with clear differences in cell proliferation, developmental timing, and dopaminergic neuron development. Additionally, we developed a method to quantitatively assess the fidelity of dopaminergic neurons derived from human pluripotent stem cells,\u00a0at a single-cell level. Thus, our study provides insight into the molecular programs controlling human midbrain development and provides a foundation for the development of cell replacement therapies.", "doi": "10.1016/j.cell.2016.09.027", "pmid": "27716510", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0092-8674(16)31309-5"}, {"db": "pmc", "key": "PMC5055122"}], "notes": [], "created": "2017-05-03T12:59:49.639Z", "modified": "2024-01-16T13:48:49.223Z"}, {"entity": "publication", "iuid": "b7cde7b362a84da3b4a7bd88f1306b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7cde7b362a84da3b4a7bd88f1306b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7cde7b362a84da3b4a7bd88f1306b69"}}, "title": "MultiQC: summarize analysis results for multiple tools and samples in a single report.", "authors": [{"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}], "type": "journal article", "published": "2016-10-01", "journal": {"volume": "32", "issn": "1367-4811", "issue": "19", "pages": "3047-3048", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.\n\nWe present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.\n\nMultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info\n\nphil.ewels@scilifelab.se.", "doi": "10.1093/bioinformatics/btw354", "pmid": "27312411", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Stockholm (Genomics Applications)": "Technology development", "NGI Stockholm (Genomics Production)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "btw354"}, {"db": "pmc", "key": "PMC5039924"}], "notes": [], "created": "2017-05-03T13:00:06.264Z", "modified": "2024-01-16T13:48:49.233Z"}, {"entity": "publication", "iuid": "0057f3529cb84e27a762d14015b4ba3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0057f3529cb84e27a762d14015b4ba3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0057f3529cb84e27a762d14015b4ba3e"}}, "title": "Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity.", "authors": [{"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Kulyt\u00e9", "given": "Agn\u00e9", "initials": "A"}, {"family": "N\u00e4slund", "given": "Erik", "initials": "E"}, {"family": "Thorell", "given": "Anders", "initials": "A"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2016-10-00", "journal": {"volume": "65", "issn": "1939-327X", "issue": "10", "pages": "2980-2989", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Identification of rare sequencing variants with a larger functional impact has the potential to highlight new pathways contributing to obesity. Using whole-exome sequencing followed by genotyping, we have identified a low-frequency coding variant rs2076349 (V527M) in the laminin subunit \u03b23 (LAMB3) gene showing strong association with morbid obesity and thereby risk of type 2 diabetes. We exome-sequenced 200 morbidly obese subjects and 100 control subjects with pooled DNA samples. After several filtering steps, we retained 439 obesity-enriched low-frequency coding variants. Associations between genetic variants and obesity were validated sequentially in two case-control cohorts. In the final analysis of 1,911 morbidly obese and 1,274 control subjects, rs2076349 showed strong association with obesity (P = 9.67 \u00d7 10(-5); odds ratio 1.84). This variant was also associated with BMI and fasting serum leptin. Moreover, LAMB3 expression in adipose tissue was positively correlated with BMI and adipose morphology (few but large fat cells). LAMB3 knockdown by small interfering RNA in human adipocytes cultured in vitro inhibited adipogenesis. In conclusion, we identified a previously not reported low-frequency coding variant that was associated with morbid obesity in the LAMB3 gene. This gene may be involved in the development of excess body fat.", "doi": "10.2337/db16-0522", "pmid": "27431458", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "db16-0522"}], "notes": [], "created": "2017-05-03T13:00:29.532Z", "modified": "2024-01-16T13:48:49.242Z"}, {"entity": "publication", "iuid": "b4fdd09afe704791807a6bd40a0a66fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4fdd09afe704791807a6bd40a0a66fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4fdd09afe704791807a6bd40a0a66fc"}}, "title": "Towards integration of population and comparative genomics in forest trees.", "authors": [{"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal article", "published": "2016-10-00", "journal": {"volume": "212", "issn": "1469-8137", "issue": "2", "pages": "338-344", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.", "doi": "10.1111/nph.14153", "pmid": "27575589", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:58:59.932Z", "modified": "2020-01-21T13:56:04.739Z"}, {"entity": "publication", "iuid": "885ef4eea0274699a8ff4fe57d743b59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/885ef4eea0274699a8ff4fe57d743b59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/885ef4eea0274699a8ff4fe57d743b59"}}, "title": "Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples.", "authors": [{"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Skoog", "given": "Tiina", "initials": "T"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Kaartokallio", "given": "Tea", "initials": "T"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}, {"family": "Grauers", "given": "Anna", "initials": "A"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}, {"family": "Hyt\u00f6nen", "given": "Marjo", "initials": "M"}, {"family": "Lohi", "given": "Hannes", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Jiao", "given": "Hong", "initials": "H"}], "type": "journal article", "published": "2016-09-16", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "33256", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "High-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data. Both GATK and Freebayes displayed high sensitivity, specificity and accuracy when detecting rare or low-frequency variants. For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data. The MAF estimates from WGS correlated well (r\u2009=\u20090.94) with those from Illumina arrays. The MAFs from the pooled WES data also showed high concordance (r\u2009=\u20090.88) with those from the individual genotyping data. In conclusion, the MAFs estimated from pooled DNA sequencing data reflect the MAFs in individually genotyped samples well. The pooling strategy can thus be a rapid and cost-effective approach for the initial screening in large-scale association studies.", "doi": "10.1038/srep33256", "pmid": "27633116", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep33256"}, {"db": "pmc", "key": "PMC5025741"}], "notes": [], "created": "2017-05-03T13:00:02.994Z", "modified": "2024-01-16T13:48:49.513Z"}, {"entity": "publication", "iuid": "41ae0a76968243e097a7cb4c95df969c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41ae0a76968243e097a7cb4c95df969c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41ae0a76968243e097a7cb4c95df969c"}}, "title": "Absence of the Autophagy Adaptor SQSTM1/p62 Causes Childhood-Onset Neurodegeneration with Ataxia, Dystonia, and Gaze Palsy.", "authors": [{"family": "Haack", "given": "Tobias B", "initials": "TB"}, {"family": "Ignatius", "given": "Erika", "initials": "E"}, {"family": "Calvo-Garrido", "given": "Javier", "initials": "J"}, {"family": "Iuso", "given": "Arcangela", "initials": "A"}, {"family": "Isohanni", "given": "Pirjo", "initials": "P"}, {"family": "Maffezzini", "given": "Camilla", "initials": "C"}, {"family": "L\u00f6nnqvist", "given": "Tuula", "initials": "T"}, {"family": "Suomalainen", "given": "Anu", "initials": "A"}, {"family": "Gorza", "given": "Matteo", "initials": "M"}, {"family": "Kremer", "given": "Laura S", "initials": "LS"}, {"family": "Graf", "given": "Elisabeth", "initials": "E"}, {"family": "Hartig", "given": "Monika", "initials": "M"}, {"family": "Berutti", "given": "Riccardo", "initials": "R"}, {"family": "Paucar", "given": "Martin", "initials": "M"}, {"family": "Svenningsson", "given": "Per", "initials": "P"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Brandberg", "given": "G\u00f6ran", "initials": "G"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Kurian", "given": "Manju A", "initials": "MA"}, {"family": "Hayflick", "given": "Susan A", "initials": "SA"}, {"family": "Venco", "given": "Paola", "initials": "P"}, {"family": "Tiranti", "given": "Valeria", "initials": "V"}, {"family": "Strom", "given": "Tim M", "initials": "TM"}, {"family": "Dichgans", "given": "Martin", "initials": "M"}, {"family": "Horvath", "given": "Rita", "initials": "R"}, {"family": "Holinski-Feder", "given": "Elke", "initials": "E"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Prokisch", "given": "Holger", "initials": "H"}, {"family": "Senderek", "given": "Jan", "initials": "J"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}, {"family": "Carroll", "given": "Christopher J", "initials": "CJ"}, {"family": "Klopstock", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2016-09-01", "journal": {"volume": "99", "issn": "1537-6605", "issue": "3", "pages": "735-743", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "SQSTM1 (sequestosome 1; also known as p62) encodes a multidomain scaffolding protein involved in various key cellular processes, including the removal of damaged mitochondria by its function as a selective autophagy receptor. Heterozygous variants in SQSTM1 have been associated with Paget disease of the bone and might contribute to neurodegeneration in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Using exome sequencing, we identified three different biallelic loss-of-function variants in SQSTM1 in nine affected individuals from four families with a childhood- or adolescence-onset neurodegenerative disorder characterized by gait abnormalities, ataxia, dysarthria, dystonia, vertical gaze palsy, and cognitive decline. We confirmed absence of the SQSTM1/p62 protein in affected individuals' fibroblasts and found evidence of a defect in the early response to mitochondrial depolarization and autophagosome formation. Our findings expand the SQSTM1-associated phenotypic spectrum and lend further support to the concept of disturbed selective autophagy pathways in neurodegenerative diseases.", "doi": "10.1016/j.ajhg.2016.06.026", "pmid": "27545679", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S0002-9297(16)30230-0"}, {"db": "pmc", "key": "PMC5010644"}], "notes": [], "created": "2017-05-03T12:58:57.260Z", "modified": "2020-01-21T13:56:01.857Z"}, {"entity": "publication", "iuid": "c6c00c2e70f14617a41efb14396898a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6c00c2e70f14617a41efb14396898a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6c00c2e70f14617a41efb14396898a1"}}, "title": "The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.", "authors": [{"family": "Lindholm", "given": "Mal\u00e9ne E", "initials": "ME"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Werne Solnestam", "given": "Beata", "initials": "B"}, {"family": "Fischer", "given": "Helene", "initials": "H"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "12", "issn": "1553-7404", "issue": "9", "pages": "e1006294", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Regularly performed endurance training has many beneficial effects on health and skeletal muscle function, and can be used to prevent and treat common diseases e.g. cardiovascular disease, type II diabetes and obesity. The molecular adaptation mechanisms regulating these effects are incompletely understood. To date, global transcriptome changes in skeletal muscles have been studied at the gene level only. Therefore, global isoform expression changes following exercise training in humans are unknown. Also, the effects of repeated interventions on transcriptional memory or training response have not been studied before. In this study, 23 individuals trained one leg for three months. Nine months later, 12 of the same subjects trained both legs in a second training period. Skeletal muscle biopsies were obtained from both legs before and after both training periods. RNA sequencing analysis of all 119 skeletal muscle biopsies showed that training altered the expression of 3,404 gene isoforms, mainly associated with oxidative ATP production. Fifty-four genes had isoforms that changed in opposite directions. Training altered expression of 34 novel transcripts, all with protein-coding potential. After nine months of detraining, no training-induced transcriptome differences were detected between the previously trained and untrained legs. Although there were several differences in the physiological and transcriptional responses to repeated training, no coherent evidence of an endurance training induced transcriptional skeletal muscle memory was found. This human lifestyle intervention induced differential expression of thousands of isoforms and several transcripts from unannotated regions of the genome. It is likely that the observed isoform expression changes reflect adaptational mechanisms and processes that provide the functional and health benefits of regular physical activity.", "doi": "10.1371/journal.pgen.1006294", "pmid": "27657503", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5033478"}, {"db": "pii", "key": "PGENETICS-D-16-01025"}], "notes": [], "created": "2017-05-03T13:00:36.166Z", "modified": "2020-01-21T13:56:16.829Z"}, {"entity": "publication", "iuid": "df6351a484c54051a38d9271dbf5bdd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/df6351a484c54051a38d9271dbf5bdd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/df6351a484c54051a38d9271dbf5bdd3"}}, "title": "Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.", "authors": [{"family": "Ni", "given": "Gaofeng", "initials": "G"}, {"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Roman", "given": "Pawel", "initials": "P"}, {"family": "Wong", "given": "Zhen Lim", "initials": "ZL"}, {"family": "Bijmans", "given": "Martijn F M", "initials": "MF"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "167", "issn": "1769-7123", "issue": "7", "pages": "568-575", "title": "Res. Microbiol.", "issn-l": "0923-2508"}, "abstract": "Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72\u00a0\u00b1\u00a09\u00a0mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105\u00a0\u00b1\u00a042\u00a0mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology.", "doi": "10.1016/j.resmic.2016.04.010", "pmid": "27155452", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0923-2508(16)30012-2"}, {"db": "pmc", "key": "PMC5015573"}], "notes": [], "created": "2017-05-03T13:00:56.683Z", "modified": "2020-01-21T13:56:05.745Z"}, {"entity": "publication", "iuid": "0f0978e8393c47ffa311daa47b6c29a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f0978e8393c47ffa311daa47b6c29a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f0978e8393c47ffa311daa47b6c29a0"}}, "title": "The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.", "authors": [{"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Hrydziuszko", "given": "Olga", "initials": "O"}, {"family": "Mileti", "given": "Enrichetta", "initials": "E"}, {"family": "Raman", "given": "Amitha", "initials": "A"}, {"family": "Bornholdt", "given": "Jette", "initials": "J"}, {"family": "Boyd", "given": "Mette", "initials": "M"}, {"family": "Toft", "given": "Eva", "initials": "E"}, {"family": "Qvist", "given": "Veronica", "initials": "V"}, {"family": "N\u00e4slund", "given": "Erik", "initials": "E"}, {"family": "Thorell", "given": "Anders", "initials": "A"}, {"family": "Andersson", "given": "Daniel P", "initials": "DP"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Sandelin", "given": "Albin", "initials": "A"}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}, {"family": "Arner", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2016-08-30", "journal": {"volume": "16", "issn": "2211-1247", "issue": "9", "pages": "2317-2326", "title": "Cell Rep", "issn-l": null}, "abstract": "Metabolically healthy obese subjects display preserved insulin sensitivity and a beneficial white adipose tissue gene expression pattern. However, this observation stems from fasting studies when insulin levels are low. We investigated adipose gene expression by 5'Cap-mRNA sequencing in 17 healthy non-obese (NO), 21 insulin-sensitive severely obese (ISO), and 30 insulin-resistant severely obese (IRO) subjects, before and 2\u00a0hr into a hyperinsulinemic euglycemic clamp. ISO and IRO subjects displayed a clear but globally similar transcriptional response to\u00a0insulin, which differed from the small effects observed in NO subjects. In the obese, 231 genes were altered; 71 were enriched in ISO subjects (e.g., phosphorylation processes), and 52 were enriched in IRO subjects (e.g., cellular stimuli). Common cardio-metabolic risk factors and gender do not influence these findings. This study demonstrates that differences in the acute transcriptional response to insulin are primarily driven by obesity per se, challenging the notion of healthy obese adipose tissue, at least in severe obesity.", "doi": "10.1016/j.celrep.2016.07.070", "pmid": "27545890", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2211-1247(16)31014-2"}], "notes": [], "created": "2017-05-03T12:59:49.929Z", "modified": "2024-01-16T13:48:49.601Z"}, {"entity": "publication", "iuid": "386e79be64ed42d2af96c60e99239ea8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/386e79be64ed42d2af96c60e99239ea8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/386e79be64ed42d2af96c60e99239ea8"}}, "title": "Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.", "authors": [{"family": "Luo", "given": "Dan", "initials": "D"}, {"family": "Callari", "given": "Roberta", "initials": "R"}, {"family": "Hamberger", "given": "Britta", "initials": "B"}, {"family": "Wubshet", "given": "Sileshi Gizachew", "initials": "SG"}, {"family": "Nielsen", "given": "Morten T", "initials": "MT"}, {"family": "Andersen-Ranberg", "given": "Johan", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Cozzi", "given": "Federico", "initials": "F"}, {"family": "Heider", "given": "Harald", "initials": "H"}, {"family": "Lindberg M\u00f8ller", "given": "Birger", "initials": "B"}, {"family": "Staerk", "given": "Dan", "initials": "D"}, {"family": "Hamberger", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal article", "published": "2016-08-23", "journal": {"volume": "113", "issn": "1091-6490", "issue": "34", "pages": "E5082-E5089", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The seed oil of Euphorbia lathyris L. contains a series of macrocyclic diterpenoids known as Euphorbia factors. They are the current industrial source of ingenol mebutate, which is approved for the treatment of actinic keratosis, a precancerous skin condition. Here, we report an alcohol dehydrogenase-mediated cyclization step in the biosynthetic pathway of Euphorbia factors, illustrating the origin of the intramolecular carbon-carbon bonds present in lathyrane and ingenane diterpenoids. This unconventional cyclization describes the ring closure of the macrocyclic diterpene casbene. Through transcriptomic analysis of E. lathyris L. mature seeds and in planta functional characterization, we identified three enzymes involved in the cyclization route from casbene to jolkinol C, a lathyrane diterpene. These enzymes include two cytochromes P450 from the CYP71 clan and an alcohol dehydrogenase (ADH). CYP71D445 and CYP726A27 catalyze regio-specific 9-oxidation and 5-oxidation of casbene, respectively. When coupled with these P450-catalyzed monooxygenations, E. lathyris ADH1 catalyzes dehydrogenation of the hydroxyl groups, leading to the subsequent rearrangement and cyclization. The discovery of this nonconventional cyclization may provide the key link to complete elucidation of the biosynthetic pathways of ingenol mebutate and other bioactive macrocyclic diterpenoids.", "doi": "10.1073/pnas.1607504113", "pmid": "27506796", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "1607504113"}, {"db": "pmc", "key": "PMC5003294"}, {"db": "GENBANK", "key": "KR350665"}, {"db": "GENBANK", "key": "KR350666"}, {"db": "GENBANK", "key": "KR350667"}, {"db": "GENBANK", "key": "KR350668"}, {"db": "GENBANK", "key": "KR350669"}, {"db": "GENBANK", "key": "KR350671"}, {"db": "GENBANK", "key": "KX428471"}], "notes": [], "created": "2017-05-03T13:01:01.786Z", "modified": "2020-01-21T13:56:01.597Z"}, {"entity": "publication", "iuid": "f1a3c1a2a30547758a422c41afef02c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1a3c1a2a30547758a422c41afef02c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1a3c1a2a30547758a422c41afef02c2"}}, "title": "Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea", "authors": [{"family": "Vaquer-Sunyer", "given": "Raquel", "initials": "R", "orcid": "0000-0003-4507-0531", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a7963c9b1be4ff788d421562722493d.json"}}, {"family": "Reader", "given": "Heather E", "initials": "HE"}, {"family": "Muthusamy", "given": "Saraladevi", "initials": "S"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Conley", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0001-9668-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d95efcbb3ce8420494cbc2260d2b1aa1.json"}}, {"family": "Kritzberg", "given": "Emma S", "initials": "ES"}], "type": "journal-article", "published": "2016-08-23", "journal": {"volume": "13", "issn": "1726-4189", "issue": "16", "pages": "4751-4765", "title": "Biogeosciences", "issn-l": "1726-4170"}, "abstract": null, "doi": "10.5194/bg-13-4751-2016", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:56:04.096Z", "modified": "2021-06-21T15:55:50.792Z"}, {"entity": "publication", "iuid": "7d3a9a83444049e8b4d26652d57f1ad6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d3a9a83444049e8b4d26652d57f1ad6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d3a9a83444049e8b4d26652d57f1ad6"}}, "title": "Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.", "authors": [{"family": "Ivanov", "given": "Maxim", "initials": "M"}, {"family": "Kals", "given": "Mart", "initials": "M"}, {"family": "Lauschke", "given": "Volker", "initials": "V"}, {"family": "Barragan", "given": "Isabel", "initials": "I"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Ingelman-Sundberg", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2016-08-19", "journal": {"volume": "44", "issn": "1362-4962", "issue": "14", "pages": "6756-6769", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.", "doi": "10.1093/nar/gkw316", "pmid": "27131363", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Clinical Proteomics Mass spectrometry": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "gkw316"}, {"db": "pmc", "key": "PMC5001587"}], "notes": [], "created": "2017-05-03T13:00:08.926Z", "modified": "2024-01-16T13:48:49.630Z"}, {"entity": "publication", "iuid": "15d098c045bc40939df7005366ac9abf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15d098c045bc40939df7005366ac9abf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15d098c045bc40939df7005366ac9abf"}}, "title": "Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.", "authors": [{"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Cohain", "given": "Ariella", "initials": "A"}, {"family": "Akers", "given": "Nicholas K", "initials": "NK"}, {"family": "Di Narzo", "given": "Antonio", "initials": "A"}, {"family": "Talukdar", "given": "Husain A", "initials": "HA"}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Giambartolomei", "given": "Claudia", "initials": "C"}, {"family": "Fullard", "given": "John F", "initials": "JF"}, {"family": "Sukhavasi", "given": "Katyayani", "initials": "K"}, {"family": "K\u00f6ks", "given": "Sulev", "initials": "S"}, {"family": "Gan", "given": "Li-Ming", "initials": "LM"}, {"family": "Giannarelli", "given": "Chiara", "initials": "C"}, {"family": "Kovacic", "given": "Jason C", "initials": "JC"}, {"family": "Betsholtz", "given": "Christer", "initials": "C"}, {"family": "Losic", "given": "Bojan", "initials": "B"}, {"family": "Michoel", "given": "Tom", "initials": "T"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Roussos", "given": "Panos", "initials": "P"}, {"family": "Skogsberg", "given": "Josefin", "initials": "J"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JL"}], "type": "journal article", "published": "2016-08-19", "journal": {"volume": "353", "issn": "1095-9203", "issue": "6301", "pages": "827-830", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Genome-wide association studies (GWAS) have identified hundreds of cardiometabolic disease (CMD) risk loci. However, they contribute little to genetic variance, and most downstream gene-regulatory mechanisms are unknown. We genotyped and RNA-sequenced vascular and metabolic tissues from 600 coronary artery disease patients in the Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task study (STARNET). Gene expression traits associated with CMD risk single-nucleotide polymorphism (SNPs) identified by GWAS were more extensively found in STARNET than in tissue- and disease-unspecific gene-tissue expression studies, indicating sharing of downstream cis-/trans-gene regulation across tissues and CMDs. In contrast, the regulatory effects of other GWAS risk SNPs were tissue-specific; abdominal fat emerged as an important gene-regulatory site for blood lipids, such as for the low-density lipoprotein cholesterol and coronary artery disease risk gene PCSK9 STARNET provides insights into gene-regulatory mechanisms for CMD risk loci, facilitating their translation into opportunities for diagnosis, therapy, and prevention.", "doi": "10.1126/science.aad6970", "pmid": "27540175", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "353/6301/827"}], "notes": [], "created": "2017-05-03T13:00:15.132Z", "modified": "2024-01-16T13:48:49.639Z"}, {"entity": "publication", "iuid": "d20029cd97e5458ba383b2a258b01fe8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d20029cd97e5458ba383b2a258b01fe8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d20029cd97e5458ba383b2a258b01fe8"}}, "title": "The genome-scale DNA-binding profile of BarR, a \u03b2-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.", "authors": [{"family": "Liu", "given": "Han", "initials": "H"}, {"family": "Wang", "given": "Kun", "initials": "K"}, {"family": "Lind\u00e5s", "given": "Ann-Christin", "initials": "AC"}, {"family": "Peeters", "given": "Eveline", "initials": "E"}], "type": "journal article", "published": "2016-08-08", "journal": {"volume": "17", "issn": "1471-2164", "issue": null, "pages": "569", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a \u03b2-alanine aminotransferase gene, which is involved in \u03b2-alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the \u03b1-amino acids but interacts specifically with \u03b2-alanine. Besides the juxtaposed \u03b2-alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although \u03b2-alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective.\n\nWe characterized the genome-wide binding profile of BarR using chromatin immunoprecipation combined with high-throughput sequencing (ChIP-seq). This revealed 21 genomic binding loci. High-enrichment binding regions were validated to interact with purified BarR protein in vitro using electrophoretic mobility shift assays and almost all targets were also shown to harbour a conserved semi-palindromic binding motif. Only a small subset of enriched genomic sites are located in intergenic regions at a relative short distance to a promoter, and qRT-PCR analysis demonstrated that only one additional operon is under activation of BarR, namely the glutamine synthase operon. The latter is also a target of other Lrp-like transcription factors. Detailed inspection of the BarR ChIP-seq profile at the \u03b2-alanine aminotransferase promoter region in combination with binding motif predictions indicate that the operator structure is more complicated than previously anticipated, consisting of multiple (major and auxiliary) operators.\n\nBarR has a limited regulon, and includes also glutamine synthase genes besides the previously characterized \u03b2-alanine aminotransferase. Regulation of glutamine synthase is suggestive of a link between \u03b2-alanine and \u03b1-amino acid metabolism in S. acidocaldarius. Furthermore, this work reveals that the BarR regulon overlaps with that of other Lrp-like regulators.", "doi": "10.1186/s12864-016-2890-0", "pmid": "27502941", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-016-2890-0"}, {"db": "pmc", "key": "PMC4977709"}], "notes": [], "created": "2017-05-03T13:01:07.294Z", "modified": "2020-01-21T13:56:05.381Z"}, {"entity": "publication", "iuid": "655d9c88a16e40798a9d335394eb0836", "links": {"self": {"href": "https://publications.scilifelab.se/publication/655d9c88a16e40798a9d335394eb0836.json"}, "display": {"href": "https://publications.scilifelab.se/publication/655d9c88a16e40798a9d335394eb0836"}}, "title": "Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum.", "authors": [{"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Costantini", "given": "Alice", "initials": "A"}, {"family": "Coles", "given": "Nicole", "initials": "N"}, {"family": "Pekkinen", "given": "Minna", "initials": "M"}, {"family": "H\u00e9on", "given": "Elise", "initials": "E"}, {"family": "\u015e\u0131klar", "given": "Zeynep", "initials": "Z"}, {"family": "Berbero\u011flu", "given": "Merih", "initials": "M"}, {"family": "K\u00e4mpe", "given": "Anders", "initials": "A"}, {"family": "K\u0131yk\u0131m", "given": "Ertu\u011frul", "initials": "E"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "T\u00fcys\u00fcz", "given": "Beyhan", "initials": "B"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "31", "issn": "1523-4681", "issue": "8", "pages": "1577-1585", "title": "J. Bone Miner. Res.", "issn-l": "0884-0431"}, "abstract": "Spondyloocular syndrome is an autosomal-recessive disorder with spinal compression fractures, osteoporosis, and cataract. Mutations in XYLT2, encoding isoform of xylosyltransferase, were recently identified as the cause of the syndrome. We report on 4 patients, 2 unrelated patients and 2 siblings, with spondyloocular syndrome and novel mutations in XYLT2. Exome sequencing revealed a homozygous nonsense mutation, NM_022167.3(XYLT2): c.2188C>T, resulting in a premature stop codon (p.Arg730*) in a female patient. The patient presents visual impairment, generalized osteoporosis, short stature with short trunk, spinal compression fractures, and increased intervertebral disc space and hearing loss. We extended our XYLT2 analysis to a cohort of 22 patients with generalized osteoporosis, mostly from consanguineous families. In this cohort, we found by Sanger sequencing 2 siblings and 1 single patient who were homozygous for missense mutations in the XYLT2 gene (p.Arg563Gly and p.Leu605Pro). The patients had osteoporosis, compression fractures, cataracts, and hearing loss. Bisphosphonate treatment in 1 patient resulted in almost complete normalization of vertebral structures by adolescence, whereas treatment response in the others was variable. This report together with a previous study shows that mutations in the XYLT2 gene result in a variable phenotype dominated by spinal osteoporosis, cataract, and hearing loss. \u00a9 2016 American Society for Bone and Mineral Research.", "doi": "10.1002/jbmr.2834", "pmid": "26987875", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:59:45.537Z", "modified": "2024-01-16T13:48:49.688Z"}, {"entity": "publication", "iuid": "9dcc622ffa634ecb881934cd870a28c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dcc622ffa634ecb881934cd870a28c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dcc622ffa634ecb881934cd870a28c2"}}, "title": "Adaptation to different types of stress converge on mitochondrial metabolism", "authors": [{"family": "Lahtvee", "given": "Petri Jaan", "initials": "PJ", "orcid": "0000-0002-3327-3190", "researcher": {"href": "https://publications.scilifelab.se/researcher/8043cd36bb0e4cf3bc8a526dd45fa311.json"}}, {"family": "Kumar", "given": "Rahul", "initials": "R"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal-article", "published": "2016-08-00", "journal": {"volume": "27", "issn": "1059-1524", "issue": "15", "pages": "2505-2514", "title": "Mol. Biol. Cell", "issn-l": null}, "abstract": "Yeast cell factories encounter physical and chemical stresses when used for industrial production of fuels and chemicals. These stresses reduce productivity and increase bioprocess costs. Understanding the mechanisms of the stress response is essential for improving cellular robustness in platform strains. We investigated the three most commonly encountered industrial stresses for yeast (ethanol, salt, and temperature) to identify the mechanisms of general and stress-specific responses under chemostat conditions in which specific growth rate-dependent changes are eliminated. By applying systems-level analysis, we found that most stress responses converge on mitochondrial processes. Our analysis revealed that stress-specific factors differ between applied stresses; however, they are underpinned by an increased ATP demand. We found that when ATP demand increases to high levels, respiration cannot provide sufficient ATP, leading to onset of respirofermentative metabolism. Although stress-specific factors increase ATP demand for cellular growth under stressful conditions, increased ATP demand for cellular maintenance underpins a general stress response and is responsible for the onset of overflow metabolism.", "doi": "10.1091/mbc.e16-03-0187", "pmid": "27307591", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4966989"}, {"db": "pii", "key": "mbc.E16-03-0187"}], "notes": [], "created": "2017-05-03T13:00:05.969Z", "modified": "2024-01-16T13:48:49.776Z"}, {"entity": "publication", "iuid": "2e7aaf67a1334b1fad955fe8439da928", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e7aaf67a1334b1fad955fe8439da928.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e7aaf67a1334b1fad955fe8439da928"}}, "title": "Profiling cancer testis antigens in non-small-cell lung cancer.", "authors": [{"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Horie", "given": "Masafumi", "initials": "M"}, {"family": "Mattsson", "given": "Johanna Sofia Margareta", "initials": "JSM"}, {"family": "La Fleur", "given": "Linnea", "initials": "L"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Madjar", "given": "Katrin", "initials": "K"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "St\u00e5hle", "given": "Elisabeth", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Hengstler", "given": "Jan G", "initials": "JG"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Saito", "given": "Akira", "initials": "A"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2016-07-07", "journal": {"volume": "1", "issn": "2379-3708", "issue": "10", "pages": "e86837", "title": "JCI Insight", "issn-l": "2379-3708"}, "abstract": "Cancer testis antigens (CTAs) are of clinical interest as biomarkers and present valuable targets for immunotherapy. To comprehensively characterize the CTA landscape of non-small-cell lung cancer (NSCLC), we compared RNAseq data from 199 NSCLC tissues to the normal transcriptome of 142 samples from 32 different normal organs. Of 232 CTAs currently annotated in the Caner Testis Database (CTdatabase), 96 were confirmed in NSCLC. To obtain an unbiased CTA profile of NSCLC, we applied stringent criteria on our RNAseq data set and defined 90 genes as CTAs, of which 55 genes were not annotated in the CTdatabase, thus representing potential new CTAs. Cluster analysis revealed that CTA expression is histology dependent and concurrent expression is common. IHC confirmed tissue-specific protein expression of selected new CTAs (TKTL1, TGIF2LX, VCX, and CXORF67). Furthermore, methylation was identified as a regulatory mechanism of CTA expression based on independent data from The Cancer Genome Atlas. The proposed prognostic impact of CTAs in lung cancer was not confirmed, neither in our RNAseq cohort nor in an independent meta-analysis of 1,117 NSCLC cases. In summary, we defined a set of 90 reliable CTAs, including information on protein expression, methylation, and survival association. The detailed RNAseq catalog can guide biomarker studies and efforts to identify targets for immunotherapeutic strategies.", "doi": "10.1172/jci.insight.86837", "pmid": "27699219", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "86837"}, {"db": "pmc", "key": "PMC5033889"}], "notes": [], "created": "2017-05-08T07:56:19.862Z", "modified": "2024-01-16T13:48:49.815Z"}, {"entity": "publication", "iuid": "a54fcff0811145f6946e924649231bf8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a54fcff0811145f6946e924649231bf8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a54fcff0811145f6946e924649231bf8"}}, "title": "Exome sequencing in pooled DNA samples to identify maternal pre-eclampsia risk variants.", "authors": [{"family": "Kaartokallio", "given": "Tea", "initials": "T"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Heinonen", "given": "Seppo", "initials": "S"}, {"family": "Kajantie", "given": "Eero", "initials": "E"}, {"family": "Kivinen", "given": "Katja", "initials": "K"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}], "type": "journal article", "published": "2016-07-07", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "29085", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Pre-eclampsia is a common pregnancy disorder that is a major cause for maternal and perinatal mortality and morbidity. Variants predisposing to pre-eclampsia might be under negative evolutionary selection that is likely to keep their population frequencies low. We exome sequenced samples from a hundred Finnish pre-eclamptic women in pools of ten to screen for low-frequency, large-effect risk variants for pre-eclampsia. After filtering and additional genotyping steps, we selected 28 low-frequency missense, nonsense and splice site variants that were enriched in the pre-eclampsia pools compared to reference data, and genotyped the variants in 1353 pre-eclamptic and 699 non-pre-eclamptic women to test the association of them with pre-eclampsia and quantitative traits relevant for the disease. Genotypes from the SISu project (n\u2009=\u20096118 exome sequenced Finnish samples) were included in the binary trait association analysis as a population reference to increase statistical power. In these analyses, none of the variants tested reached genome-wide significance. In conclusion, the genetic risk for pre-eclampsia is likely complex even in a population isolate like Finland, and larger sample sizes will be necessary to detect risk variants.", "doi": "10.1038/srep29085", "pmid": "27384325", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep29085"}, {"db": "pmc", "key": "PMC4935848"}], "notes": [], "created": "2017-05-03T13:00:02.106Z", "modified": "2024-01-16T13:48:49.832Z"}, {"entity": "publication", "iuid": "5eb535697db247e48ae113f2bc551f7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5eb535697db247e48ae113f2bc551f7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5eb535697db247e48ae113f2bc551f7a"}}, "title": "Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem.", "authors": [{"family": "Asplund-Samuelsson", "given": "Johannes", "initials": "J"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Dupont", "given": "Chris L", "initials": "CL"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "McCrow", "given": "John P", "initials": "JP"}, {"family": "Celepli", "given": "Narin A", "initials": "NA"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Ekman", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2016-07-06", "journal": {"volume": "7", "issn": "1664-302X", "issue": null, "pages": "1043", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (>0.8 \u03bcm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.", "doi": "10.3389/fmicb.2016.01043", "pmid": "27458440", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4933709"}], "notes": [], "created": "2017-05-03T13:00:30.711Z", "modified": "2024-01-16T13:48:49.840Z"}, {"entity": "publication", "iuid": "4be007a3a4414a64b991907f260116cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4be007a3a4414a64b991907f260116cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4be007a3a4414a64b991907f260116cc"}}, "title": "Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.", "authors": [{"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Salm\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-8728-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/32ce477474f8488ea726ed1214d8e568.json"}}, {"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Navarro", "given": "Jos\u00e9 Fern\u00e1ndez", "initials": "JF"}, {"family": "Magnusson", "given": "Jens", "initials": "J"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Asp", "given": "Michaela", "initials": "M"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Codeluppi", "given": "Simone", "initials": "S"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Costea", "given": "Paul Igor", "initials": "PI"}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Bergmann", "given": "Olaf", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2016-07-01", "journal": {"volume": "353", "issn": "1095-9203", "issue": "6294", "pages": "78-82", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Analysis of the pattern of proteins or messengerRNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call \"spatial transcriptomics,\" that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.", "doi": "10.1126/science.aaf2403", "pmid": "27365449", "labels": {"Fluorescence Tissue Profiling": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "353/6294/78"}], "notes": [], "created": "2017-05-03T12:59:11.066Z", "modified": "2024-01-16T13:48:49.862Z"}, {"entity": "publication", "iuid": "73fb4760d9374f6ba0ea45f9bbce78f3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73fb4760d9374f6ba0ea45f9bbce78f3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73fb4760d9374f6ba0ea45f9bbce78f3"}}, "title": "Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.", "authors": [{"family": "Scott", "given": "Alison Dawn", "initials": "AD"}, {"family": "Stenz", "given": "Noah W M", "initials": "NW"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Baum", "given": "David A", "initials": "DA"}], "type": "journal article", "published": "2016-07-00", "journal": {"volume": "211", "issn": "1469-8137", "issue": "1", "pages": "186-193", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "Polyploidy is common and an important evolutionary factor in most land plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia sempervirens) is one of just two polyploid conifer species and the only hexaploid. Evidence from fossil guard cell size suggests that polyploidy in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of polyploidy and parental genome donors have been proposed, based primarily on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and close relatives. Our data show that hexaploidy in coast redwood is best explained by autopolyploidy or, if there was allopolyploidy, it happened within the Californian redwood clade. We found that duplicate genes have more similar sequences than expected, given the age of the inferred polyploidization. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following polyploidization. We extrapolate from this to suggest that the rarity of polyploidy in gymnosperms may be due to slow diploidization in this clade.", "doi": "10.1111/nph.13930", "pmid": "26996245", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:58:51.976Z", "modified": "2020-01-21T13:56:03.006Z"}, {"entity": "publication", "iuid": "0b270065144c45d3be7bb731e39ef1e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b270065144c45d3be7bb731e39ef1e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b270065144c45d3be7bb731e39ef1e1"}}, "title": "Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.", "authors": [{"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}], "type": "journal article", "published": "2016-07-00", "journal": {"volume": "33", "issn": "1537-1719", "issue": "7", "pages": "1754-1767", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged \u223c2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.", "doi": "10.1093/molbev/msw051", "pmid": "26983554", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "msw051"}, {"db": "pmc", "key": "PMC4915356"}], "notes": [], "created": "2017-05-08T07:57:57.486Z", "modified": "2024-01-16T13:48:49.870Z"}, {"entity": "publication", "iuid": "f9f0e902f6c047979bcacdce63d41ded", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9f0e902f6c047979bcacdce63d41ded.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9f0e902f6c047979bcacdce63d41ded"}}, "title": "The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.", "authors": [{"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Engstr\u00f6m", "given": "P\u00e4r G", "initials": "PG", "orcid": "0000-0001-5265-2121", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce330ec225f4a8595932d092ab8c8d1.json"}}, {"family": "Helgadottir", "given": "Hildur", "initials": "H"}, {"family": "Eriksson", "given": "Hanna", "initials": "H"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Kjellqvist", "given": "Sanela", "initials": "S"}, {"family": "Yang", "given": "Muyi", "initials": "M"}, {"family": "Lind\u00e9n", "given": "Diana", "initials": "D"}, {"family": "Edsg\u00e4rd", "given": "Daniel", "initials": "D"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}], "type": "journal article", "published": "2016-07-00", "journal": {"volume": "55", "issn": "1098-2264", "issue": "7", "pages": "601-611", "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "We applied a targeted sequencing approach to identify germline mutations conferring a moderately to highly increased risk of cutaneous and uveal melanoma. Ninety-two high-risk melanoma patients were screened for inherited variation in 120 melanoma candidate genes. Observed gene variants were filtered based on frequency in reference populations, cosegregation with melanoma in families and predicted functional effect. Several novel or rare genetic variants in genes involved in DNA damage response, cell-cycle regulation and transcriptional control were identified in melanoma patients. Among identified genetic alterations was an extremely rare variant (minor allele frequency of 0.00008) in the BRIP1 gene that was found to cosegregate with the melanoma phenotype. We also found a rare nonsense variant in the BRCA2 gene (rs11571833), previously associated with cancer susceptibility but not with melanoma, which showed weak association with melanoma susceptibility in the Swedish population. Our results add to the growing knowledge about genetic factors associated with melanoma susceptibility and also emphasize the role of DNA damage response as an important factor in melanoma etiology. \u00a9 2016 Wiley Periodicals, Inc.", "doi": "10.1002/gcc.22363", "pmid": "27074266", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:33.369Z", "modified": "2021-06-16T15:35:27.441Z"}, {"entity": "publication", "iuid": "3b52e3c7526943d1b8b54ff7a20ccc28", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b52e3c7526943d1b8b54ff7a20ccc28.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b52e3c7526943d1b8b54ff7a20ccc28"}}, "title": "The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes.", "authors": [{"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Zettermark", "given": "Sofia", "initials": "S"}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Behrendtz", "given": "Mikael", "initials": "M"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "journal article", "published": "2016-07-00", "journal": {"volume": "174", "issn": "1365-2141", "issue": "2", "pages": "292-301", "title": "Br. J. Haematol.", "issn-l": "0007-1048"}, "abstract": "Cytogenetic analyses of a consecutive series of 67 paediatric (median age 8\u00a0years; range 0-17) de novo acute myeloid leukaemia (AML) patients revealed aberrations in 55 (82%) cases. The most common subgroups were KMT2A rearrangement (29%), normal karyotype (15%), RUNX1-RUNX1T1 (10%), deletions of 5q, 7q and/or 17p (9%), myeloid leukaemia associated with Down syndrome (7%), PML-RARA (7%) and CBFB-MYH11 (5%). Single nucleotide polymorphism array (SNP-A) analysis and exon sequencing of 100 genes, performed in 52 and 40 cases, respectively (39 overlapping), revealed \u22651 aberration in 89%; when adding cytogenetic data, this frequency increased to 98%. Uniparental isodisomies (UPIDs) were detected in 13% and copy number aberrations (CNAs) in 63% (median 2/case); three UPIDs and 22 CNAs were recurrent. Twenty-two genes were targeted by focal CNAs, including AEBP2 and PHF6 deletions and genes involved in AML-associated gene fusions. Deep sequencing identified mutations in 65% of cases (median 1/case). In total, 60 mutations were found in 30 genes, primarily those encoding signalling proteins (47%), transcription factors (25%), or epigenetic modifiers (13%). Twelve genes (BCOR, CEBPA, FLT3, GATA1, KIT, KRAS, NOTCH1, NPM1, NRAS, PTPN11, SMC3 and TP53) were recurrently mutated. We conclude that SNP-A and deep sequencing analyses complement the cytogenetic diagnosis of paediatric AML.", "doi": "10.1111/bjh.14056", "pmid": "27022003", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:12.784Z", "modified": "2024-01-16T13:48:49.878Z"}, {"entity": "publication", "iuid": "7f184b2951e849249cd85c696ebbe9df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f184b2951e849249cd85c696ebbe9df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f184b2951e849249cd85c696ebbe9df"}}, "title": "Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.", "authors": [{"family": "Yau", "given": "Anthony C Y", "initials": "AC"}, {"family": "Tuncel", "given": "Jonatan", "initials": "J"}, {"family": "Haag", "given": "Sabrina", "initials": "S"}, {"family": "Norin", "given": "Ulrika", "initials": "U"}, {"family": "Houtman", "given": "Miranda", "initials": "M"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Holmdahl", "given": "Rikard", "initials": "R"}], "type": "journal article", "published": "2016-06-28", "journal": {"volume": "113", "issn": "1091-6490", "issue": "26", "pages": "E3716-E3724", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Genome-wide association studies have revealed many genetic loci associated with complex autoimmune diseases. In rheumatoid arthritis (RA), the MHC gene HLA-DRB1 is the strongest candidate predicting disease development. It has been suggested that other immune-regulating genes in the MHC contribute to the disease risk, but this contribution has been difficult to show because of the strong linkage disequilibrium within the MHC. We isolated genomic regions in the form of congenic fragments in rats to test whether there are additional susceptibility loci in the MHC. By both congenic mapping in inbred strains and SNP typing in wild rats, we identified a conserved, 33-kb large haplotype Ltab-Ncr3 in the MHC-III region, which regulates the onset, severity, and chronicity of arthritis. The Ltab-Ncr3 haplotype consists of five polymorphic immunoregulatory genes: Lta (lymphotoxin-\u03b1), Tnf, Ltb (lymphotoxin-\u03b2), Lst1 (leukocyte-specific transcript 1), and Ncr3 (natural cytotoxicity-triggering receptor 3). Significant correlation in the expression of the Ltab-Ncr3 genes suggests that interaction of these genes may be important in keeping these genes clustered together as a conserved haplotype. We studied the arthritis association and the spliceo-transcriptome of four different Ltab-Ncr3 haplotypes and showed that higher Ltb and Ncr3 expression, lower Lst1 expression, and the expression of a shorter splice variant of Lst1 correlate with reduced arthritis severity in rats. Interestingly, patients with mild RA also showed higher NCR3 expression and lower LST1 expression than patients with severe RA. These data demonstrate the importance of a conserved haplotype in the regulation of complex diseases such as arthritis.", "doi": "10.1073/pnas.1600567113", "pmid": "27303036", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1600567113"}, {"db": "pmc", "key": "PMC4932949"}], "notes": [], "created": "2017-05-03T13:00:04.787Z", "modified": "2024-01-16T13:48:49.914Z"}, {"entity": "publication", "iuid": "ef398bc7e3dd48a38a05d94d36cd4787", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef398bc7e3dd48a38a05d94d36cd4787.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef398bc7e3dd48a38a05d94d36cd4787"}}, "title": "Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d15be15c484e6a99f22b466bf99166.json"}}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications.scilifelab.se/researcher/badb913f91e14489aca247ee841e1608.json"}}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "Engstrand", "given": "Lars", "initials": "L", "orcid": "0000-0002-7713-2373", "researcher": {"href": "https://publications.scilifelab.se/researcher/857abb528bdb4661803b77b4deb693e0.json"}}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ERB"}], "type": "journal article", "published": "2016-06-16", "journal": {"title": "Genome Announc", "issn": "2169-8287", "issn-l": "2169-8287", "volume": "4", "issue": "3", "pages": "e00552-16"}, "abstract": "Moraxella catarrhalis is a Gram-negative commensal and pathogenic bacterium found in the human respiratory tract. It is associated with otitis media and respiratory tract infections. Here, we report the draft genome sequence of M. catarrhalis type strain CCUG 353(T), composed of 18 contigs and a total size of 1.89 Mb.", "doi": "10.1128/genomeA.00552-16", "pmid": "27313296", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4/3/e00552-16"}, {"db": "pmc", "key": "PMC4911475"}], "notes": [], "created": "2017-05-08T07:58:54.487Z", "modified": "2023-05-15T16:46:23.175Z"}, {"entity": "publication", "iuid": "883f1bc7adcc44ecb1c8c23a7f1a2360", "links": {"self": {"href": "https://publications.scilifelab.se/publication/883f1bc7adcc44ecb1c8c23a7f1a2360.json"}, "display": {"href": "https://publications.scilifelab.se/publication/883f1bc7adcc44ecb1c8c23a7f1a2360"}}, "title": "Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.", "authors": [{"family": "Marques", "given": "Sueli", "initials": "S"}, {"family": "Zeisel", "given": "Amit", "initials": "A"}, {"family": "Codeluppi", "given": "Simone", "initials": "S"}, {"family": "van Bruggen", "given": "David", "initials": "D"}, {"family": "Mendanha Falc\u00e3o", "given": "Ana", "initials": "A"}, {"family": "Xiao", "given": "Lin", "initials": "L"}, {"family": "Li", "given": "Huiliang", "initials": "H"}, {"family": "H\u00e4ring", "given": "Martin", "initials": "M"}, {"family": "Hochgerner", "given": "Hannah", "initials": "H"}, {"family": "Romanov", "given": "Roman A", "initials": "RA"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Mu\u00f1oz-Manchado", "given": "Ana B", "initials": "AB"}, {"family": "La Manno", "given": "Gioele", "initials": "G"}, {"family": "L\u00f6nnerberg", "given": "Peter", "initials": "P"}, {"family": "Floriddia", "given": "Elisa M", "initials": "EM"}, {"family": "Rezayee", "given": "Fatemah", "initials": "F"}, {"family": "Ernfors", "given": "Patrik", "initials": "P"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}, {"family": "Hjerling-Leffler", "given": "Jens", "initials": "J"}, {"family": "Harkany", "given": "Tibor", "initials": "T"}, {"family": "Richardson", "given": "William D", "initials": "WD"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Castelo-Branco", "given": "Gon\u00e7alo", "initials": "G"}], "type": "journal article", "published": "2016-06-10", "journal": {"volume": "352", "issn": "1095-9203", "issue": "6291", "pages": "1326-1329", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Oligodendrocytes have been considered as a functionally homogeneous population in the central nervous system (CNS). We performed single-cell RNA sequencing on 5072 cells of the oligodendrocyte lineage from 10 regions of the mouse juvenile and adult CNS. Thirteen distinct populations were identified, 12 of which represent a continuum from Pdgfra(+) oligodendrocyte precursor cells (OPCs) to distinct mature oligodendrocytes. Initial stages of differentiation were similar across the juvenile CNS, whereas subsets of mature oligodendrocytes were enriched in specific regions in the adult brain. Newly formed oligodendrocytes were detected in the adult CNS and were responsive to complex motor learning. A second Pdgfra(+) population, distinct from OPCs, was found along vessels. Our study reveals the dynamics of oligodendrocyte differentiation and maturation, uncoupling them at a transcriptional level and highlighting oligodendrocyte heterogeneity in the CNS.", "doi": "10.1126/science.aaf6463", "pmid": "27284195", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "352/6291/1326"}, {"db": "pmc", "key": "PMC5221728"}, {"db": "mid", "key": "EMS70326"}], "notes": [], "created": "2017-05-03T13:00:15.943Z", "modified": "2024-01-16T13:48:49.941Z"}, {"entity": "publication", "iuid": "d6566bda63754a63b60586649f4d755f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6566bda63754a63b60586649f4d755f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6566bda63754a63b60586649f4d755f"}}, "title": "GPR44 is a pancreatic protein restricted to the human beta cell.", "authors": [{"family": "Hellstr\u00f6m-Lindahl", "given": "Ewa", "initials": "E"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Czernichow", "given": "Paul", "initials": "P"}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Eriksson", "given": "Olof", "initials": "O"}], "type": "journal article", "published": "2016-06-00", "journal": {"volume": "53", "issn": "1432-5233", "issue": "3", "pages": "413-421", "title": "Acta Diabetol", "issn-l": "0940-5429"}, "abstract": "To address questions regarding onset and progression of types 1 and 2 diabetes (T1D/T2D), surrogate imaging biomarkers for beta cell function and mass are needed. Here, we assess the potential of GPR44 as a surrogate marker for beta cells, in a direct comparison with clinically used biomarker VMAT2.\n\nGPR44 surface availability was assessed by flow cytometry of human beta cells. RNA transcription levels in different pancreas compartments were evaluated. The density of GPR44 receptor in endocrine and exocrine tissues was assessed by the radiolabeled GPR44 ligand [(3)H]AZD 3825. A direct comparison with the established beta cell marker VMAT2 was performed by radiolabeled [(3)H]DTBZ.\n\nGPR44 was available on the cell surface, and pancreatic RNA levels were restricted to the islets of Langerhans. [(3)H]AZD 3825 had nanomolar affinity for GPR44 in human islets and EndoC-\u03b2H1 beta cells, and the specific binding to human beta cells was close to 50 times higher than in exocrine preparations. The endocrine-to-exocrine binding ratio was approximately 10 times higher for [(3)H]AZD 3825 than for [(3)H]DTBZ.\n\nGPR44 is a highly beta cell-specific target, which potentially offers improved imaging contrast between the human beta cell and the exocrine pancreas.", "doi": "10.1007/s00592-015-0811-3", "pmid": "26467464", "labels": {"National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00592-015-0811-3"}], "notes": [], "created": "2017-05-02T12:57:14.826Z", "modified": "2024-01-16T13:48:50.009Z"}, {"entity": "publication", "iuid": "983e3dc201174745abf9b9631372f639", "links": {"self": {"href": "https://publications.scilifelab.se/publication/983e3dc201174745abf9b9631372f639.json"}, "display": {"href": "https://publications.scilifelab.se/publication/983e3dc201174745abf9b9631372f639"}}, "title": "The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila.", "authors": [{"family": "Dantoft", "given": "Widad", "initials": "W"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Esfahani", "given": "Shiva Seyedoleslami", "initials": "SS"}, {"family": "Engstr\u00f6m", "given": "Ylva", "initials": "Y"}], "type": "journal article", "published": "2016-05-28", "journal": {"volume": "8", "issn": "1662-8128", "issue": "4", "pages": "412-426", "title": "J Innate Immun", "issn-l": "1662-811X"}, "abstract": "Maintenance of a stable gut microbial community relies on a delicate balance between immune defense and immune tolerance. We have used Drosophila to study how the microbial gut flora is affected by changes in host genetic factors and immunity. Flies with a constitutively active gut immune system, due to a mutation in the POU transcriptional regulator Pdm1/nubbin (nub) gene, had higher loads of bacteria and a more diverse taxonomic composition than controls. In addition, the microbial composition shifted considerably during the short lifespan of the nub1 mutants. This shift was characterized by a loss of relatively few OTUs (operational taxonomic units) and a remarkable increase in a large number of Acetobacter spp. and Leuconostoc spp. Treating nub1 mutant flies with antibiotics prolonged their lifetime survival by more than 100%. Immune gene expression was also persistently high in the presence of antibiotics, indicating that the early death was not a direct consequence of an overactive immune defense but rather an indirect consequence of the microbial load and composition. Thus, changes in host genotype and an inability to regulate the normal growth and composition of the gut microbiota leads to a shift in the microbial community, dysbiosis and early death.", "doi": "10.1159/000446368", "pmid": "27231014", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "000446368"}], "notes": [], "created": "2017-05-03T13:01:06.196Z", "modified": "2020-01-21T13:56:03.921Z"}, {"entity": "publication", "iuid": "1f569b02fad4412093fb86a85265123f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f569b02fad4412093fb86a85265123f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f569b02fad4412093fb86a85265123f"}}, "title": "Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30\u2009\u00b0C.", "authors": [{"family": "Caspeta", "given": "Luis", "initials": "L"}, {"family": "Chen", "given": "Yun", "initials": "Y"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2016-05-27", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "27003", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Exposure to long-term environmental changes across >100s of generations results in adapted phenotypes, but little is known about how metabolic and transcriptional responses are optimized in these processes. Here, we show that thermotolerant yeast strains selected by adaptive laboratory evolution to grow at increased temperature, activated a constitutive heat stress response when grown at the optimal ancestral temperature, and that this is associated with a reduced growth rate. This preventive response was perfected by additional transcriptional changes activated when the cultivation temperature is increased. Remarkably, the sum of global transcriptional changes activated in the thermotolerant strains when transferred from the optimal to the high temperature, corresponded, in magnitude and direction, to the global changes observed in the ancestral strain exposed to the same transition. This demonstrates robustness of the yeast transcriptional program when exposed to heat, and that the thermotolerant strains streamlined their path to rapidly and optimally reach post-stress transcriptional and metabolic levels. Thus, long-term adaptation to heat improved yeasts ability to rapidly adapt to increased temperatures, but this also causes a trade-off in the growth rate at the optimal ancestral temperature.", "doi": "10.1038/srep27003", "pmid": "27229477", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep27003"}, {"db": "pmc", "key": "PMC4882594"}], "notes": [], "created": "2017-05-03T13:00:01.805Z", "modified": "2024-01-16T13:48:50.050Z"}, {"entity": "publication", "iuid": "79b25de8804c4969841cf047609ff26d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79b25de8804c4969841cf047609ff26d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79b25de8804c4969841cf047609ff26d"}}, "title": "Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.", "authors": [{"family": "D\u00edez", "given": "Beatriz", "initials": "B"}, {"family": "Nylander", "given": "Johan A A", "initials": "JA"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Allen", "given": "Andrew E", "initials": "AE"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Rusch", "given": "Douglas B", "initials": "DB"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2016-05-19", "journal": {"volume": "11", "issn": "1932-6203", "issue": "5", "pages": "e0155757", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 \u03bcm to 20 \u03bcm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.", "doi": "10.1371/journal.pone.0155757", "pmid": "27196065", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "PONE-D-15-30061"}, {"db": "pmc", "key": "PMC4890579"}, {"db": "ENA", "description": "sequences", "key": "PRJEB8968"}], "notes": [], "created": "2017-05-03T13:00:49.533Z", "modified": "2020-01-21T13:56:17.073Z"}, {"entity": "publication", "iuid": "ec806726683e4a7494d288ba74b669a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec806726683e4a7494d288ba74b669a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec806726683e4a7494d288ba74b669a2"}}, "title": "Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.", "authors": [{"family": "Lundstr\u00f6m", "given": "Sara V", "initials": "SV"}, {"family": "\u00d6stman", "given": "Marcus", "initials": "M"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J"}, {"family": "Rutgersson", "given": "Carolin", "initials": "C"}, {"family": "Thoudal", "given": "Malin", "initials": "M"}, {"family": "Sircar", "given": "Triranta", "initials": "T"}, {"family": "Blanck", "given": "Hans", "initials": "H"}, {"family": "Eriksson", "given": "K Martin", "initials": "KM"}, {"family": "Tysklind", "given": "Mats", "initials": "M"}, {"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2016-05-15", "journal": {"volume": "553", "issn": "1879-1026", "issue": null, "pages": "587-595", "title": "Sci. Total Environ.", "issn-l": "0048-9697"}, "abstract": "Selection pressure generated by antibiotics released into the environment could enrich for antibiotic resistance genes and antibiotic resistant bacteria, thereby increasing the risk for transmission to humans and animals. Tetracyclines comprise an antibiotic class of great importance to both human and animal health. Accordingly, residues of tetracycline are commonly detected in aquatic environments. To assess if tetracycline pollution in aquatic environments promotes development of resistance, we determined minimal selective concentrations (MSCs) in biofilms of complex aquatic bacterial communities using both phenotypic and genotypic assays. Tetracycline significantly increased the relative abundance of resistant bacteria at 10 \u03bcg/L, while specific tet genes (tetA and tetG) increased significantly at the lowest concentration tested (1 \u03bcg/L). Taxonomic composition of the biofilm communities was altered with increasing tetracycline concentrations. Metagenomic analysis revealed a concurrent increase of several tet genes and a range of other genes providing resistance to different classes of antibiotics (e.g. cmlA, floR, sul1, and mphA), indicating potential for co-selection. Consequently, MSCs for the tet genes of \u2264 1 \u03bcg/L suggests that current exposure levels in e.g. sewage treatment plants could be sufficient to promote resistance. The methodology used here to assess MSCs could be applied in risk assessment of other antibiotics as well.", "doi": "10.1016/j.scitotenv.2016.02.103", "pmid": "26938321", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(16)30314-X"}], "notes": [], "created": "2017-05-03T13:00:56.981Z", "modified": "2020-01-21T13:56:06.026Z"}, {"entity": "publication", "iuid": "3c259f153b554630b916ce50992daf0f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c259f153b554630b916ce50992daf0f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c259f153b554630b916ce50992daf0f"}}, "title": "Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.", "authors": [{"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Karlson", "given": "Bengt", "initials": "B"}, {"family": "Charvet", "given": "Sophie", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2016-05-12", "journal": {"volume": "7", "issn": "1664-302X", "issue": null, "pages": "679", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 10(5) sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Emiliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.", "doi": "10.3389/fmicb.2016.00679", "pmid": "27242706", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4864665"}], "notes": [], "created": "2017-05-08T07:58:31.569Z", "modified": "2024-01-16T13:48:50.066Z"}, {"entity": "publication", "iuid": "832d8fd531da49888ca05b6cff3ee534", "links": {"self": {"href": "https://publications.scilifelab.se/publication/832d8fd531da49888ca05b6cff3ee534.json"}, "display": {"href": "https://publications.scilifelab.se/publication/832d8fd531da49888ca05b6cff3ee534"}}, "title": "Determining breast cancer histological grade from RNA-sequencing data.", "authors": [{"family": "Wang", "given": "Mei", "initials": "M"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}], "type": "journal article", "published": "2016-05-10", "journal": {"volume": "18", "issn": "1465-542X", "issue": "1", "pages": "48", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "The histologic grade (HG) of breast cancer is an established prognostic factor. The grade is usually reported on a scale ranging from 1 to 3, where grade 3 tumours are the most aggressive. However, grade 2 is associated with an intermediate risk of recurrence, and carries limited information for clinical decision-making. Patients classified as grade 2 are at risk of both under- and over-treatment.\n\nRNA-sequencing analysis was conducted in a cohort of 275 women diagnosed with invasive breast cancer. Multivariate prediction models were developed to classify tumours into high and low transcriptomic grade (TG) based on gene- and isoform-level expression data from RNA-sequencing. HG2 tumours were reclassified according to the prediction model and a recurrence-free survival analysis was performed by the multivariate Cox proportional hazards regression model to assess to what extent the TG model could be used to stratify patients. The prediction model was validated in N=487 breast cancer cases from the The Cancer Genome Atlas (TCGA) data set. Differentially expressed genes and isoforms associated with HGs were analysed using linear models.\n\nThe classification of grade 1 and grade 3 tumours based on RNA-sequencing data achieved high accuracy (area under the receiver operating characteristic curve = 0.97). The association between recurrence-free survival rate and HGs was confirmed in the study population (hazard ratio of grade 3 versus 1 was 2.62 with 95 % confidence interval = 1.04-6.61). The TG model enabled us to reclassify grade 2 tumours as high TG and low TG gene or isoform grade. The risk of recurrence in the high TG group of grade 2 tumours was higher than in low TG group (hazard ratio = 2.43, 95 % confidence interval = 1.13-5.20). We found 8200 genes and 13,809 isoforms that were differentially expressed between HG1 and HG3 breast cancer tumours.\n\nGene- and isoform-level expression data from RNA-sequencing could be utilised to differentiate HG1 and HG3 tumours with high accuracy. We identified a large number of novel genes and isoforms associated with HG. Grade 2 tumours could be reclassified as high and low TG, which has the potential to reduce over- and under-treatment if implemented clinically.", "doi": "10.1186/s13058-016-0710-8", "pmid": "27165105", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s13058-016-0710-8"}, {"db": "pmc", "key": "PMC4862203"}], "notes": [], "created": "2017-05-03T13:00:22.821Z", "modified": "2024-01-16T13:48:50.091Z"}, {"entity": "publication", "iuid": "d0637b5a89034eb7bce40c4c349988f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0637b5a89034eb7bce40c4c349988f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0637b5a89034eb7bce40c4c349988f9"}}, "title": "Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors.", "authors": [{"family": "Bertos-Fortis", "given": "Mireia", "initials": "M"}, {"family": "Farnelid", "given": "Hanna M", "initials": "HM"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Casini", "given": "Michele", "initials": "M"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}], "type": "journal article", "published": "2016-05-09", "journal": {"volume": "7", "issn": "1664-302X", "issue": null, "pages": "625", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Future climate scenarios in the Baltic Sea project an increase of cyanobacterial bloom frequency and duration, attributed to eutrophication and climate change. Some cyanobacteria can be toxic and their impact on ecosystem services is relevant for a sustainable sea. Yet, there is limited understanding of the mechanisms regulating cyanobacterial diversity and biogeography. Here we unravel successional patterns and changes in cyanobacterial community structure using a 2-year monthly time- series during the productive season in a 100 km coastal-offshore transect using microscopy and high-throughput sequencing of 16S rRNA gene fragments. A total of 565 cyanobacterial OTUs were found, of which 231 where filamentous/colonial and 334 picocyanobacterial. Spatial differences in community structure between coastal and offshore waters were minor. An \"epidemic population structure\" (dominance of asingle cluster) was found for Aphanizomenon/Dolichospermum within the filamentous/colonial cyanobacterial community. In summer, this clusters imultaneously occurred with opportunistic clusters/OTUs, e.g., Nodularia spumigena and Pseudanabaena. Picocyanobacteria, Synechococcus/Cyanobium, formeda consistent but highly diverse group. Overall, the potential drivers structuring summer cyanobacterial communities were temperature and salinity. However, the different responses to environmental factors among and within genera suggest high niche specificity for individual OTUs. The recruitment and occurrence of potentially toxic filamentous/colonial clusters was likely related to disturbance such as mixing events and short-term shifts in salinity, and not solely dependent on increasing temperature and nitrogen-limiting conditions. Nutrients did not explain further the changes in cyanobacterial community composition. Novel occurrence patterns were identified as a strong seasonal succession revealing a tight coupling between the emergence of opportunistic picocynobacteria and the bloom offilamentous/colonialclusters. These findings highlight that if environmental conditions can partially explain the presence of opportunistic picocyanobacteria, microbial and trophic interactions with filamentous/colonial cyanobacteria should also be considered as potential shaping factors for single-celled communities. Regional climate change scenarios in the Baltic Sea predict environmental shifts leading to higher temperature and lower salinity; conditions identified here as favorable for opportunistic filamentous/colonial cyanobacteria. Altogether, the diversity and complexity of cyanobacterial communities reported here is far greater than previously known, emphasizing the importance of microbial interactions between filamentous and picocyanobacteria in the context of environmental disturbances.", "doi": "10.3389/fmicb.2016.00625", "pmid": "27242679", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4860504"}], "notes": [], "created": "2017-05-03T13:00:30.417Z", "modified": "2024-01-16T13:48:50.098Z"}, {"entity": "publication", "iuid": "f081819507c347dcba39244e2fbb4517", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f081819507c347dcba39244e2fbb4517.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f081819507c347dcba39244e2fbb4517"}}, "title": "nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs.", "authors": [{"family": "Gandin", "given": "Valentina", "initials": "V"}, {"family": "Masvidal", "given": "Laia", "initials": "L"}, {"family": "Hulea", "given": "Laura", "initials": "L"}, {"family": "Gravel", "given": "Simon-Pierre", "initials": "SP"}, {"family": "Cargnello", "given": "Marie", "initials": "M"}, {"family": "McLaughlan", "given": "Shannon", "initials": "S"}, {"family": "Cai", "given": "Yutian", "initials": "Y"}, {"family": "Balanathan", "given": "Preetika", "initials": "P"}, {"family": "Morita", "given": "Masahiro", "initials": "M"}, {"family": "Rajakumar", "given": "Arjuna", "initials": "A"}, {"family": "Furic", "given": "Luc", "initials": "L"}, {"family": "Pollak", "given": "Michael", "initials": "M"}, {"family": "Porco", "given": "John A", "initials": "JA"}, {"family": "St-Pierre", "given": "Julie", "initials": "J"}, {"family": "Pelletier", "given": "Jerry", "initials": "J"}, {"family": "Larsson", "given": "Ola", "initials": "O"}, {"family": "Topisirovic", "given": "Ivan", "initials": "I"}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "26", "issn": "1549-5469", "issue": "5", "pages": "636-648", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "The diversity of MTOR-regulated mRNA translation remains unresolved. Whereas ribosome-profiling suggested that MTOR almost exclusively stimulates translation of the TOP (terminal oligopyrimidine motif) and TOP-like mRNAs, polysome-profiling indicated that MTOR also modulates translation of mRNAs without the 5' TOP motif (non-TOP mRNAs). We demonstrate that in ribosome-profiling studies, detection of MTOR-dependent changes in non-TOP mRNA translation was obscured by low sensitivity and methodology biases. Transcription start site profiling using nano-cap analysis of gene expression (nanoCAGE) revealed that not only do many MTOR-sensitive mRNAs lack the 5' TOP motif but that 5' UTR features distinguish two functionally and translationally distinct subsets of MTOR-sensitive mRNAs: (1) mRNAs with short 5' UTRs enriched for mitochondrial functions, which require EIF4E but are less EIF4A1-sensitive; and (2) long 5' UTR mRNAs encoding proliferation- and survival-promoting proteins, which are both EIF4E- and EIF4A1-sensitive. Selective inhibition of translation of mRNAs harboring long 5' UTRs via EIF4A1 suppression leads to sustained expression of proteins involved in respiration but concomitant loss of those protecting mitochondrial structural integrity, resulting in apoptosis. Conversely, simultaneous suppression of translation of both long and short 5' UTR mRNAs by MTOR inhibitors results in metabolic dormancy and a predominantly cytostatic effect. Thus, 5' UTR features define different modes of MTOR-sensitive translation of functionally distinct subsets of mRNAs, which may explain the diverse impact of MTOR and EIF4A inhibitors on neoplastic cells.", "doi": "10.1101/gr.197566.115", "pmid": "26984228", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "gr.197566.115"}, {"db": "pmc", "key": "PMC4864462"}], "notes": [], "created": "2017-05-03T12:58:55.732Z", "modified": "2020-01-21T13:56:06.186Z"}, {"entity": "publication", "iuid": "8bfa76ca5efa41d383fee1ee7352c204", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bfa76ca5efa41d383fee1ee7352c204.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bfa76ca5efa41d383fee1ee7352c204"}}, "title": "Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.", "authors": [{"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Baca", "given": "Mateusz", "initials": "M"}, {"family": "Abramson", "given": "Natalia I", "initials": "NI"}, {"family": "Sablin", "given": "Mikhail", "initials": "M"}, {"family": "Socha", "given": "Pawe\u0142", "initials": "P"}, {"family": "Nadachowski", "given": "Adam", "initials": "A"}, {"family": "Prost", "given": "Stefan", "initials": "S"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Kosintsev", "given": "Pavel", "initials": "P"}, {"family": "Smirnov", "given": "Nickolay G", "initials": "NG"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Ponomarev", "given": "Dmitry", "initials": "D"}, {"family": "Nystr\u00f6m", "given": "Johanna", "initials": "J"}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Jass", "given": "Christopher N", "initials": "CN"}, {"family": "Litvinov", "given": "Yuriy N", "initials": "YN"}, {"family": "Kalthoff", "given": "Daniela C", "initials": "DC"}, {"family": "Grigoriev", "given": "Semyon", "initials": "S"}, {"family": "Fadeeva", "given": "Tatyana", "initials": "T"}, {"family": "Douka", "given": "Aikaterini", "initials": "A"}, {"family": "Higham", "given": "Thomas F G", "initials": "TF"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Pitulko", "given": "Vladimir", "initials": "V"}, {"family": "Pavlova", "given": "Elena", "initials": "E"}, {"family": "Stewart", "given": "John R", "initials": "JR"}, {"family": "W\u0119gle\u0144ski", "given": "Piotr", "initials": "P"}, {"family": "Stankovic", "given": "Anna", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "22", "issn": "1365-2486", "issue": "5", "pages": "1710-1721", "title": "Glob Chang Biol", "issn-l": "1354-1013"}, "abstract": "Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.", "doi": "10.1111/gcb.13214", "pmid": "26919067", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "GENBANK", "key": "KT867379"}, {"db": "GENBANK", "key": "KT867537"}], "notes": [], "created": "2017-05-03T12:58:56.967Z", "modified": "2021-07-07T20:31:10.863Z"}, {"entity": "publication", "iuid": "aa0e8bfde19a4e24a95d64a836030d3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa0e8bfde19a4e24a95d64a836030d3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa0e8bfde19a4e24a95d64a836030d3a"}}, "title": "Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes.", "authors": [{"family": "Hyt\u00f6nen", "given": "Marjo K", "initials": "MK"}, {"family": "Arumilli", "given": "Meharji", "initials": "M"}, {"family": "Lappalainen", "given": "Anu K", "initials": "AK"}, {"family": "Owczarek-Lipska", "given": "Marta", "initials": "M"}, {"family": "Jagannathan", "given": "Vidhya", "initials": "V"}, {"family": "Hundi", "given": "Sruthi", "initials": "S"}, {"family": "Salmela", "given": "Elina", "initials": "E"}, {"family": "Venta", "given": "Patrick", "initials": "P"}, {"family": "Sarkiala", "given": "Eva", "initials": "E"}, {"family": "Jokinen", "given": "Tarja", "initials": "T"}, {"family": "Gorgas", "given": "Daniela", "initials": "D"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Nieminen", "given": "Pekka", "initials": "P"}, {"family": "Dr\u00f6gem\u00fcller", "given": "Cord", "initials": "C"}, {"family": "Lohi", "given": "Hannes", "initials": "H"}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "12", "issn": "1553-7404", "issue": "5", "pages": "e1006037", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "One to two percent of all children are born with a developmental disorder requiring pediatric hospital admissions. For many such syndromes, the molecular pathogenesis remains poorly characterized. Parallel developmental disorders in other species could provide complementary models for human rare diseases by uncovering new candidate genes, improving the understanding of the molecular mechanisms and opening possibilities for therapeutic trials. We performed various experiments, e.g. combined genome-wide association and next generation sequencing, to investigate the clinico-pathological features and genetic causes of three developmental syndromes in dogs, including craniomandibular osteopathy (CMO), a previously undescribed skeletal syndrome, and dental hypomineralization, for which we identified pathogenic variants in the canine SLC37A2 (truncating splicing enhancer variant), SCARF2 (truncating 2-bp deletion) and FAM20C (missense variant) genes, respectively. CMO is a clinical equivalent to an infantile cortical hyperostosis (Caffey disease), for which SLC37A2 is a new candidate gene. SLC37A2 is a poorly characterized member of a glucose-phosphate transporter family without previous disease associations. It is expressed in many tissues, including cells of the macrophage lineage, e.g. osteoclasts, and suggests a disease mechanism, in which an impaired glucose homeostasis in osteoclasts compromises their function in the developing bone, leading to hyperostosis. Mutations in SCARF2 and FAM20C have been associated with the human van den Ende-Gupta and Raine syndromes that include numerous features similar to the affected dogs. Given the growing interest in the molecular characterization and treatment of human rare diseases, our study presents three novel physiologically relevant models for further research and therapy approaches, while providing the molecular identity for the canine conditions.", "doi": "10.1371/journal.pgen.1006037", "pmid": "27187611", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-15-02896"}, {"db": "pmc", "key": "PMC4871343"}], "notes": [], "created": "2017-05-03T13:00:24.302Z", "modified": "2024-01-16T13:48:50.159Z"}, {"entity": "publication", "iuid": "b634e1e31191430db96f61d49dd10ab5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b634e1e31191430db96f61d49dd10ab5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b634e1e31191430db96f61d49dd10ab5"}}, "title": "Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.", "authors": [{"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Holmfeldt", "given": "Karin", "initials": "K"}, {"family": "Hubalek", "given": "Valerie", "initials": "V"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "\u00c5str\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-05-00", "journal": {"volume": "10", "issn": "1751-7370", "issue": "5", "pages": "1192-1203", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448\u2009m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22\u2009\u03bcm filter. Such cells of <0.22\u2009\u03bcm would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22\u2009\u03bcm populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.", "doi": "10.1038/ismej.2015.185", "pmid": "26484735", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ismej2015185"}, {"db": "pmc", "key": "PMC5029217"}], "notes": [], "created": "2017-05-02T12:58:58.147Z", "modified": "2024-01-16T13:48:50.167Z"}, {"entity": "publication", "iuid": "c2e9a4bcfdd0465ca1c3498e7c4e1619", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2e9a4bcfdd0465ca1c3498e7c4e1619.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2e9a4bcfdd0465ca1c3498e7c4e1619"}}, "title": "Biotin and Thiamine Responsive Basal Ganglia Disease--A vital differential diagnosis in infants with severe encephalopathy.", "authors": [{"family": "Ygberg", "given": "Sofia", "initials": "S"}, {"family": "Naess", "given": "Karin", "initials": "K"}, {"family": "Eriksson", "given": "Mats", "initials": "M"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Barbaro", "given": "Michela", "initials": "M"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Wang", "given": "Chen", "initials": "C"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Wickstr\u00f6m", "given": "Ronny", "initials": "R"}], "type": "case reports", "published": "2016-05-00", "journal": {"volume": "20", "issn": "1532-2130", "issue": "3", "pages": "457-461", "title": "Eur. J. Paediatr. Neurol.", "issn-l": "1090-3798"}, "abstract": "We report two siblings of Swedish origin with infantile Biotin and Thiamine Responsive Basal Ganglia Disease (BTRBG).\n\nInitial symptoms were in both cases lethargia, with reduced contact and poor feeding from the age of 5 weeks. Magnetic resonance imaging showed altered signal in the basal ganglia, along with grey and white matter abnormalities. The diagnosis BTRBG was not recognized in the first sibling who died at the age of 8 weeks. The second sibling was started on biotin and thiamine immediately upon development of symptoms, leading to clinical improvement and partial reversion of the magnetic resonance imaging findings. Genetic analysis of the SLC19A3 gene identified two mutations, c.74dupT and c.1403delA, carried in compound heterozygous form in both boys, each inherited from one parent.\n\nThe first mutation has previously been described in children with BTRBG, and the second mutation is novel. Although the clinical picture in BTRGB is very severe it is also rather unspecific and the diagnosis may be missed.\n\nThis report highlights the importance of considering biotin and thiamine treatment also in a European infant born to non-consanguineous parents, who presents with symptoms of acute/subacute encephalopathy.", "doi": "10.1016/j.ejpn.2016.01.009", "pmid": "26975589", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "S1090-3798(16)00027-1"}], "notes": [], "created": "2017-05-03T12:59:51.425Z", "modified": "2024-01-16T13:48:50.210Z"}, {"entity": "publication", "iuid": "69b221ea9a2f454992db3b424ea930ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69b221ea9a2f454992db3b424ea930ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69b221ea9a2f454992db3b424ea930ad"}}, "title": "Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom.", "authors": [{"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Bertos-Fortis", "given": "Mireia", "initials": "M"}, {"family": "Sassenhagen", "given": "Ingrid", "initials": "I"}, {"family": "Sildever", "given": "Sirje", "initials": "S"}, {"family": "Sj\u00f6qvist", "given": "Conny", "initials": "C"}, {"family": "Godhe", "given": "Anna", "initials": "A"}, {"family": "Gross", "given": "Susanna", "initials": "S"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Lips", "given": "Inga", "initials": "I"}, {"family": "Lundholm", "given": "Nina", "initials": "N"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}, {"family": "Sefbom", "given": "Josefin", "initials": "J"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}], "type": "journal article", "published": "2016-04-21", "journal": {"volume": "7", "issn": "1664-302X", "issue": null, "pages": "517", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "In temperate systems, phytoplankton spring blooms deplete inorganic nutrients and are major sources of organic matter for the microbial loop. In response to phytoplankton exudates and environmental factors, heterotrophic microbial communities are highly dynamic and change their abundance and composition both on spatial and temporal scales. Yet, most of our understanding about these processes comes from laboratory model organism studies, mesocosm experiments or single temporal transects. Spatial-temporal studies examining interactions of phytoplankton blooms and bacterioplankton community composition and function, though being highly informative, are scarce. In this study, pelagic microbial community dynamics (bacteria and phytoplankton) and environmental variables were monitored during a spring bloom across the Baltic Proper (two cruises between North Germany to Gulf of Finland). To test to what extent bacterioplankton community composition relates to the spring bloom, we used next generation amplicon sequencing of the 16S rRNA gene, phytoplankton diversity analysis based on microscopy counts and population genotyping of the dominating diatom Skeletonema marinoi. Several phytoplankton bloom related and environmental variables were identified to influence bacterial community composition. Members of Bacteroidetes and Alphaproteobacteria dominated the bacterial community composition but the bacterial groups showed no apparent correlation with direct bloom related variables. The less abundant bacterial phyla Actinobacteria, Planctomycetes, and Verrucomicrobia, on the other hand, were strongly associated with phytoplankton biomass, diatom:dinoflagellate ratio, and colored dissolved organic matter (cDOM). Many bacterial operational taxonomic units (OTUs) showed high niche specificities. For example, particular Bacteroidetes OTUs were associated with two distinct genetic clusters of S. marinoi. Our study revealed the complexity of interactions of bacterial taxa with inter- and intraspecific genetic variation in phytoplankton. Overall, our findings imply that biotic and abiotic factors during spring bloom influence bacterial community dynamics in a hierarchical manner.", "doi": "10.3389/fmicb.2016.00517", "pmid": "27148206", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC4838809"}], "notes": [], "created": "2017-05-03T13:00:30.123Z", "modified": "2024-01-16T13:48:50.239Z"}, {"entity": "publication", "iuid": "5e59df9d21b3446d9c4c3b2203017537", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5e59df9d21b3446d9c4c3b2203017537.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5e59df9d21b3446d9c4c3b2203017537"}}, "title": "Mutations in histone modulators are associated with prolonged survival during azacitidine therapy.", "authors": [{"family": "Tobiasson", "given": "Magnus", "initials": "M"}, {"family": "McLornan", "given": "Donal P", "initials": "DP"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Dimitriou", "given": "Marios", "initials": "M"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Ben Azenkoud", "given": "Asmaa", "initials": "A"}, {"family": "J\u00e4dersten", "given": "Martin", "initials": "M"}, {"family": "Lindberg", "given": "Greger", "initials": "G"}, {"family": "Abdulkadir", "given": "Hani", "initials": "H"}, {"family": "Kulasekararaj", "given": "Austin", "initials": "A"}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Mufti", "given": "Ghulam J", "initials": "GJ"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2016-04-19", "journal": {"volume": "7", "issn": "1949-2553", "issue": "16", "pages": "22103-22115", "title": "Oncotarget", "issn-l": "1949-2553"}, "abstract": "Early therapeutic decision-making is crucial in patients with higher-risk MDS. We evaluated the impact of clinical parameters and mutational profiles in 134 consecutive patients treated with azacitidine using a combined cohort from Karolinska University Hospital (n=89) and from King's College Hospital, London (n=45). While neither clinical parameters nor mutations had a significant impact on response rate, both karyotype and mutational profile were strongly associated with survival from the start of treatment. IPSS high-risk cytogenetics negatively impacted overall survival (median 20 vs 10 months; p<0.001), whereas mutations in histone modulators (ASXL1, EZH2) were associated with prolonged survival (22 vs 12 months, p=0.01). This positive association was present in both cohorts and remained highly significant in the multivariate cox model. Importantly, patients with mutations in histone modulators lacking high-risk cytogenetics showed a survival of 29 months compared to only 10 months in patients with the opposite pattern. While TP53 was negatively associated with survival, neither RUNX1-mutations nor the number of mutations appeared to influence survival in this cohort. We propose a model combining histone modulator mutational screening with cytogenetics in the clinical decision-making process for higher-risk MDS patients eligible for treatment with azacitidine.", "doi": "10.18632/oncotarget.7899", "pmid": "26959885", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "7899"}, {"db": "pmc", "key": "PMC5008347"}], "notes": [], "created": "2017-05-08T07:58:57.167Z", "modified": "2020-01-21T13:56:02.559Z"}, {"entity": "publication", "iuid": "67ac778e0c844b0a9a23b0c36737692f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67ac778e0c844b0a9a23b0c36737692f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67ac778e0c844b0a9a23b0c36737692f"}}, "title": "Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast.", "authors": [{"family": "Gowda", "given": "Naveen Kumar Chandappa", "initials": "NK"}, {"family": "Kaimal", "given": "Jayasankar Mohanakrishnan", "initials": "JM"}, {"family": "Masser", "given": "Anna E", "initials": "AE"}, {"family": "Kang", "given": "Wenjing", "initials": "W"}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR"}, {"family": "Andr\u00e9asson", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2016-04-15", "journal": {"volume": "27", "issn": "1939-4586", "issue": "8", "pages": "1210-1219", "title": "Mol. Biol. Cell", "issn-l": "1059-1524"}, "abstract": "Cells maintain proteostasis by selectively recognizing and targeting misfolded proteins for degradation. InSaccharomyces cerevisiae, the Hsp70 nucleotide exchange factor Fes1 is essential for the degradation of chaperone-associated misfolded proteins by the ubiquitin-proteasome system. Here we show that theFES1transcript undergoes unique 3' alternative splicing that results in two equally active isoforms with alternative C-termini, Fes1L and Fes1S. Fes1L is actively targeted to the nucleus and represents the first identified nuclear Hsp70 nucleotide exchange factor. In contrast, Fes1S localizes to the cytosol and is essential to maintain proteostasis. In the absence of Fes1S, the heat-shock response is constitutively induced at normally nonstressful conditions. Moreover, cells display severe growth defects when elevated temperatures, amino acid analogues, or the ectopic expression of misfolded proteins, induce protein misfolding. Importantly, misfolded proteins are not targeted for degradation by the ubiquitin-proteasome system. These observations support the notion that cytosolic Fes1S maintains proteostasis by supporting the removal of toxic misfolded proteins by proteasomal degradation. This study provides key findings for the understanding of the organization of protein quality control mechanisms in the cytosol and nucleus.", "doi": "10.1091/mbc.E15-10-0697", "pmid": "26912797", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "mbc.E15-10-0697"}, {"db": "pmc", "key": "PMC4831876"}], "notes": [], "created": "2017-05-08T07:57:50.459Z", "modified": "2024-01-16T13:48:50.251Z"}, {"entity": "publication", "iuid": "5da8c8b6ed79477ba89c81ae7013ac7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5da8c8b6ed79477ba89c81ae7013ac7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5da8c8b6ed79477ba89c81ae7013ac7f"}}, "title": "Transcriptomics resources of human tissues and\u00a0organs.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2016-04-04", "journal": {"volume": "12", "issn": "1744-4292", "issue": "4", "pages": "862", "title": "Mol. Syst. Biol.", "issn-l": "1744-4292"}, "abstract": "Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome-wide transcriptome analyses of different tissues. Gene expression measurements from these independent datasets, generated using samples from fresh frozen surgical specimens and postmortem tissues, are consistent. Overall, the different genome-wide analyses support a distribution in which many proteins are found in all tissues and relatively few in a tissue-restricted manner. Moreover, we discuss the applications of publicly available omics data for building genome-scale metabolic models, used for analyzing cell and tissue functions both in physiological and in disease contexts.", "doi": "10.15252/msb.20155865", "pmid": "27044256", "labels": {"Systems Biology": "Technology development", "National Genomics Infrastructure": "Service", "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC4848759"}], "notes": [], "created": "2017-05-03T12:58:59.635Z", "modified": "2021-07-08T13:44:33.307Z"}, {"entity": "publication", "iuid": "9c7992409f3d425cb633929d763c1cc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c7992409f3d425cb633929d763c1cc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c7992409f3d425cb633929d763c1cc2"}}, "title": "RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.", "authors": [{"family": "Christel", "given": "Stephan", "initials": "S"}, {"family": "Fridlund", "given": "Jimmy", "initials": "J"}, {"family": "Buetti-Dinh", "given": "Antoine", "initials": "A"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Watkin", "given": "Elizabeth L", "initials": "EL"}, {"family": "Dopson", "given": "Mark", "initials": "M"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "363", "issn": "1574-6968", "issue": "7", "title": "FEMS Microbiol. Lett.", "issn-l": "0378-1097"}, "abstract": "Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.", "doi": "10.1093/femsle/fnw057", "pmid": "26956550", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "fnw057"}], "notes": [], "created": "2017-05-03T13:00:06.848Z", "modified": "2024-01-16T13:48:50.282Z"}, {"entity": "publication", "iuid": "37aec34c32ae4409972c0b6085bf7614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37aec34c32ae4409972c0b6085bf7614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37aec34c32ae4409972c0b6085bf7614"}}, "title": "Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.", "authors": [{"family": "Rodr\u00edguez", "given": "Sof\u00eda A", "initials": "SA"}, {"family": "Grochov\u00e1", "given": "Diana", "initials": "D"}, {"family": "McKenna", "given": "Tom\u00e1s", "initials": "T"}, {"family": "Borate", "given": "Bhavesh", "initials": "B"}, {"family": "Trivedi", "given": "Niraj S", "initials": "NS"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Eriksson", "given": "Maria", "initials": "M"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "15", "issn": "1474-9726", "issue": "2", "pages": "267-278", "title": "Aging Cell", "issn-l": "1474-9718"}, "abstract": "Alternative splicing (AS) is a key regulatory mechanism for the development of different tissues; however, not much is known about changes to alternative splicing during aging. Splicing events may become more frequent and widespread genome-wide as tissues age and the splicing machinery stringency decreases. Using skin, skeletal muscle, bone, thymus, and white adipose tissue from wild-type C57BL6/J male mice (4 and 18 months old), we examined the effect of age on splicing by AS analysis of the differential exon usage of the genome. The results identified a considerable number of AS genes in skeletal muscle, thymus, bone, and white adipose tissue between the different age groups (ranging from 27 to 246 AS genes corresponding to 0.3-3.2% of the total number of genes analyzed). For skin, skeletal muscle, and bone, we included a later age group (28 months old) that showed that the number of alternatively spliced genes increased with age in all three tissues (P < 0.01). Analysis of alternatively spliced genes across all tissues by gene ontology and pathway analysis identified 158 genes involved in RNA processing. Additional analysis of AS in a mouse model for the premature aging disease Hutchinson-Gilford progeria syndrome was performed. The results show that expression of the mutant protein, progerin, is associated with an impaired developmental splicing. As progerin accumulates, the number of genes with AS increases compared to in wild-type skin. Our results indicate the existence of a mechanism for increased AS during aging in several tissues, emphasizing that AS has a more important role in the aging process than previously known.", "doi": "10.1111/acel.12433", "pmid": "26685868", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pmc", "key": "PMC4783335"}], "notes": [], "created": "2017-05-02T12:58:25.017Z", "modified": "2024-01-16T13:48:50.295Z"}, {"entity": "publication", "iuid": "7f33e523cbec42fd9934929c0d78f1ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f33e523cbec42fd9934929c0d78f1ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f33e523cbec42fd9934929c0d78f1ac"}}, "title": "Digital image analysis outperforms manual biomarker assessment in breast cancer.", "authors": [{"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "Fuentes Martinez", "given": "Nelson", "initials": "N"}, {"family": "Lippert", "given": "Michael", "initials": "M"}, {"family": "Tobin", "given": "Nicholas P", "initials": "NP"}, {"family": "M\u00f8lholm", "given": "Ida", "initials": "I"}, {"family": "Kis", "given": "Lorand", "initials": "L"}, {"family": "Rosin", "given": "Gustaf", "initials": "G"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Pedersen", "given": "Lars", "initials": "L"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Grunkin", "given": "Michael", "initials": "M"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2016-04-00", "journal": {"volume": "29", "issn": "1530-0285", "issue": "4", "pages": "318-329", "title": "Mod. Pathol.", "issn-l": "0893-3952"}, "abstract": "In the spectrum of breast cancers, categorization according to the four gene expression-based subtypes 'Luminal A,' 'Luminal B,' 'HER2-enriched,' and 'Basal-like' is the method of choice for prognostic and predictive value. As gene expression assays are not yet universally available, routine immunohistochemical stains act as surrogate markers for these subtypes. Thus, congruence of surrogate markers and gene expression tests is of utmost importance. In this study, 3 cohorts of primary breast cancer specimens (total n=436) with up to 28 years of survival data were scored for Ki67, ER, PR, and HER2 status manually and by digital image analysis (DIA). The results were then compared for sensitivity and specificity for the Luminal B subtype, concordance to PAM50 assays in subtype classification and prognostic power. The DIA system used was the Visiopharm Integrator System. DIA outperformed manual scoring in terms of sensitivity and specificity for the Luminal B subtype, widely considered the most challenging distinction in surrogate subclassification, and produced slightly better concordance and Cohen's \u03ba agreement with PAM50 gene expression assays. Manual biomarker scores and DIA essentially matched each other for Cox regression hazard ratios for all-cause mortality. When the Nottingham combined histologic grade (Elston-Ellis) was used as a prognostic surrogate, stronger Spearman's rank-order correlations were produced by DIA. Prognostic value of Ki67 scores in terms of likelihood ratio \u03c7(2) (LR \u03c7(2)) was higher for DIA that also added significantly more prognostic information to the manual scores (LR-\u0394\u03c7(2)). In conclusion, the system for DIA evaluated here was in most aspects a superior alternative to manual biomarker scoring. It also has the potential to reduce time consumption for pathologists, as many of the steps in the workflow are either automatic or feasible to manage without pathological expertise.", "doi": "10.1038/modpathol.2016.34", "pmid": "26916072", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "modpathol201634"}], "notes": [], "created": "2017-05-03T12:59:55.502Z", "modified": "2024-01-16T13:48:50.319Z"}, {"entity": "publication", "iuid": "fb98d3f536834077b00b62f27053a8a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb98d3f536834077b00b62f27053a8a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb98d3f536834077b00b62f27053a8a2"}}, "title": "Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.", "authors": [{"family": "Salv\u00e0-Serra", "given": "Francisco", "initials": "F", "orcid": "0000-0003-0173-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/49d15be15c484e6a99f22b466bf99166.json"}}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Thorell", "given": "Kaisa", "initials": "K", "orcid": "0000-0002-4447-8968", "researcher": {"href": "https://publications.scilifelab.se/researcher/badb913f91e14489aca247ee841e1608.json"}}, {"family": "Gonzales-Siles", "given": "Lucia", "initials": "L"}, {"family": "Hallb\u00e4ck", "given": "Erika T", "initials": "ET"}, {"family": "Ja\u00e9n-Luchoro", "given": "Daniel", "initials": "D"}, {"family": "Boulund", "given": "Fredrik", "initials": "F"}, {"family": "Sikora", "given": "Per", "initials": "P", "orcid": "0000-0002-0049-1562", "researcher": {"href": "https://publications.scilifelab.se/researcher/beeaccd4a7ab4105be077ee778cf0507.json"}}, {"family": "Karlsson", "given": "Roger", "initials": "R"}, {"family": "Svensson", "given": "Liselott", "initials": "L"}, {"family": "Bennasar", "given": "Antoni", "initials": "A"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Moore", "given": "Edward R B", "initials": "ER", "orcid": "0000-0001-7693-924X", "researcher": {"href": "https://publications.scilifelab.se/researcher/10b1c68436094391bfefd7de22757aba.json"}}], "type": "journal article", "published": "2016-03-24", "journal": {"volume": "4", "issn": "2169-8287", "issue": "2", "pages": "e00175-16", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Streptococcus gordoniitype strain CCUG 33482(T)is a member of theStreptococcus mitisgroup, isolated from a case of subacute bacterial endocarditis. Here, we report the draft genome sequence ofS. gordoniiCCUG 33482(T), composed of 41 contigs of a total size of 2.15 Mb with 2,061 annotated coding sequences.", "doi": "10.1128/genomeA.00175-16", "pmid": "27013051", "labels": {"National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "4/2/e00175-16"}, {"db": "pmc", "key": "PMC4807240"}], "notes": [], "created": "2017-05-08T07:58:11.637Z", "modified": "2024-01-16T13:48:50.326Z"}, {"entity": "publication", "iuid": "21e3b46404d64b53b70917d735291b2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21e3b46404d64b53b70917d735291b2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21e3b46404d64b53b70917d735291b2c"}}, "title": "The chemosensory receptors of codling moth Cydia pomonella-expression in larvae and adults.", "authors": [{"family": "Walker", "given": "William B", "initials": "WB"}, {"family": "Gonzalez", "given": "Francisco", "initials": "F"}, {"family": "Garczynski", "given": "Stephen F", "initials": "SF"}, {"family": "Witzgall", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2016-03-23", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "23518", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Olfaction and gustation play critical roles in the life history of insects, mediating vital behaviors such as food, mate and host seeking. Chemosensory receptor proteins, including odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) function to interface the insect with its chemical environment. Codling moth, Cydia pomonella, is a worldwide pest of apple, pear and walnut, and behavior-modifying semiochemicals are used for environmentally safe control. We produced an Illumina-based transcriptome from antennae of males and females as well as neonate head tissue, affording a qualitative and quantitative analysis of the codling moth chemosensory receptor repertoire. We identified 58 ORs, 20 GRs and 21 IRs, and provide a revised nomenclature that is consistent with homologous sequences in related species. Importantly, we have identified several OR transcripts displaying sex-biased expression in adults, as well as larval-enriched transcripts. Our analyses have expanded annotations of the chemosensory receptor gene families, and provide first-time transcript abundance estimates for codling moth. The results presented here provide a strong foundation for future work on codling moth behavioral physiology and ecology at the molecular level, and may lead to the development of more precise biorational control strategies.", "doi": "10.1038/srep23518", "pmid": "27006164", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep23518"}, {"db": "pmc", "key": "PMC4804390"}], "notes": [], "created": "2017-05-03T13:00:01.511Z", "modified": "2024-01-16T13:48:50.341Z"}, {"entity": "publication", "iuid": "13a79f3ecf9e4607999f5cbcab5393fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13a79f3ecf9e4607999f5cbcab5393fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13a79f3ecf9e4607999f5cbcab5393fb"}}, "title": "Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.", "authors": [{"family": "Gyarmati", "given": "P", "initials": "P"}, {"family": "Kjellander", "given": "C", "initials": "C"}, {"family": "Aust", "given": "C", "initials": "C"}, {"family": "Song", "given": "Y", "initials": "Y"}, {"family": "\u00d6hrmalm", "given": "L", "initials": "L"}, {"family": "Giske", "given": "C G", "initials": "CG"}], "type": "journal article", "published": "2016-03-21", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "23532", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Leukemic patients are often immunocompromised due to underlying conditions, comorbidities and the effects of chemotherapy, and thus at risk for developing systemic infections. Bloodstream infection (BSI) is a severe complication in neutropenic patients, and is associated with increased mortality. BSI is routinely diagnosed with blood culture, which only detects culturable pathogens. We analyzed 27 blood samples from 9 patients with acute leukemia and suspected BSI at different time points of their antimicrobial treatment using shotgun metagenomics sequencing in order to detect unculturable and non-bacterial pathogens. Our findings confirm the presence of bacterial, fungal and viral pathogens alongside antimicrobial resistance genes. Decreased white blood cell (WBC) counts were associated with the presence of microbial DNA, and was inversely proportional to the number of sequencing reads. This study could indicate the use of high-throughput sequencing for personalized antimicrobial treatments in BSIs.", "doi": "10.1038/srep23532", "pmid": "26996149", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep23532"}, {"db": "pmc", "key": "PMC4800731"}], "notes": [], "created": "2017-05-03T12:58:56.671Z", "modified": "2020-01-21T13:56:00.833Z"}, {"entity": "publication", "iuid": "c76b9b8a177c4cd4addd6e1f5eb0e960", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c76b9b8a177c4cd4addd6e1f5eb0e960.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c76b9b8a177c4cd4addd6e1f5eb0e960"}}, "title": "Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.", "authors": [{"family": "Celorio-Mancera", "given": "Maria de la Paz", "initials": "Mde L"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}, {"family": "Janz", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2016-03-08", "journal": {"volume": "16", "issn": "1471-2148", "issue": null, "pages": "59", "title": "BMC Evol. Biol.", "issn-l": "1471-2148"}, "abstract": "Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to feed on a wide repertoire of plants is crucial for the control of pest species and for the elucidation of the macroevolutionary mechanisms of speciation and diversification of insect herbivores. Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were reared on different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness.\n\nUsing both unsupervised and supervised methods of data analysis, we found that the tissue-specific patterns of caterpillar gene expression are better explained by the evolutionary history of adaptation of the insects to the plants than by plant phylogeny.\n\nOur findings suggest that V. cardui may use two sets of expressed genes to achieve polyphagy, one associated with the ancestral capability to consume Rosids and Asterids, and another allowing the caterpillar to incorporate a wide range of novel host-plants.", "doi": "10.1186/s12862-016-0627-y", "pmid": "26956800", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12862-016-0627-y"}, {"db": "pmc", "key": "PMC4782335"}, {"db": "ArrayExpress", "description": "RNA-seq data", "key": "E-MTAB-3861"}], "notes": [], "created": "2017-05-08T07:58:17.816Z", "modified": "2024-01-16T13:48:50.357Z"}, {"entity": "publication", "iuid": "845967e99a9241bb9066d04642cd73bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/845967e99a9241bb9066d04642cd73bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/845967e99a9241bb9066d04642cd73bb"}}, "title": "Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.", "authors": [{"family": "Zangenah", "given": "Salah", "initials": "S"}, {"family": "Abbasi", "given": "Nasir", "initials": "N"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bergman", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2016-03-07", "journal": {"volume": "6", "issn": "2045-2322", "issue": null, "pages": "22919", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "C. canimorsus and C. cynodegmi are dog and cat commensals which can be transmitted to humans via bites or scratches and can cause sepsis, meningitis, endocarditis, and eye- or wound infections. Recently an additional Capnocytophaga species was identified as part of the oral flora of healthy dogs and was given the name \"C. canis\". We previously identified a Capnocytophaga isolate that could not be typed with available diagnostic tests including MALDI-TOF, 16S rRNA sequencing or species-specific PCR. This strain and 21 other Capnocytophaga spp isolated in Sweden from clinical blood- or wound-cultures were subjected to whole genome sequencing using the Illumina platform. Phylogenetic analysis revealed that the previously non-typable isolate belongs to the putative new species \"C. canis\". Since this strain was isolated from a wound it also shows that members of \"C. canis\" have the potential to be pathogenic. In addition, our phylogenetic analysis uncovered an additional species of Capnocytophaga, which can be transmitted from dogs and cats to humans, suggesting a speciation within the Capnocytophaga family that has not been observed before. We propose the name of \"C. stomatis\" for this putative novel species.", "doi": "10.1038/srep22919", "pmid": "26947740", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "srep22919"}, {"db": "pmc", "key": "PMC4780008"}], "notes": [], "created": "2017-05-03T13:00:01.213Z", "modified": "2024-01-16T13:48:50.364Z"}, {"entity": "publication", "iuid": "047ee868b5db45eca47e6761a67fbe44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/047ee868b5db45eca47e6761a67fbe44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/047ee868b5db45eca47e6761a67fbe44"}}, "title": "Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.", "authors": [{"family": "Prezza", "given": "Nicola", "initials": "N"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Policriti", "given": "Alberto", "initials": "A"}], "type": "journal article", "published": "2016-03-02", "journal": {"volume": "17 Suppl 4", "issn": "1471-2105", "issue": null, "pages": "69", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of low-methylated genomic regions, and C-to-T mismatches may reflect cytosine unmethylation rather than SNPs or sequencing errors. Further challenges arise both during and after the alignment phase: data structures used by the aligner should be fast and should fit into main memory, and the methylation-caller output should be somehow compressed, due to its significant size.\n\nAs far as data structures employed to align bisulfite-treated reads are concerned, solutions proposed in the literature can be roughly grouped into two main categories: those storing pointers at each text position (e.g. hash tables, suffix trees/arrays), and those using the information-theoretic minimum number of bits (e.g. FM indexes and compressed suffix arrays). The former are fast and memory consuming. The latter are much slower and light. In this paper, we try to close this gap proposing a data structure for aligning bisulfite-treated reads which is at the same time fast, light, and very accurate. We reach this objective by combining a recent theoretical result on succinct hashing with a bisulfite-aware hash function. Furthermore, the new versions of the tools implementing our ideas|the aligner ERNE-BS5 2 and the caller ERNE-METH 2|have been extended with increased downstream compatibility (EPP/Bismark cov output formats), output compression, and support for target enrichment protocols.\n\nExperimental results on public and simulated WGBS libraries show that our algorithmic solution is a competitive tradeoff between hash-based and BWT-based indexes, being as fast and accurate as the former, and as memory-efficient as the latter.\n\nThe new functionalities of our bisulfite aligner and caller make it a fast and memory efficient tool, useful to analyze big datasets with little computational resources, to easily process target enrichment data, and produce statistics such as protocol efficiency and coverage as a function of the distance from target regions.", "doi": "10.1186/s12859-016-0910-3", "pmid": "26961371", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12859-016-0910-3"}, {"db": "pmc", "key": "PMC4896272"}], "notes": [], "created": "2017-05-03T13:01:06.997Z", "modified": "2021-07-07T15:22:42.670Z"}, {"entity": "publication", "iuid": "c4d1e196683a48cd8d3d587d687dbf4d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4d1e196683a48cd8d3d587d687dbf4d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4d1e196683a48cd8d3d587d687dbf4d"}}, "title": "The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae).", "authors": [{"family": "Kryvokhyzha", "given": "Dmytro", "initials": "D"}, {"family": "Holm", "given": "Karl", "initials": "K"}, {"family": "Chen", "given": "Jun", "initials": "J"}, {"family": "Cornille", "given": "Amandine", "initials": "A"}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "Wright", "given": "Stephen I", "initials": "SI"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "Lascoux", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "25", "issn": "1365-294X", "issue": "5", "pages": "1106-1121", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.", "doi": "10.1111/mec.13537", "pmid": "26797895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "Q83PT"}], "notes": [], "created": "2017-05-03T13:00:14.249Z", "modified": "2024-01-16T13:48:50.371Z"}, {"entity": "publication", "iuid": "dc2cd11e7ff44704ad1f5e7c52f309bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc2cd11e7ff44704ad1f5e7c52f309bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc2cd11e7ff44704ad1f5e7c52f309bc"}}, "title": "T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.", "authors": [{"family": "Grunewald", "given": "Johan", "initials": "J"}, {"family": "Kaiser", "given": "Ylva", "initials": "Y"}, {"family": "Ostadkarampour", "given": "Mahyar", "initials": "M"}, {"family": "Rivera", "given": "Natalia V", "initials": "NV"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Sylwan", "given": "Lina", "initials": "L"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Sandalova", "given": "Tatiana", "initials": "T"}, {"family": "Ahlgren", "given": "Kerstin M", "initials": "KM"}, {"family": "Wahlstr\u00f6m", "given": "Jan", "initials": "J"}, {"family": "Achour", "given": "Adnane", "initials": "A"}, {"family": "Ronninger", "given": "Marcus", "initials": "M"}, {"family": "Eklund", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "47", "issn": "1399-3003", "issue": "3", "pages": "898-909", "title": "Eur. Respir. J.", "issn-l": "0903-1936"}, "abstract": "In pulmonary sarcoidosis, CD4(+) T-cells expressing T-cell receptor V\u03b12.3 accumulate in the lungs of HLA-DRB1*03(+) patients. To investigate T-cell receptor-HLA-DRB1*03 interactions underlying recognition of hitherto unknown antigens, we performed detailed analyses of T-cell receptor expression on bronchoalveolar lavage fluid CD4(+) T-cells from sarcoidosis patients.Pulmonary sarcoidosis patients (n=43) underwent bronchoscopy with bronchoalveolar lavage. T-cell receptor \u03b1 and \u03b2 chains of CD4(+) T-cells were analysed by flow cytometry, DNA-sequenced, and three-dimensional molecular models of T-cell receptor-HLA-DRB1*03 complexes generated.Simultaneous expression of V\u03b12.3 with the V\u03b222 chain was identified in the lungs of all HLA-DRB1*03(+) patients. Accumulated V\u03b12.3/V\u03b222-expressing T-cells were highly clonal, with identical or near-identical V\u03b12.3 chain sequences and inter-patient similarities in V\u03b222 chain amino acid distribution. Molecular modelling revealed specific T-cell receptor-HLA-DRB1*03-peptide interactions, with a previously identified, sarcoidosis-associated vimentin peptide, (Vim)429-443 DSLPLVDTHSKRTLL, matching both the HLA peptide-binding cleft and distinct T-cell receptor features perfectly.We demonstrate, for the first time, the accumulation of large clonal populations of specific V\u03b12.3/V\u03b222 T-cell receptor-expressing CD4(+) T-cells in the lungs of HLA-DRB1*03(+) sarcoidosis patients. Several distinct contact points between V\u03b12.3/V\u03b222 receptors and HLA-DRB1*03 molecules suggest presentation of prototypic vimentin-derived peptides.", "doi": "10.1183/13993003.01209-2015", "pmid": "26585430", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "13993003.01209-2015"}], "notes": [], "created": "2017-05-02T12:57:09.283Z", "modified": "2024-01-16T13:48:50.378Z"}, {"entity": "publication", "iuid": "c739409284804dc9a4e4c5d063c8fd00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c739409284804dc9a4e4c5d063c8fd00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c739409284804dc9a4e4c5d063c8fd00"}}, "title": "Reclassification of Wolbachia persica as Francisella persica comb. nov. and emended description of the family Francisellaceae.", "authors": [{"family": "Larson", "given": "Marilynn A", "initials": "MA"}, {"family": "Nalbantoglu", "given": "Ufuk", "initials": "U"}, {"family": "Sayood", "given": "Khalid", "initials": "K"}, {"family": "Zentz", "given": "Emily B", "initials": "EB"}, {"family": "Cer", "given": "Regina Zing", "initials": "RZ"}, {"family": "Iwen", "given": "Peter C", "initials": "PC"}, {"family": "Francesconi", "given": "Stephen C", "initials": "SC"}, {"family": "Bishop-Lilly", "given": "Kimberly A", "initials": "KA"}, {"family": "Mokashi", "given": "Vishwesh P", "initials": "VP"}, {"family": "Sj\u00f6stedt", "given": "Anders", "initials": "A"}, {"family": "Hinrichs", "given": "Steven H", "initials": "SH"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "66", "issn": "1466-5034", "issue": "3", "pages": "1200-1205", "title": "Int. J. Syst. Evol. Microbiol.", "issn-l": "1466-5026"}, "abstract": "The taxonomic status of the bacterium Wolbachia persica is described, and based on the evidence presented, transfer of this species to the genus Francisella as Francisella persica comb. nov. is proposed. This reclassification is supported by data generated from genomic comparisons of W. persica ATCC VR-331T (\u2009=\u2009FSC845T\u2009=\u2009DSM 101678T) to other near neighbours, including Francisella tularensis subsp. novicida. The full-length 16S rRNA gene sequence of strain ATCC VR-331T had 98.5\u2009% nucleotide identity to the cognate gene in F. tularensis, with the highest similarity to subspecies novicida. Phylogenetic trees of full-length 16S rRNA gene, gyrA and recA sequences from species of the genera Wolbachia (class Alphaproteobacteria) and Francisella (class Gammaproteobacteria) indicated that W. persica ATCC VR-331T was most closely related to members of the genus Francisella and not Wolbachia. Local collinear blocks within the chromosome of strain ATCC VR-331T had considerable similarity with F. tularensis subsp. novicida, but not with any Wolbachia strain. The genomes of strain ATCC VR-331T and F. tularensis subsp. novicida Utah 112T (\u2009=\u2009ATCC 15482T) contained an average nucleotide identity mean of 88.72\u2009% and median of 89.18\u2009%. Importantly, the genome of strain ATCC VR-331T contained one Francisella Pathogenicity Island, similar to F. tularensis subsp. novicida, as well as the Francisella-specific gene fopA1 and F. tularensis-specific genes fopA2 and lpnA (also referred to as tul4). In contrast to the obligate intracellular genus Wolbachia, strain ATCC VR-331T and facultative intracellular Francisella can replicate in specialized cell-free media. Collectively, these results demonstrate that Wolbachia persica should be reclassified in the genus Francisella as Francisella persica comb. nov. The type strain of Francisella persica comb. nov. is ATCC VR-331T (\u2009=\u2009FSC845T\u2009=\u2009DSM 101678T). An emended description of the family Francisellaceae is also provided.", "doi": "10.1099/ijsem.0.000855", "pmid": "26747442", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T12:58:56.046Z", "modified": "2020-01-21T13:56:05.130Z"}, {"entity": "publication", "iuid": "d3f3b77df7bb441495c74fa77e664015", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3f3b77df7bb441495c74fa77e664015.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3f3b77df7bb441495c74fa77e664015"}}, "title": "Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.", "authors": [{"family": "Wang", "given": "Jing", "initials": "J"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}], "type": "journal article", "published": "2016-03-00", "journal": {"volume": "202", "issn": "1943-2631", "issue": "3", "pages": "1185-1200", "title": "Genetics", "issn-l": "0016-6731"}, "abstract": "A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.", "doi": "10.1534/genetics.115.183152", "pmid": "26721855", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "genetics.115.183152"}, {"db": "pmc", "key": "PMC4788117"}], "notes": [], "created": "2017-05-02T12:58:54.740Z", "modified": "2024-01-16T13:48:50.392Z"}, {"entity": "publication", "iuid": "892bdf3f53a0496c86931dd5f23ff8e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/892bdf3f53a0496c86931dd5f23ff8e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/892bdf3f53a0496c86931dd5f23ff8e1"}}, "title": "Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma.", "authors": [{"family": "Fransson", "given": "Susanne", "initials": "S"}, {"family": "\u00d6stensson", "given": "Malin", "initials": "M"}, {"family": "Djos", "given": "Anna", "initials": "A"}, {"family": "Javanmardi", "given": "Niloufar", "initials": "N"}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}], "type": "comparative study", "published": "2016-03-00", "journal": {"volume": "48", "issn": "1791-2423", "issue": "3", "pages": "1103-1116", "title": "Int. J. Oncol.", "issn-l": "1791-2423"}, "abstract": "In the pediatric cancer neuroblastoma, analysis of recurrent chromosomal aberrations such as loss of chromosome 1p, 11q, gain of 17q and MYCN amplification are used for patient stratification and subsequent therapy decision making. Different analysis techniques have been used for detection of segmental abnormalities, including fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH)-microarrays and multiplex ligation-dependent probe amplification (MLPA). However, as next-generation sequencing becomes available for clinical use, this technique could also be used for assessment of copy number alterations simultaneously with mutational analysis. In this study we compare genomic profiles generated through exome sequencing data with profiles generated from high resolution Affymetrix single nucleotide polymorphism (SNP) microarrays on 30 neuroblastoma tumors of different stages. Normalized coverage reads for tumors were calculated using Control-FREEC software and visualized through a web based Shiny application, prior to comparison with corresponding SNP-microarray data. The two methods show high-level agreement for breakpoints and copy number of larger segmental aberrations and numerical aneuploidies. However, several smaller gene containing deletions that could not readily be detected through the SNP-microarray analyses were identified through exome profiling, most likely due to difference between spatial distribution of microarray probes and targeted regions of the exome capture. These smaller aberrations included focal ATRX deletion in two tumors and three cases of novel deletions in chromosomal region 19q13.2 causing homozygous loss of multiple genes including the CIC (Capicua) gene. In conclusion, genomic profiles generated from normalized coverage of exome sequencing show concordance with SNP microarray generated genomic profiles. Exome sequencing is therefore a useful diagnostic tool for copy number variant (CNV) detection in neuroblastoma tumors, especially considering the combination with mutational screening. This enables detection of theranostic targets such as ALK and ATRX together with detection of significant segmental aneuploidies, such as 2p-gain, 17q-gain, 11q-deletion as well as MYCN amplification.", "doi": "10.3892/ijo.2016.3349", "pmid": "26794043", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:31.893Z", "modified": "2024-01-16T13:48:50.417Z"}, {"entity": "publication", "iuid": "fb94ae6f65904c328ae523aa3f1d88d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb94ae6f65904c328ae523aa3f1d88d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb94ae6f65904c328ae523aa3f1d88d5"}}, "title": "Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.", "authors": [{"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Sun", "given": "Li", "initials": "L"}, {"family": "Westerholm", "given": "Maria", "initials": "M"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2016-02-27", "journal": {"volume": "9", "issn": "1754-6834", "issue": null, "pages": "48", "title": "Biotechnol Biofuels", "issn-l": "1754-6834"}, "abstract": "Syntrophic acetate oxidation (SAO) is the predominant pathway for methane production in high ammonia anaerobic digestion processes. The bacteria (SAOB) occupying this niche and the metabolic pathway are poorly understood. Phylogenetic diversity and strict cultivation requirements hinder comprehensive research and discovery of novel SAOB. Most SAOB characterised to date are affiliated to the physiological group of acetogens. Formyltetrahydrofolate synthetase is a key enzyme of both acetogenic and SAO metabolism. The encoding fhs gene has therefore been identified as a suitable functional marker, using a newly designed primer pair. In this comparative study, we used a combination of terminal restriction fragment length polymorphism profiling, clone-based comparison, qPCR and Illumina amplicon sequencing to assess the bacterial community and acetogenic sub-community prevailing in high- and low-ammonia laboratory-scale digesters in order to delineate potential SAOB communities. Potential candidates identified were further tracked in a number of low-ammonia and high-ammonia laboratory-scale and large-scale digesters in order to reveal a potential function in SAO.\n\nAll methodical approaches revealed significant changes in the bacterial community composition concurrently with increasing ammonia and predominance of SAO. The acetogenic community under high ammonia conditions was revealed to be generally heterogeneous, but formed distinct phylogenetic clusters. The clusters differed clearly from those found under low-ammonia conditions and represented an acetogenic assemblage unique for biogas processes and recurring in a number of high-ammonia processes, indicating potential involvement in SAO.\n\nThe phylogenetic affiliation and population dynamics observed point to a key community, belonging mainly to the Clostridia class, in particular to the orders Clostridiales and Thermoanaerobacterales, which appear to specialise in SAO rather than being metabolically versatile. Overall, the results reported here provide evidence of functional importance of the bacterial families identified in high-ammonia systems and extend existing knowledge of bacterial and acetogenic assemblages at low and high ammonia levels. This information will be of help in monitoring and assessing the impacts on the SAOB community in order to identify characteristics of robust and productive high ammonia biogas processes.", "doi": "10.1186/s13068-016-0454-9", "pmid": "26925165", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service"}, "xrefs": [{"db": "pii", "key": "454"}, {"db": "pmc", "key": "PMC4769498"}], "notes": [], "created": "2017-05-03T12:58:54.888Z", "modified": "2020-01-21T13:56:06.461Z"}, {"entity": "publication", "iuid": "31ea5863739a459198d553aad06f3aaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31ea5863739a459198d553aad06f3aaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31ea5863739a459198d553aad06f3aaa"}}, "title": "Xenacoelomorpha is the sister group to Nephrozoa.", "authors": [{"family": "Cannon", "given": "Johanna Taylor", "initials": "JT"}, {"family": "Vellutini", "given": "Bruno Cossermelli", "initials": "BC"}, {"family": "Smith", "given": "Julian", "initials": "J"}, {"family": "Ronquist", "given": "Fredrik", "initials": "F"}, {"family": "Jondelius", "given": "Ulf", "initials": "U"}, {"family": "Hejnol", "given": "Andreas", "initials": "A"}], "type": "journal article", "published": "2016-02-04", "journal": {"volume": "530", "issn": "1476-4687", "issue": "7588", "pages": "89-93", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "The position of Xenacoelomorpha in the tree of life remains a major unresolved question in the study of deep animal relationships. Xenacoelomorpha, comprising Acoela, Nemertodermatida, and Xenoturbella, are bilaterally symmetrical marine worms that lack several features common to most other bilaterians, for example an anus, nephridia, and a circulatory system. Two conflicting hypotheses are under debate: Xenacoelomorpha is the sister group to all remaining Bilateria (=\u2009Nephrozoa, namely protostomes and deuterostomes) or is a clade inside Deuterostomia. Thus, determining the phylogenetic position of this clade is pivotal for understanding the early evolution of bilaterian features, or as a case of drastic secondary loss of complexity. Here we show robust phylogenomic support for Xenacoelomorpha as the sister taxon of Nephrozoa. Our phylogenetic analyses, based on 11 novel xenacoelomorph transcriptomes and using different models of evolution under maximum likelihood and Bayesian inference analyses, strongly corroborate this result. Rigorous testing of 25 experimental data sets designed to exclude data partitions and taxa potentially prone to reconstruction biases indicates that long-branch attraction, saturation, and missing data do not influence these results. The sister group relationship between Nephrozoa and Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.", "doi": "10.1038/nature16520", "pmid": "26842059", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "nature16520"}, {"db": "BioProject", "key": "PRJNA295688"}, {"db": "Dryad", "key": "493B7"}], "notes": [], "created": "2017-05-03T12:59:56.096Z", "modified": "2024-01-16T13:48:50.472Z"}, {"entity": "publication", "iuid": "0a636ef1f1294f3e95502f73cdace59e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0a636ef1f1294f3e95502f73cdace59e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0a636ef1f1294f3e95502f73cdace59e"}}, "title": "Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1.", "authors": [{"family": "Massinen", "given": "Satu", "initials": "S"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Laivuori", "given": "Krista", "initials": "K"}, {"family": "Bieder", "given": "Andrea", "initials": "A"}, {"family": "Tapia Paez", "given": "Isabel", "initials": "I"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2016-01-27", "journal": {"volume": "8", "issn": "1866-1947", "issue": null, "pages": "4", "title": "J Neurodev Disord", "issn-l": null}, "abstract": "The DYX5 locus for developmental dyslexia was mapped to chromosome 3 by linkage study of a large Finnish family, and later, roundabout guidance receptor 1 (ROBO1) was implicated as a candidate gene at DYX5 with suppressed expression from the segregating rare haplotype. A functional magnetoencephalographic study of several family members revealed abnormal auditory processing of interaural interaction, supporting a defect in midline crossing of auditory pathways. In the current study, we have characterized genetic variation in the broad ROBO1 gene region in the DYX5-linked family, aiming to identify variants that would increase our understanding of the altered expression of ROBO1.\n\nWe have used a whole genome sequencing strategy on a pooled sample of 19 individuals in combination with two individually sequenced genomes. The discovered genetic variants were annotated and filtered. Subsequently, the most interesting variants were functionally tested using relevant methods, including electrophoretic mobility shift assay (EMSA), luciferase assay, and gene knockdown by lentiviral small hairpin RNA (shRNA) in lymphoblasts.\n\nWe found one novel intronic single nucleotide variant (SNV) and three novel intergenic SNVs in the broad region of ROBO1 that were specific to the dyslexia susceptibility haplotype. Functional testing by EMSA did not support the binding of transcription factors to three of the SNVs, but one of the SNVs was bound by the LIM homeobox 2 (LHX2) protein, with increased binding affinity for the non-reference allele. Knockdown of LHX2 in lymphoblast cell lines extracted from subjects from the DYX5-linked family showed decreasing expression of ROBO1, supporting the idea that LHX2 regulates ROBO1 also in human.\n\nThe discovered variants may explain the segregation of dyslexia in this family, but the effect appears subtle in the experimental settings. Their impact on the developing human brain remains suggestive based on the association and subtle experimental support.", "doi": "10.1186/s11689-016-9136-y", "pmid": "26877820", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "9136"}, {"db": "pmc", "key": "PMC4751651"}], "notes": [], "created": "2017-05-03T13:00:20.246Z", "modified": "2024-01-16T13:48:50.560Z"}, {"entity": "publication", "iuid": "06a7f813e778488ca2802234eb311211", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06a7f813e778488ca2802234eb311211.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06a7f813e778488ca2802234eb311211"}}, "title": "Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.", "authors": [{"family": "Thureborn", "given": "Petter", "initials": "P"}, {"family": "Franzetti", "given": "Andrea", "initials": "A"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Sj\u00f6ling", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2016-01-19", "journal": {"volume": "4", "issn": "2167-8359", "issue": null, "pages": "e1593", "title": "PeerJ", "issn-l": "2167-8359"}, "abstract": "Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning.", "doi": "10.7717/peerj.1593", "pmid": "26823996", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1593"}, {"db": "pmc", "key": "PMC4730985"}], "notes": [], "created": "2017-05-03T13:00:51.830Z", "modified": "2020-01-21T13:56:16.842Z"}, {"entity": "publication", "iuid": "708227d54b854bada883a69b636e8610", "links": {"self": {"href": "https://publications.scilifelab.se/publication/708227d54b854bada883a69b636e8610.json"}, "display": {"href": "https://publications.scilifelab.se/publication/708227d54b854bada883a69b636e8610"}}, "title": "Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.", "authors": [{"family": "Gr\u00e9en", "given": "Henrik", "initials": "H"}, {"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Kupershmidt", "given": "Ilya", "initials": "I"}, {"family": "Edsg\u00e4rd", "given": "Daniel", "initials": "D"}, {"family": "de Petris", "given": "Luigi", "initials": "L"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "Blackhall", "given": "Fiona", "initials": "F"}, {"family": "Vikingsson", "given": "Svante", "initials": "S"}, {"family": "Besse", "given": "Benjamin", "initials": "B"}, {"family": "Lindgren", "given": "Andrea", "initials": "A"}, {"family": "Brand\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Koyi", "given": "Hirsh", "initials": "H"}, {"family": "Peterson", "given": "Curt", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2016-01-15", "journal": {"volume": "22", "issn": "1557-3265", "issue": "2", "pages": "366-373", "title": "Clin. Cancer Res.", "issn-l": "1078-0432"}, "abstract": "Chemotherapies are associated with significant interindividual variability in therapeutic effect and adverse drug reactions. In lung cancer, the use of gemcitabine and carboplatin induces grade 3 or 4 myelosuppression in about a quarter of the patients, while an equal fraction of patients is basically unaffected in terms of myelosuppressive side effects. We therefore set out to identify genetic markers for gemcitabine/carboplatin-induced myelosuppression.\n\nWe exome sequenced 32 patients that suffered extremely high neutropenia and thrombocytopenia (grade 3 or 4 after first chemotherapy cycle) or were virtually unaffected (grade 0 or 1). The genetic differences/polymorphism between the groups were compared using six different bioinformatics strategies: (i) whole-exome nonsynonymous single-nucleotide variants association analysis, (ii) deviation from Hardy-Weinberg equilibrium, (iii) analysis of genes selected by a priori biologic knowledge, (iv) analysis of genes selected from gene expression meta-analysis of toxicity datasets, (v) Ingenuity Pathway Analysis, and (vi) FunCoup network enrichment analysis.\n\nA total of 53 genetic variants that differed among these groups were validated in an additional 291 patients and were correlated to the patients' myelosuppression. In the validation, we identified rs1453542 in OR4D6 (P = 0.0008; OR, 5.2; 95% CI, 1.8-18) as a marker for gemcitabine/carboplatin-induced neutropenia and rs5925720 in DDX53 (P = 0.0015; OR, 0.36; 95% CI, 0.17-0.71) as a marker for thrombocytopenia. Patients homozygous for the minor allele of rs1453542 had a higher risk of neutropenia, and for rs5925720 the minor allele was associated with a lower risk for thrombocytopenia.\n\nWe have identified two new genetic markers with the potential to predict myelosuppression induced by gemcitabine/carboplatin chemotherapy.", "doi": "10.1158/1078-0432.CCR-15-0964", "pmid": "26378035", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "1078-0432.CCR-15-0964"}], "notes": [], "created": "2017-05-02T12:57:08.106Z", "modified": "2024-01-16T13:48:50.593Z"}, {"entity": "publication", "iuid": "568c8a1dbacc4b2fbf572abcbe5346a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/568c8a1dbacc4b2fbf572abcbe5346a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/568c8a1dbacc4b2fbf572abcbe5346a9"}}, "title": "Pathogenenic variant in the COL2A1 gene is associated with Spondyloepiphyseal dysplasia type Stanescu.", "authors": [{"family": "Hammarsj\u00f6", "given": "Anna", "initials": "A"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Malmgren", "given": "Helena", "initials": "H"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Wedr\u00e9n", "given": "Sara", "initials": "S"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Nishimura", "given": "Gen", "initials": "G"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}], "type": "case reports", "published": "2016-01-00", "journal": {"volume": "170A", "issn": "1552-4833", "issue": "1", "pages": "266-269", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": null, "doi": "10.1002/ajmg.a.37387", "pmid": "26420734", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-02T12:56:31.054Z", "modified": "2024-01-16T13:48:50.638Z"}, {"entity": "publication", "iuid": "15c7426884f84985aa16df8c0e95c064", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15c7426884f84985aa16df8c0e95c064.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15c7426884f84985aa16df8c0e95c064"}}, "title": "Mutations in FLVCR2 associated with Fowler syndrome and survival beyond infancy.", "authors": [{"family": "Kvarnung", "given": "M", "initials": "M"}, {"family": "Taylan", "given": "F", "initials": "F"}, {"family": "Nilsson", "given": "D", "initials": "D"}, {"family": "Alb\u00e5ge", "given": "M", "initials": "M"}, {"family": "Nordenskj\u00f6ld", "given": "M", "initials": "M"}, {"family": "Anderlid", "given": "B M", "initials": "BM"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Syk Lundberg", "given": "E", "initials": "E"}], "type": "case reports", "published": "2016-01-00", "journal": {"volume": "89", "issn": "1399-0004", "issue": "1", "pages": "99-103", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": "Proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome (PVHH, OMIM 225790), also known as Fowler syndrome, is a rare autosomal recessive disorder, caused by mutations in FLVCR2. Hallmarks of the syndrome are glomerular vasculopathy in the central nervous system, severe hydrocephaly, hypokinesia and arthrogryphosis. The disorder is considered prenatally lethal. We report the first patients, a brother and a sister, with Fowler syndrome and survival beyond infancy. The patients present a phenotype of severe intellectual and neurologic disability with seizures, absence of functional movements, and no means of communication. Imaging of the brain showed calcifications, profound ventriculomegaly with only a thin edging of the cerebral cortex and hypoplastic cerebellum. Investigation with whole-exome sequencing (WES) revealed, in both patients, a homozygous pathogenic mutation in FLVCR2, c.1289C>T, compatible with a diagnosis of Fowler syndrome. The results highlight the power of combining WES with a thorough clinical examination in order to identify disease-causing mutations in patients whose clinical presentation differs from previously described cases. Specifically, the findings demonstrate that Fowler syndrome is a diagnosis to consider, not only prenatally but also in severely affected children with gross ventriculomegaly on brain imaging.", "doi": "10.1111/cge.12565", "pmid": "25677735", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:40.994Z", "modified": "2020-01-21T13:56:00.852Z"}, {"entity": "publication", "iuid": "bf5c2ea2906c4e23b6b43047310133b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf5c2ea2906c4e23b6b43047310133b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf5c2ea2906c4e23b6b43047310133b9"}}, "title": "Composition of human faecal microbiota in resistance to Campylobacter infection.", "authors": [{"family": "Kampmann", "given": "C", "initials": "C"}, {"family": "Dicksved", "given": "J", "initials": "J"}, {"family": "Engstrand", "given": "L", "initials": "L"}, {"family": "Rautelin", "given": "H", "initials": "H"}], "type": "journal article", "published": "2016-01-00", "journal": {"volume": "22", "issn": "1469-0691", "issue": "1", "pages": "61.e1-61.e8", "title": "Clin. Microbiol. Infect.", "issn-l": "1198-743X"}, "abstract": "In mice, specific species composition of gut microbiota enhances susceptibility to Campylobacter jejuni but little is known about the specific composition of the human gut microbiota in providing protection from infections caused by enteropathogens. Healthy adult individuals, who travelled in groups from Sweden to destinations with an estimated high risk for acquisition of Campylobacter infection, were enrolled. Faecal samples, collected before travelling and after returning home, were cultured for bacterial enteropathogens, and analysed for Campylobacter by PCR and for the species composition of the microbiota by 16S amplicon massive parallel sequencing. The microbiota compositions were compared between persons who became infected during their travel and those who did not. A total of 63 participants completed the study; 14 became infected with Campylobacter, two with Salmonella and 47 remained negative for the enteropathogens tested. After exclusion of samples taken after antimicrobial treatment, 49 individuals were included in the final analyses. Intra-individual stability of the microbiota was demonstrated for samples taken before travelling. The original diversity of the faecal microbiota was significantly lower among individuals who later became infected compared with those who remained uninfected. The relative abundances of bacteria belonging to the family Lachnospiraceae, and more specifically its two genera Dorea and Coprococcus, were significantly higher among those who remained uninfected. The travel-related infection did not significantly modify the faecal microbiota composition. Species composition of human gut microbiota is important for colonization resistance to Campylobacter infection. Especially individuals with a lower diversity are more susceptible to Campylobacter infection.", "doi": "10.1016/j.cmi.2015.09.004", "pmid": "26369602", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S1198-743X(15)00819-8"}], "notes": [], "created": "2017-05-03T12:58:55.433Z", "modified": "2020-01-21T13:56:04.978Z"}, {"entity": "publication", "iuid": "ba916d96df4d409ab5b060a1e1af3b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba916d96df4d409ab5b060a1e1af3b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba916d96df4d409ab5b060a1e1af3b7e"}}, "title": "Overexpression of Trypanosoma rangeli trypanothione reductase increases parasite survival under oxidative stress", "authors": [{"family": "BELTRAME-BOTELHO", "given": "I T", "initials": "IT"}, {"family": "STOCO", "given": "P H", "initials": "PH"}, {"family": "STEINDEL", "given": "M", "initials": "M"}, {"family": "ANDERSSON", "given": "B", "initials": "B"}, {"family": "PELOSO", "given": "E F", "initials": "EF"}, {"family": "GADELHA", "given": "F R", "initials": "FR"}, {"family": "GRISARD", "given": "E C", "initials": "EC"}], "type": "journal-article", "published": "2016-00-00", "journal": {"volume": "2", "issn": "2055-7094", "issue": null, "pages": null, "title": "Parasitology Open", "issn-l": "2055-7094"}, "abstract": null, "doi": "10.1017/pao.2016.14", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:58:49.379Z", "modified": "2023-06-19T13:52:58.139Z"}, {"entity": "publication", "iuid": "d852a0e2b7b34fdd8fe46a5d3b682ca7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d852a0e2b7b34fdd8fe46a5d3b682ca7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d852a0e2b7b34fdd8fe46a5d3b682ca7"}}, "title": "The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Habuka", "given": "Masato", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Yamamoto", "given": "Tadashi", "initials": "T"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2015-12-22", "journal": {"volume": "10", "issn": "1932-6203", "issue": "12", "pages": "e0145301", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To understand functions and diseases of urinary bladder, it is important to define its molecular constituents and their roles in urinary bladder biology. Here, we performed genome-wide deep RNA sequencing analysis of human urinary bladder samples and identified genes up-regulated in the urinary bladder by comparing the transcriptome data to those of all other major human tissue types. 90 protein-coding genes were elevated in the urinary bladder, either with enhanced expression uniquely in the urinary bladder or elevated expression together with at least one other tissue (group enriched). We further examined the localization of these proteins by immunohistochemistry and tissue microarrays and 20 of these 90 proteins were localized to the whole urothelium with a majority not yet described in the context of the urinary bladder. Four additional proteins were found specifically in the umbrella cells (Uroplakin 1a, 2, 3a, and 3b), and three in the intermediate/basal cells (KRT17, PCP4L1 and ATP1A4). 61 of the 90 elevated genes have not been previously described in the context of urinary bladder and the corresponding proteins are interesting targets for more in-depth studies. In summary, an integrated omics approach using transcriptomics and antibody-based profiling has been used to define a comprehensive list of proteins elevated in the urinary bladder.", "doi": "10.1371/journal.pone.0145301", "pmid": "26694548", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-11078"}, {"db": "pmc", "key": "PMC4687928"}], "notes": [], "created": "2017-05-02T12:57:10.743Z", "modified": "2021-07-08T13:44:33.679Z"}, {"entity": "publication", "iuid": "831286c09f7e42ce987b6b5b948920dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/831286c09f7e42ce987b6b5b948920dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/831286c09f7e42ce987b6b5b948920dd"}}, "title": "Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.", "authors": [{"family": "Lundmark", "given": "Anna", "initials": "A"}, {"family": "Davanian", "given": "Haleh", "initials": "H"}, {"family": "B\u00e5ge", "given": "Tove", "initials": "T"}, {"family": "Johannsen", "given": "Gunnar", "initials": "G"}, {"family": "Koro", "given": "Catalin", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Yucel-Lindberg", "given": "T\u00fclay", "initials": "T"}], "type": "journal article", "published": "2015-12-21", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "18475", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "The multifactorial chronic inflammatory disease periodontitis, which is characterized by destruction of tooth-supporting tissues, has also been implicated as a risk factor for various systemic diseases. Although periodontitis has been studied extensively, neither disease-specific biomarkers nor therapeutic targets have been identified, nor its link with systemic diseases. Here, we analyzed the global transcriptome of periodontitis and compared its gene expression profile with those of other inflammatory conditions, including cardiovascular disease (CVD), rheumatoid arthritis (RA), and ulcerative colitis (UC). Gingival biopsies from 62 patients with periodontitis and 62 healthy subjects were subjected to RNA sequencing. The up-regulated genes in periodontitis were related to inflammation, wounding and defense response, and apoptosis, whereas down-regulated genes were related to extracellular matrix organization and structural support. The most highly up-regulated gene was mucin 4 (MUC4), and its protein product was confirmed to be over-expressed in periodontitis. When comparing the expression profile of periodontitis with other inflammatory diseases, several gene ontology categories, including inflammatory response, cell death, cell motion, and homeostatic processes, were identified as common to all diseases. Only one gene, pleckstrin (PLEK), was significantly overexpressed in periodontitis, CVD, RA, and UC, implicating this gene as an important networking link between these chronic inflammatory diseases.", "doi": "10.1038/srep18475", "pmid": "26686060", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep18475"}, {"db": "pmc", "key": "PMC4685297"}], "notes": [], "created": "2017-05-02T12:57:54.257Z", "modified": "2021-07-08T13:26:08.230Z"}, {"entity": "publication", "iuid": "b545e90c796a469a8e13301f4d18b22b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b545e90c796a469a8e13301f4d18b22b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b545e90c796a469a8e13301f4d18b22b"}}, "title": "Metagenome-assembled genomes uncover a global brackish microbiome.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Larsson", "given": "John", "initials": "J"}, {"family": "Alneberg", "given": "Johannes", "initials": "J"}, {"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2015-12-14", "journal": {"volume": "16", "issn": "1474-760X", "issue": null, "pages": "279", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them.\n\nWe use automatic binning to reconstruct a large number of bacterioplankton genomes from a metagenomic time-series from the Baltic Sea, one of world's largest brackish water bodies. These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. Signs of streamlining are evident in most genomes, and estimated genome sizes correlate with abundance variation across filter size fractions. Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. This suggests the existence of a global brackish metacommunity whose populations diverged from freshwater and marine relatives over 100,000 years ago, long before the Baltic Sea was formed (8000 years ago). This markedly contrasts to most Baltic Sea multicellular organisms, which are locally adapted populations of freshwater or marine counterparts.\n\nWe describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. We propose that brackish environments exert such strong selection that lineages adapted to them flourish globally with limited influence from surrounding aquatic communities.", "doi": "10.1186/s13059-015-0834-7", "pmid": "26667648", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-015-0834-7"}, {"db": "pmc", "key": "PMC4699468"}], "notes": [], "created": "2017-05-02T12:57:20.814Z", "modified": "2020-01-21T13:56:04.745Z"}, {"entity": "publication", "iuid": "48ed6c13b74743b99137d081483ca574", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48ed6c13b74743b99137d081483ca574.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48ed6c13b74743b99137d081483ca574"}}, "title": "Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.", "authors": [{"family": "Kovatcheva-Datchary", "given": "Petia", "initials": "P"}, {"family": "Nilsson", "given": "Anne", "initials": "A"}, {"family": "Akrami", "given": "Rozita", "initials": "R"}, {"family": "Lee", "given": "Ying Shiuan", "initials": "YS"}, {"family": "De Vadder", "given": "Filipe", "initials": "F"}, {"family": "Arora", "given": "Tulika", "initials": "T"}, {"family": "Hallen", "given": "Anna", "initials": "A"}, {"family": "Martens", "given": "Eric", "initials": "E"}, {"family": "Bj\u00f6rck", "given": "Inger", "initials": "I"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "clinical trial", "published": "2015-12-01", "journal": {"volume": "22", "issn": "1932-7420", "issue": "6", "pages": "971-982", "title": "Cell Metab.", "issn-l": "1550-4131"}, "abstract": "The gut microbiota plays an important role in human health by interacting with host diet, but there is substantial inter-individual variation in the response to diet. Here we compared the gut microbiota composition of healthy subjects who exhibited improved glucose metabolism following 3-day consumption of\u00a0barley kernel-based bread (BKB) with those who\u00a0responded least to this dietary intervention. The Prevotella/Bacteroides ratio was higher in responders than non-responders after BKB. Metagenomic analysis showed that the gut microbiota of responders was enriched in Prevotella copri and had increased potential to ferment complex polysaccharides after BKB. Finally, germ-free mice transplanted with microbiota from responder human donors exhibited improved glucose metabolism and\u00a0increased abundance of Prevotella and liver glycogen content compared with germ-free mice that received non-responder microbiota. Our findings indicate that Prevotella plays a role in the BKB-induced improvement in glucose metabolism observed in certain individuals, potentially by promoting increased glycogen storage.", "doi": "10.1016/j.cmet.2015.10.001", "pmid": "26552345", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1550-4131(15)00517-3"}], "notes": [], "created": "2017-05-02T12:57:39.236Z", "modified": "2020-01-21T13:56:02.120Z"}, {"entity": "publication", "iuid": "6a635f8a475444aa920906cddc9098d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a635f8a475444aa920906cddc9098d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a635f8a475444aa920906cddc9098d1"}}, "title": "The Plant Genome Integrative Explorer Resource: PlantGenIE.org.", "authors": [{"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Mannapperuma", "given": "Chanaka", "initials": "C"}, {"family": "Netotea", "given": "Sergiu", "initials": "S"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal article", "published": "2015-12-00", "journal": {"volume": "208", "issn": "1469-8137", "issue": "4", "pages": "1149-1156", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.", "doi": "10.1111/nph.13557", "pmid": "26192091", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:42.331Z", "modified": "2020-01-21T13:56:02.812Z"}, {"entity": "publication", "iuid": "8b87b5ee37664544bb8815eb84b8e509", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b87b5ee37664544bb8815eb84b8e509.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b87b5ee37664544bb8815eb84b8e509"}}, "title": "Oral microbiota in patients with atherosclerosis.", "authors": [{"family": "F\u00e5k", "given": "Frida", "initials": "F"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Bergstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2015-12-00", "journal": {"volume": "243", "issn": "1879-1484", "issue": "2", "pages": "573-578", "title": "Atherosclerosis", "issn-l": "0021-9150"}, "abstract": "Recent evidence suggests that the microbiota may be considered as an environmental factor that contributes to the development of atherosclerosis. Periodontal disease has been associated with cardio- and cerebrovascular events, and inflammation in the periodontium is suggested to increase the systemic inflammatory level of the host, which may in turn influence plaque composition and rupture. We previously showed that bacteria from the oral cavity and the gut could be found in atherosclerotic plaques.\n\nTo elucidate whether the oral microbiota composition differed between patients with asymptomatic and symptomatic atherosclerosis we performed pyrosequencing of the oral microbiota of 92 individuals including patients with asymptomatic and symptomatic atherosclerosis and control individuals without carotid plaques or previous stroke or myocardial infarction.\n\nThe overall microbial structure was similar in controls and atherosclerosis patients, but patients with symptomatic atherosclerosis had higher relative abundance of Anaeroglobus (mean 0.040% (SD 0.049)) than the control group (0.010% (SD 0.028)) (P\u00a0=\u00a00.03). Using linear regression analysis, we found that Parvimonas associated positively with uCRP and Capnocytophaga, Catonella and Lactobacillus associated with blood lipid markers. In conclusion, abundance of Anaeroglobus in the oral cavity could be associated with symptomatic atherosclerosis.", "doi": "10.1016/j.atherosclerosis.2015.10.097", "pmid": "26536303", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0021-9150(15)30181-7"}], "notes": [], "created": "2017-05-02T12:56:58.154Z", "modified": "2020-01-21T13:56:03.611Z"}, {"entity": "publication", "iuid": "93acb4cd31914e1a856c9a41b08fd8c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93acb4cd31914e1a856c9a41b08fd8c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93acb4cd31914e1a856c9a41b08fd8c3"}}, "title": "Experiences with workflows for automating data-intensive bioinformatics", "authors": [{"family": "Spjuth", "given": "Ola", "initials": "O"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Hern\u00e1ndez", "given": "Guillermo Carrasco", "initials": "GC"}, {"family": "Forer", "given": "Lukas", "initials": "L"}, {"family": "Giovacchini", "given": "Mario", "initials": "M"}, {"family": "Guimera", "given": "Roman Valls", "initials": "RV"}, {"family": "Kallio", "given": "Aleksi", "initials": "A"}, {"family": "Korpelainen", "given": "Eija", "initials": "E"}, {"family": "Ka\u0144du\u0142a", "given": "Maciej M", "initials": "MM"}, {"family": "Krachunov", "given": "Milko", "initials": "M"}, {"family": "Kreil", "given": "David P", "initials": "DP"}, {"family": "Kulev", "given": "Ognyan", "initials": "O"}, {"family": "\u0141abaj", "given": "Pawe\u0142 P", "initials": "PP"}, {"family": "Lampa", "given": "Samuel", "initials": "S"}, {"family": "Pireddu", "given": "Luca", "initials": "L"}, {"family": "Sch\u00f6nherr", "given": "Sebastian", "initials": "S"}, {"family": "Siretskiy", "given": "Alexey", "initials": "A"}, {"family": "Vassilev", "given": "Dimitar", "initials": "D"}], "type": "journal-article", "published": "2015-12-00", "journal": {"volume": "10", "issn": "1745-6150", "issue": "1", "pages": null, "title": "Biol. Direct", "issn-l": "1745-6150"}, "abstract": null, "doi": "10.1186/s13062-015-0071-8", "pmid": "26282399", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": "Service", "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:38.115Z", "modified": "2020-01-21T13:56:16.974Z"}, {"entity": "publication", "iuid": "42f4c093ad4944ef8a0a2edfeea4ff25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42f4c093ad4944ef8a0a2edfeea4ff25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42f4c093ad4944ef8a0a2edfeea4ff25"}}, "title": "De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.", "authors": [{"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Tiukova", "given": "Ievgeniia", "initials": "I"}, {"family": "Holmberg", "given": "Kicki", "initials": "K"}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}], "type": "journal article", "published": "2015-11-26", "journal": {"volume": "4", "issn": "2047-217X", "issue": null, "pages": "56", "title": "Gigascience", "issn-l": "2047-217X"}, "abstract": "It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to assemble new genomes at chromosome resolution (i.e., one sequence per chromosome). Obtaining high quality draft assemblies is extremely important in the case of yeast genomes to better characterise major events in their evolutionary history. The aim of this work is two-fold: on the one hand we want to show how combining different and somewhat complementary technologies is key to improving assembly quality and correctness, and on the other hand we present a de novo assembly pipeline we believe to be beneficial to core facility bioinformaticians. To demonstrate both the effectiveness of combining technologies and the simplicity of the pipeline, here we present the results obtained using the Dekkera bruxellensis genome.\n\nIn this work we used short-read Illumina data and long-read PacBio data combined with the extreme long-range information from OpGen optical maps in the task of de novo genome assembly and finishing. Moreover, we developed NouGAT, a semi-automated pipeline for read-preprocessing, de novo assembly and assembly evaluation, which was instrumental for this work.\n\nWe obtained a high quality draft assembly of a yeast genome, resolved on a chromosomal level. Furthermore, this assembly was corrected for mis-assembly errors as demonstrated by resolving a large collapsed repeat and by receiving higher scores by assembly evaluation tools. With the inclusion of PacBio data we were able to fill about 5 % of the optical mapped genome not covered by the Illumina data.", "doi": "10.1186/s13742-015-0094-1", "pmid": "26617983", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "94"}, {"db": "pmc", "key": "PMC4661999"}], "notes": [], "created": "2017-05-02T12:58:21.226Z", "modified": "2021-07-07T15:22:42.719Z"}, {"entity": "publication", "iuid": "7d10a225ec71482a8ce9383ffcd11050", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d10a225ec71482a8ce9383ffcd11050.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d10a225ec71482a8ce9383ffcd11050"}}, "title": "A Conserved Odorant Receptor Detects the Same 1-Indanone Analogs in a Tortricid and a Noctuid Moth", "authors": [{"family": "Gonzalez", "given": "Francisco", "initials": "F"}, {"family": "Bengtsson", "given": "Jonas M", "initials": "JM"}, {"family": "Walker", "given": "William B", "initials": "WB"}, {"family": "Sousa", "given": "Maria F R", "initials": "MFR"}, {"family": "Cattaneo", "given": "Alberto M", "initials": "AM"}, {"family": "Montagn\u00e9", "given": "Nicolas", "initials": "N"}, {"family": "de Fouchier", "given": "Arthur", "initials": "A"}, {"family": "Anfora", "given": "Gianfranco", "initials": "G"}, {"family": "Jacquin-Joly", "given": "Emmanuelle", "initials": "E"}, {"family": "Witzgall", "given": "Peter", "initials": "P"}, {"family": "Ignell", "given": "Rickard", "initials": "R"}, {"family": "Bengtsson", "given": "Marie", "initials": "M"}], "type": "journal-article", "published": "2015-11-19", "journal": {"volume": "3", "issn": "2296-701X", "issue": null, "pages": null, "title": "Front. Ecol. Evol.", "issn-l": "2296-701X"}, "abstract": null, "doi": "10.3389/fevo.2015.00131", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-05T12:47:25.024Z", "modified": "2021-06-22T11:35:14.943Z"}, {"entity": "publication", "iuid": "9529d31ff6fd4e1ca213ed3b76d4c1fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9529d31ff6fd4e1ca213ed3b76d4c1fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9529d31ff6fd4e1ca213ed3b76d4c1fb"}}, "title": "Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.", "authors": [{"family": "Kvastad", "given": "L", "initials": "L"}, {"family": "Werne Solnestam", "given": "B", "initials": "B"}, {"family": "Johansson", "given": "E", "initials": "E"}, {"family": "Nygren", "given": "A O", "initials": "AO"}, {"family": "Laddach", "given": "N", "initials": "N"}, {"family": "Sahl\u00e9n", "given": "P", "initials": "P"}, {"family": "Vickovic", "given": "S", "initials": "S"}, {"family": "Bendigtsen", "given": "Schirmer C", "initials": "SC"}, {"family": "Aaserud", "given": "M", "initials": "M"}, {"family": "Floer", "given": "L", "initials": "L"}, {"family": "Borgen", "given": "E", "initials": "E"}, {"family": "Schwind", "given": "C", "initials": "C"}, {"family": "Himmelreich", "given": "R", "initials": "R"}, {"family": "Latta", "given": "D", "initials": "D"}, {"family": "Lundeberg", "given": "J", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2015-11-12", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "16519", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Single cell analysis techniques have great potential in the cancer genomics field. The detection and characterization of circulating tumour cells are important for identifying metastatic disease at an early stage and monitoring it. This protocol is based on transcript profiling using Reverse Transcriptase Multiplex Ligation-dependent Probe Amplification (RT-MLPA), which is a specific method for simultaneous detection of multiple mRNA transcripts. Because of the small amount of (circulating) tumour cells, a pre-amplification reaction is performed after reverse transcription to generate a sufficient number of target molecules for the MLPA reaction. We designed a highly sensitive method for detecting and quantifying a panel of seven genes whose expression patterns are associated with breast cancer, and optimized the method for single cell analysis. For detection we used a fluorescence-dependent semi-quantitative method involving hybridization of unique barcodes to an array. We evaluated the method using three human breast cancer cell lines and identified specific gene expression profiles for each line. Furthermore, we applied the method to single cells and confirmed the heterogeneity of a cell population. Successful gene detection from cancer cells in human blood from metastatic breast cancer patients supports the use of RT-MLPA as a diagnostic tool for cancer genomics.", "doi": "10.1038/srep16519", "pmid": "26558529", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep16519"}, {"db": "pmc", "key": "PMC4642268"}], "notes": [], "created": "2017-05-02T12:57:41.587Z", "modified": "2021-07-08T13:26:08.246Z"}, {"entity": "publication", "iuid": "d6ec9bcf4db045aead4f29f223439363", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d6ec9bcf4db045aead4f29f223439363.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d6ec9bcf4db045aead4f29f223439363"}}, "title": "Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization.", "authors": [{"family": "Johansson", "given": "Malin E V", "initials": "ME"}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Holm\u00e9n-Larsson", "given": "Jessica", "initials": "J"}, {"family": "Sch\u00fctte", "given": "Andr\u00e9", "initials": "A"}, {"family": "Ermund", "given": "Anna", "initials": "A"}, {"family": "Rodr\u00edguez-Pi\u00f1eiro", "given": "Ana M", "initials": "AM"}, {"family": "Arike", "given": "Liisa", "initials": "L"}, {"family": "Wising", "given": "Catharina", "initials": "C"}, {"family": "Svensson", "given": "Frida", "initials": "F"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC"}], "type": "journal article", "published": "2015-11-11", "journal": {"volume": "18", "issn": "1934-6069", "issue": "5", "pages": "582-592", "title": "Cell Host Microbe", "issn-l": "1931-3128"}, "abstract": "The intestinal mucus layer provides a barrier limiting bacterial contact with the underlying epithelium. Mucus structure is shaped by intestinal location and the microbiota. To understand how commensals modulate gut mucus, we examined mucus properties under germ-free (GF) conditions and during microbial colonization. Although the colon mucus organization of GF mice was similar to that of conventionally raised (Convr) mice, the GF inner mucus layer was penetrable to bacteria-sized beads. During colonization, in which GF mice were gavaged with Convr microbiota, the small intestine mucus required 5 weeks to be normally detached and colonic inner mucus 6 weeks to become impenetrable. The composition of the small intestinal microbiota during colonization was similar to Convr donors until 3 weeks, when Bacteroides increased, Firmicutes decreased, and segmented filamentous bacteria became undetectable. These findings highlight the dynamics of mucus layer development and indicate that studies of mature microbe-mucus interactions should be conducted weeks after colonization.", "doi": "10.1016/j.chom.2015.10.007", "pmid": "26526499", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1931-3128(15)00417-5"}, {"db": "pmc", "key": "PMC4648652"}, {"db": "mid", "key": "NIHMS730023"}], "notes": [], "created": "2017-05-02T12:57:28.771Z", "modified": "2020-01-21T13:56:05.513Z"}, {"entity": "publication", "iuid": "1988d3d3ea4940688583a3c7799c7ea6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1988d3d3ea4940688583a3c7799c7ea6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1988d3d3ea4940688583a3c7799c7ea6"}}, "title": "Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.", "authors": [{"family": "Kishita", "given": "Yoshihito", "initials": "Y"}, {"family": "Pajak", "given": "Aleksandra", "initials": "A"}, {"family": "Bolar", "given": "Nikhita Ajit", "initials": "NA"}, {"family": "Marobbio", "given": "Carlo M T", "initials": "CM"}, {"family": "Maffezzini", "given": "Camilla", "initials": "C"}, {"family": "Miniero", "given": "Daniela V", "initials": "DV"}, {"family": "Monn\u00e9", "given": "Magnus", "initials": "M"}, {"family": "Kohda", "given": "Masakazu", "initials": "M"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Murayama", "given": "Kei", "initials": "K"}, {"family": "Naess", "given": "Karin", "initials": "K"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Bruhn", "given": "Helene", "initials": "H"}, {"family": "Mourier", "given": "Arnaud", "initials": "A"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Nennesmo", "given": "Inger", "initials": "I"}, {"family": "Jespers", "given": "Ann", "initials": "A"}, {"family": "Govaert", "given": "Paul", "initials": "P"}, {"family": "Ohtake", "given": "Akira", "initials": "A"}, {"family": "Van Laer", "given": "Lut", "initials": "L"}, {"family": "Loeys", "given": "Bart L", "initials": "BL"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Palmieri", "given": "Ferdinando", "initials": "F"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}, {"family": "Okazaki", "given": "Yasushi", "initials": "Y"}, {"family": "Wedell", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2015-11-05", "journal": {"volume": "97", "issn": "1537-6605", "issue": "5", "pages": "761-768", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "S-adenosylmethionine (SAM) is the predominant methyl group donor and has a large spectrum of target substrates. As such, it is essential for nearly all biological methylation reactions. SAM is synthesized by methionine adenosyltransferase from methionine and ATP in the cytoplasm and subsequently distributed throughout the different cellular compartments, including mitochondria, where methylation is mostly required for nucleic-acid modifications and respiratory-chain function. We report a syndrome in three families affected by reduced intra-mitochondrial methylation caused by recessive mutations in the gene encoding the only known mitochondrial SAM transporter, SLC25A26. Clinical findings ranged from neonatal mortality resulting from respiratory insufficiency and hydrops to childhood acute episodes of cardiopulmonary failure and slowly progressive muscle weakness. We show that SLC25A26 mutations cause various mitochondrial defects, including those affecting RNA stability, protein modification, mitochondrial translation, and the biosynthesis of CoQ10 and lipoic acid.", "doi": "10.1016/j.ajhg.2015.09.013", "pmid": "26522469", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Clinical Genomics Stockholm": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(15)00402-4"}, {"db": "pmc", "key": "PMC4667130"}], "notes": [], "created": "2017-05-02T12:57:36.953Z", "modified": "2020-01-21T13:56:00.921Z"}, {"entity": "publication", "iuid": "dedf0d2c3af14564a3d83c4999f11ea1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dedf0d2c3af14564a3d83c4999f11ea1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dedf0d2c3af14564a3d83c4999f11ea1"}}, "title": "Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma.", "authors": [{"family": "Huang", "given": "Jiaqi", "initials": "J"}, {"family": "L\u00f6hr", "given": "Johannes-Matthias", "initials": "JM"}, {"family": "Nilsson", "given": "Magnus", "initials": "M"}, {"family": "Segersv\u00e4rd", "given": "Ralf", "initials": "R"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Verbeke", "given": "Caroline", "initials": "C"}, {"family": "Heuchel", "given": "Rainer", "initials": "R"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Iafrate", "given": "A John", "initials": "AJ"}, {"family": "Zheng", "given": "Zongli", "initials": "Z"}, {"family": "Ye", "given": "Weimin", "initials": "W"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "61", "issn": "1530-8561", "issue": "11", "pages": "1408-1416", "title": "Clin. Chem.", "issn-l": "0009-9147"}, "abstract": "Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. Variant profiling is crucial for developing personalized treatment and elucidating the etiology of this disease.\n\nPatients with PDAC undergoing surgery from 2007 to 2012 (n = 73) were followed from diagnosis until death or the end of the study. We applied an anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) method to a panel of 65 selected genes and assessed analytical performance by sequencing a quantitative multiplex DNA reference standard. In clinical PDAC samples, detection of low-level KRAS (Kirsten rat sarcoma viral oncogene homolog) mutations was validated by allele-specific PCR and digital PCR. We compared overall survival of patients according to KRAS mutation status by log-rank test and applied logistic regression to evaluate the association between smoking and tumor variant types.\n\nThe AMP-based NGS method could detect variants with allele frequencies as low as 1% given sufficient sequencing depth (>1500\u00d7). Low-frequency KRAS G12 mutations (allele frequency 1%-5%) were all confirmed by allele-specific PCR and digital PCR. The most prevalent genetic alterations were in KRAS (78% of patients), TP53 (tumor protein p53) (25%), and SMAD4 (SMAD family member 4) (8%). Overall survival in T3-stage PDAC patients differed among KRAS mutation subtypes (P = 0.019). Transversion variants were more common in ever-smokers than in never-smokers (odds ratio 5.7; 95% CI 1.2-27.8).\n\nThe AMP-based NGS method is applicable for profiling tumor variants. Using this approach, we demonstrated that in PDAC patients, KRAS mutant subtype G12V is associated with poorer survival, and that transversion variants are more common among smokers.", "doi": "10.1373/clinchem.2015.238543", "pmid": "26378065", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "clinchem.2015.238543"}], "notes": [], "created": "2017-05-02T12:57:19.327Z", "modified": "2021-07-07T13:50:46.757Z"}, {"entity": "publication", "iuid": "599626457fda4ba3b2d8135ec113c389", "links": {"self": {"href": "https://publications.scilifelab.se/publication/599626457fda4ba3b2d8135ec113c389.json"}, "display": {"href": "https://publications.scilifelab.se/publication/599626457fda4ba3b2d8135ec113c389"}}, "title": "The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.", "authors": [{"family": "Zieba", "given": "Agata", "initials": "A"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Olovsson", "given": "Matts", "initials": "M"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Oskarsson", "given": "Linda", "initials": "L"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Tolf", "given": "Anna", "initials": "A"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-11-00", "journal": {"volume": "19", "issn": "1557-8100", "issue": "11", "pages": "659-668", "title": "OMICS", "issn-l": "1536-2310"}, "abstract": "The human uterus includes the complex endometrial mucosa, the endometrium that undergoes dynamic, hormone-dependent alterations throughout the life of fertile females. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to analyze gene expression patterns in the normal endometrium. Human endometrial tissues from five women were used for deep sequencing (RNA-Seq). The mRNA and protein expression data from the endometrium were compared to 31 (RNA) and 44 (protein) other normal tissue types, to identify genes with elevated expression in the endometrium and to localize the expression of corresponding proteins at a cellular resolution. Based on the expression levels of transcripts, we could classify all putative human protein coding genes into categories defined by expression patterns and found altogether 101 genes that showed an elevated pattern of expression in the endometrium, with only four genes showing more than five-fold higher expression levels in the endometrium compared to other tissues. In conclusion, our analysis based on transcriptomics and antibody-based protein profiling reports here comprehensive lists of genes with elevated expression levels in the endometrium, providing important starting points for a better molecular understanding of human reproductive biology and disease.", "doi": "10.1089/omi.2015.0115", "pmid": "26488136", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:59:02.026Z", "modified": "2021-07-08T13:44:33.285Z"}, {"entity": "publication", "iuid": "81e02282dce74f98b8458cd248f99c32", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81e02282dce74f98b8458cd248f99c32.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81e02282dce74f98b8458cd248f99c32"}}, "title": "Rescue of primary ubiquinone deficiency due to a novel COQ7 defect using 2,4-dihydroxybensoic acid.", "authors": [{"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Naess", "given": "Karin", "initials": "K"}, {"family": "Mourier", "given": "Arnaud", "initials": "A"}, {"family": "Felser", "given": "Andrea", "initials": "A"}, {"family": "Maffezzini", "given": "Camilla", "initials": "C"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Bruhn", "given": "Helene", "initials": "H"}, {"family": "Engvall", "given": "Martin", "initials": "M"}, {"family": "Wibom", "given": "Rolf", "initials": "R"}, {"family": "Barbaro", "given": "Michela", "initials": "M"}, {"family": "Hinze", "given": "Yvonne", "initials": "Y"}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M"}, {"family": "Andeer", "given": "Robin", "initials": "R"}, {"family": "Zetterstr\u00f6m", "given": "Rolf H", "initials": "RH"}, {"family": "von D\u00f6beln", "given": "Ulrika", "initials": "U"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}, {"family": "Wedell", "given": "Anna", "initials": "A"}], "type": "case reports", "published": "2015-11-00", "journal": {"volume": "52", "issn": "1468-6244", "issue": "11", "pages": "779-783", "title": "J. Med. Genet.", "issn-l": "0022-2593"}, "abstract": "Coenzyme Q is an essential mitochondrial electron carrier, redox cofactor and a potent antioxidant in the majority of cellular membranes. Coenzyme Q deficiency has been associated with a range of metabolic diseases, as well as with some drug treatments and ageing.\n\nWe used whole exome sequencing (WES) to investigate patients with inherited metabolic diseases and applied a novel ultra-pressure liquid chromatography-mass spectrometry approach to measure coenzyme Q in patient samples.\n\nWe identified a homozygous missense mutation in the COQ7 gene in a patient with complex mitochondrial deficiency, resulting in severely reduced coenzyme Q levels We demonstrate that the coenzyme Q analogue 2,4-dihydroxybensoic acid (2,4DHB) was able to specifically bypass the COQ7 deficiency, increase cellular coenzyme Q levels and rescue the biochemical defect in patient fibroblasts.\n\nWe report the first patient with primary coenzyme Q deficiency due to a homozygous COQ7 mutation and a potentially beneficial treatment using 2,4DHB.", "doi": "10.1136/jmedgenet-2015-102986", "pmid": "26084283", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Clinical Genomics Stockholm": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "jmedgenet-2015-102986"}, {"db": "pmc", "key": "PMC4680133"}], "notes": [], "created": "2017-05-02T12:57:02.012Z", "modified": "2020-01-21T13:56:03.375Z"}, {"entity": "publication", "iuid": "3b72969774f042d0910c8a938ceb5fdf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b72969774f042d0910c8a938ceb5fdf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b72969774f042d0910c8a938ceb5fdf"}}, "title": "Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.", "authors": [{"family": "Wu", "given": "Guangxi", "initials": "G"}, {"family": "Zhao", "given": "He", "initials": "H"}, {"family": "Li", "given": "Chenhao", "initials": "C"}, {"family": "Rajapakse", "given": "Menaka Priyadarsani", "initials": "MP"}, {"family": "Wong", "given": "Wing Cheong", "initials": "WC"}, {"family": "Xu", "given": "Jun", "initials": "J"}, {"family": "Saunders", "given": "Charles W", "initials": "CW"}, {"family": "Reeder", "given": "Nancy L", "initials": "NL"}, {"family": "Reilman", "given": "Raymond A", "initials": "RA"}, {"family": "Scheynius", "given": "Annika", "initials": "A"}, {"family": "Sun", "given": "Sheng", "initials": "S"}, {"family": "Billmyre", "given": "Blake Robert", "initials": "BR"}, {"family": "Li", "given": "Wenjun", "initials": "W"}, {"family": "Averette", "given": "Anna Floyd", "initials": "AF"}, {"family": "Mieczkowski", "given": "Piotr", "initials": "P"}, {"family": "Heitman", "given": "Joseph", "initials": "J"}, {"family": "Theelen", "given": "Bart", "initials": "B"}, {"family": "Schr\u00f6der", "given": "Markus S", "initials": "MS"}, {"family": "De Sessions", "given": "Paola Florez", "initials": "PF"}, {"family": "Butler", "given": "Geraldine", "initials": "G"}, {"family": "Maurer-Stroh", "given": "Sebastian", "initials": "S"}, {"family": "Boekhout", "given": "Teun", "initials": "T"}, {"family": "Nagarajan", "given": "Niranjan", "initials": "N"}, {"family": "Dawson", "given": "Thomas L", "initials": "TL"}], "type": "comparative study", "published": "2015-11-00", "journal": {"volume": "11", "issn": "1553-7404", "issue": "11", "pages": "e1005614", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.", "doi": "10.1371/journal.pgen.1005614", "pmid": "26539826", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-15-02180"}, {"db": "pmc", "key": "PMC4634964"}], "notes": [], "created": "2017-05-02T12:58:57.557Z", "modified": "2020-01-21T13:56:01.677Z"}, {"entity": "publication", "iuid": "1b2aca9d2d7c4d25a074fd670c0e2291", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b2aca9d2d7c4d25a074fd670c0e2291.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b2aca9d2d7c4d25a074fd670c0e2291"}}, "title": "Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.", "authors": [{"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Angelin", "given": "Martin", "initials": "M"}, {"family": "Marathe", "given": "Nachiket", "initials": "N"}, {"family": "Shouche", "given": "Yogesh S", "initials": "YS"}, {"family": "Johansson", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2015-10-24", "journal": {"volume": "15", "issn": "1471-2180", "issue": null, "pages": "235", "title": "BMC Microbiol.", "issn-l": "1471-2180"}, "abstract": "International travel contributes to the spread of antibiotic resistant bacteria over the world. Most studies addressing travel-related changes in the faecal flora have focused on specific mobile resistance genes, or depended on culturing of individual bacterial isolates. Antibiotic resistance can, however, also spread via travellers colonized by bacteria carrying chromosomal antibiotic resistance mutations, but this has received little attention so far. Here we aimed at exploring the abundance of chromosomal quinolone resistance mutations in Escherichia communities residing in the gut of Swedish travellers, and to determine potential changes after visiting India. Sweden is a country with a comparably low degree of quinolone use and quinolone resistance, whereas the opposite is true for India.\n\nMassively parallel amplicon sequencing targeting the quinolone-resistance determining region of gyrA and parC was applied to total DNA extracted from faecal samples. Paired samples were collected from 12 Swedish medical students before and after a 4-15 week visit to India. Twelve Indian residents were included for additional comparisons. Methods known resistance mutations were common in Swedes before travel as well as in Indians, with a trend for all mutations to be more common in the Indian sub group. There was a significant increase in the abundance of the most common amino acid substitution in GyrA (S83L, from 44 to 72%, p=0.036) in the samples collected after return to Sweden. No other substitution, including others commonly associated with quinolone resistance (D87N in GyrA, S80I in ParC) changed significantly. The number of distinct genotypes encoded in each traveller was significantly reduced after their visit to India for both GyrA (p=0.0020) and ParC (p=0.0051), indicating a reduced genetic diversity, similar to that found in the Indians.\n\nInternational travel can alter the composition of the Escherichia communities in the faecal flora, favouring bacteria carrying certain resistance mutations, and, thereby, contributes to the global spread of antibiotic resistance. A high abundance of specific mutations in Swedish travellers before visiting India is consistent with the hypothesis that these mutation have no fitness cost even in the absence of an antibiotic selection pressure.", "doi": "10.1186/s12866-015-0574-6", "pmid": "26498929", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12866-015-0574-6"}, {"db": "pmc", "key": "PMC4619388"}, {"db": "BioProject", "key": "PRJNA241337"}], "notes": [], "created": "2017-05-02T12:57:29.368Z", "modified": "2020-01-21T13:56:00.939Z"}, {"entity": "publication", "iuid": "7b1d9e0720374cf5905addfea62090f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7b1d9e0720374cf5905addfea62090f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7b1d9e0720374cf5905addfea62090f5"}}, "title": "Nurr1 and Retinoid X Receptor Ligands Stimulate Ret Signaling in Dopamine Neurons and Can Alleviate \u03b1-Synuclein Disrupted Gene Expression.", "authors": [{"family": "Volakakis", "given": "Nikolaos", "initials": "N"}, {"family": "Tiklova", "given": "Katarina", "initials": "K"}, {"family": "Decressac", "given": "Mickael", "initials": "M"}, {"family": "Papathanou", "given": "Maria", "initials": "M"}, {"family": "Mattsson", "given": "Bengt", "initials": "B"}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Nobre", "given": "Andr\u00e9", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "Anders", "initials": "A"}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}], "type": "journal article", "published": "2015-10-21", "journal": {"volume": "35", "issn": "1529-2401", "issue": "42", "pages": "14370-14385", "title": "J. Neurosci.", "issn-l": "0270-6474"}, "abstract": "\u03b1-synuclein, a protein enriched in Lewy bodies and highly implicated in neurotoxicity in Parkinson's disease, is distributed both at nerve terminals and in the cell nucleus. Here we show that a nuclear derivative of \u03b1-synuclein induces more pronounced changes at the gene expression level in mouse primary dopamine (DA) neurons compared to a derivative that is excluded from the nucleus. Moreover, by RNA sequencing we analyzed the extent of genome-wide effects on gene expression resulting from expression of human \u03b1-synuclein in primary mouse DA neurons. The results implicated the transcription factor Nurr1 as a key dysregulated target of \u03b1-synuclein toxicity. Forced Nurr1 expression restored the expression of hundreds of dysregulated genes in primary DA neurons expressing \u03b1-synuclein, and therefore prompted us to test the possibility that Nurr1 can be pharmacologically targeted by bexarotene, a ligand for the retinoid X receptor that forms heterodimers with Nurr1. Although our data demonstrated that bexarotene was ineffective in neuroprotection in rats in vivo, the results revealed that bexarotene has the capacity to coregulate subsets of Nurr1 target genes including the receptor tyrosine kinase subunit Ret. Moreover, bexarotene was able to restore dysfunctional Ret-dependent neurotrophic signaling in \u03b1-synuclein-overexpressing mouse DA neurons. These data highlight the role of the Nurr1-Ret signaling pathway as a target of \u03b1-synuclein toxicity and suggest that retinoid X receptor ligands with appropriate pharmacological properties could have therapeutic potential in Parkinson's disease.\n\nHow \u03b1-synuclein, a protein enriched in Lewy bodies in Parkinson's disease, is causing neuropathology in dopamine neurons remains unclear. This study elucidated how \u03b1-synuclein is influencing gene expression and how Nurr1, a transcription factor known to protect dopamine neurons against \u03b1-synuclein toxicity, can counteract these effects. Moreover, given the protective role of Nurr1, this study also investigated how Nurr1 could be pharmacologically targeted via bexarotene, a ligand of Nurr1's heterodimerization partner retinoid X receptor (RXR). The results showed that RXR ligands could increase neurotrophic signaling, but provided a mixed picture of its potential in a Parkinson's disease rat model in vivo. However, this study clearly emphasized Nurr1's neuroprotective role and indicated that other RXR ligands could have therapeutic potential in Parkinson's disease.", "doi": "10.1523/JNEUROSCI.1155-15.2015", "pmid": "26490873", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "35/42/14370"}], "notes": [], "created": "2017-05-02T12:58:52.960Z", "modified": "2020-01-21T13:56:03.190Z"}, {"entity": "publication", "iuid": "5f7c7606992b450da99343109742d3ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f7c7606992b450da99343109742d3ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f7c7606992b450da99343109742d3ed"}}, "title": "Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.", "authors": [{"family": "Caesar", "given": "Robert", "initials": "R"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Kovatcheva-Datchary", "given": "Petia", "initials": "P"}, {"family": "Cani", "given": "Patrice D", "initials": "PD"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-10-06", "journal": {"volume": "22", "issn": "1932-7420", "issue": "4", "pages": "658-668", "title": "Cell Metab.", "issn-l": "1550-4131"}, "abstract": "Dietary lipids may influence the abundance of circulating inflammatory microbial factors. Hence, inflammation in white adipose tissue (WAT) induced by dietary lipids may be partly dependent on their interaction with the gut microbiota. Here, we show that mice fed lard for 11 weeks have increased Toll-like receptor (TLR) activation and WAT inflammation and reduced insulin sensitivity compared with mice fed fish oil and that phenotypic differences between the dietary groups can be partly attributed to differences in microbiota composition. Trif(-/-) and Myd88(-/-) mice are protected against lard-induced WAT inflammation and impaired insulin sensitivity. Experiments in germ-free mice show that an interaction between gut microbiota and saturated lipids promotes WAT inflammation independent of adiposity. Finally, we demonstrate that the chemokine CCL2 contributes to microbiota-induced WAT inflammation in lard-fed mice. These results indicate that gut microbiota exacerbates metabolic inflammation through TLR signaling upon challenge with a diet rich in saturated lipids.", "doi": "10.1016/j.cmet.2015.07.026", "pmid": "26321659", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1550-4131(15)00389-7"}, {"db": "pmc", "key": "PMC4598654"}, {"db": "GEO", "key": "GSE70922"}], "notes": [], "created": "2017-05-02T12:56:40.561Z", "modified": "2020-01-21T13:56:02.579Z"}, {"entity": "publication", "iuid": "3e0b0a7e857349bfbdb91d2e125f45c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e0b0a7e857349bfbdb91d2e125f45c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e0b0a7e857349bfbdb91d2e125f45c6"}}, "title": "Candidate gene analysis and exome sequencing confirm LBX1 as a susceptibility gene for idiopathic scoliosis.", "authors": [{"family": "Grauers", "given": "Anna", "initials": "A"}, {"family": "Wang", "given": "Jingwen", "initials": "J"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Simony", "given": "Ane", "initials": "A"}, {"family": "Danielsson", "given": "Aina", "initials": "A"}, {"family": "\u00c5kesson", "given": "Kristina", "initials": "K"}, {"family": "Ohlin", "given": "Acke", "initials": "A"}, {"family": "Halldin", "given": "Klas", "initials": "K"}, {"family": "Grabowski", "given": "Pawel", "initials": "P"}, {"family": "Tenne", "given": "Max", "initials": "M"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Andersen", "given": "Mikkel", "initials": "M"}, {"family": "Christensen", "given": "Steen Bach", "initials": "SB"}, {"family": "Karlsson", "given": "Magnus K", "initials": "MK"}, {"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2015-10-01", "journal": {"volume": "15", "issn": "1878-1632", "issue": "10", "pages": "2239-2246", "title": "Spine J", "issn-l": "1529-9430"}, "abstract": "Idiopathic scoliosis is a spinal deformity affecting approximately 3% of otherwise healthy children or adolescents. The etiology is still largely unknown but has an important genetic component. Genome-wide association studies have identified a number of common genetic variants that are significantly associated with idiopathic scoliosis in Asian and Caucasian populations, rs11190870 close to the LBX1 gene being the most replicated finding.\n\nThe aim of the present study was to investigate the genetics of idiopathic scoliosis in a Scandinavian cohort by performing a candidate gene study of four variants previously shown to be associated with idiopathic scoliosis and exome sequencing of idiopathic scoliosis patients with a severe phenotype to identify possible novel scoliosis risk variants.\n\nThis was a case control study.\n\nA total of 1,739 patients with idiopathic scoliosis and 1,812 controls were included.\n\nThe outcome measure was idiopathic scoliosis.\n\nThe variants rs10510181, rs11190870, rs12946942, and rs6570507 were genotyped in 1,739 patients with idiopathic scoliosis and 1,812 controls. Exome sequencing was performed on pooled samples from 100 surgically treated idiopathic scoliosis patients. Novel or rare missense, nonsense, or splice site variants were selected for individual genotyping in the 1,739 cases and 1,812 controls. In addition, the 5'UTR, noncoding exon and promoter regions of LBX1, not covered by exome sequencing, were Sanger sequenced in the 100 pooled samples.\n\nOf the four candidate genes, an intergenic variant, rs11190870, downstream of the LBX1 gene, showed a highly significant association to idiopathic scoliosis in 1,739 cases and 1,812 controls (p=7.0\u00d710(-18)). We identified 20 novel variants by exome sequencing after filtration and an initial genotyping validation. However, we could not verify any association to idiopathic scoliosis in the large cohort of 1,739 cases and 1,812 controls. We did not find any variants in the 5'UTR, noncoding exon and promoter regions of LBX1.\n\nHere, we confirm LBX1 as a susceptibility gene for idiopathic scoliosis in a Scandinavian population and report that we are unable to find evidence of other genes of similar or stronger effect.", "doi": "10.1016/j.spinee.2015.05.013", "pmid": "25987191", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1529-9430(15)00478-7"}], "notes": [], "created": "2017-05-02T12:57:07.284Z", "modified": "2020-01-21T13:56:01.767Z"}, {"entity": "publication", "iuid": "ddeb8ed71db84e7ca42ea51082686059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddeb8ed71db84e7ca42ea51082686059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddeb8ed71db84e7ca42ea51082686059"}}, "title": "Profound parental bias associated with chromosome 14 acquired uniparental disomy indicates targeting of an imprinted locus.", "authors": [{"family": "Chase", "given": "A", "initials": "A"}, {"family": "Leung", "given": "W", "initials": "W"}, {"family": "Tapper", "given": "W", "initials": "W"}, {"family": "Jones", "given": "A V", "initials": "AV"}, {"family": "Knoops", "given": "L", "initials": "L"}, {"family": "Rasi", "given": "C", "initials": "C"}, {"family": "Forsberg", "given": "L A", "initials": "LA"}, {"family": "Guglielmelli", "given": "P", "initials": "P"}, {"family": "Zoi", "given": "K", "initials": "K"}, {"family": "Hall", "given": "V", "initials": "V"}, {"family": "Chiecchio", "given": "L", "initials": "L"}, {"family": "Eder-Azanza", "given": "L", "initials": "L"}, {"family": "Bryant", "given": "C", "initials": "C"}, {"family": "Lannfelt", "given": "L", "initials": "L"}, {"family": "Docherty", "given": "L", "initials": "L"}, {"family": "White", "given": "H E", "initials": "HE"}, {"family": "Score", "given": "J", "initials": "J"}, {"family": "Mackay", "given": "D J G", "initials": "DJ"}, {"family": "Vannucchi", "given": "A M", "initials": "AM"}, {"family": "Dumanski", "given": "J P", "initials": "JP"}, {"family": "Cross", "given": "N C P", "initials": "NC"}], "type": "journal article", "published": "2015-10-00", "journal": {"volume": "29", "issn": "1476-5551", "issue": "10", "pages": "2069-2074", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "Acquired uniparental disomy (aUPD) is a common finding in myeloid malignancies and typically acts to convert a somatically acquired heterozygous mutation to homozygosity. We sought to identify the target of chromosome 14 aUPD (aUPD14), a recurrent abnormality in myeloid neoplasms and population cohorts of elderly individuals. We identified 29 cases with aUPD14q that defined a minimal affected region (MAR) of 11.2\u2009Mb running from 14q32.12 to the telomere. Exome sequencing (n=7) did not identify recurrently mutated genes, but methylation-specific PCR at the imprinted MEG3-DLK1 locus located within the MAR demonstrated loss of maternal chromosome 14 and gain of paternal chromosome 14 (P<0.0001), with the degree of methylation imbalance correlating with the level of aUPD (r=0.76; P=0.0001). The absence of driver gene mutations in the exomes of three individuals with aUPD14q but no known haematological disorder suggests that aUPD14q may be sufficient to drive clonal haemopoiesis. Analysis of cases with both aUPD14q and JAK2 V617F (n=11) indicated that aUPD14q may be an early event in some cases but a late event in others. We conclude that aUPD14q is a recurrent abnormality that targets an imprinted locus and may promote clonal haemopoiesis either as an initiating event or as a secondary change.", "doi": "10.1038/leu.2015.130", "pmid": "26114957", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "leu2015130"}, {"db": "pmc", "key": "PMC4687469"}], "notes": [], "created": "2017-05-02T12:56:43.808Z", "modified": "2020-01-21T13:56:05.688Z"}, {"entity": "publication", "iuid": "b7471af7523142ec8e6284d21fb6277c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7471af7523142ec8e6284d21fb6277c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7471af7523142ec8e6284d21fb6277c"}}, "title": "Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.", "authors": [{"family": "Flach", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Johnning", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Ida", "initials": "I"}, {"family": "Smalla", "given": "Kornelia", "initials": "K"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Larsson", "given": "D G Joakim", "initials": "DG"}], "type": "journal article", "published": "2015-10-00", "journal": {"volume": "70", "issn": "1460-2091", "issue": "10", "pages": "2709-2717", "title": "J. Antimicrob. Chemother.", "issn-l": "0305-7453"}, "abstract": "Antibiotic-polluted environments may function as reservoirs for novel resistance plasmids not yet encountered in pathogens. The aims of this study were to assess the potential of resistance transfer between bacteria from such environments and Escherichia coli, and to characterize the conjugative elements involved.\n\nSediment samples from Kazipally lake and Asanikunta tank, two Indian lakes with a history of severe pollution with fluoroquinolones, were investigated. Proportions of resistant bacteria were determined by selective cultivation, while horizontal gene transfer was studied using a GFP-tagged E. coli as recipient. Retrieved transconjugants were tested for susceptibility by Etest(\u00ae) and captured conjugative resistance elements were characterized by WGS.\n\nThe polluted lakes harboured considerably higher proportions of ciprofloxacin-resistant and sulfamethoxazole-resistant bacteria than did other Indian and Swedish lakes included for comparison (52% versus 2% and 60% versus 7%, respectively). Resistance plasmids were captured from Kazipally lake, but not from any of the other lakes; in the case of Asanikunta tank because of high sediment toxicity. Eight unique IncA/C and IncN resistance plasmids were identified among 11 sequenced transconjugants. Five plasmids were fully assembled, and four of these carried the quinolone resistance gene qnrVC1, which has previously only been found on chromosomes. Acquired resistance genes, in the majority of cases associated with class 1 integrons, could be linked to decreased susceptibility to several different classes of antibiotics.\n\nOur study shows that environments heavily polluted with antibiotics contain novel multiresistance plasmids transferrable to E. coli.", "doi": "10.1093/jac/dkv167", "pmid": "26124213", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "dkv167"}], "notes": [], "created": "2017-05-02T12:57:00.230Z", "modified": "2020-01-21T13:56:04.785Z"}, {"entity": "publication", "iuid": "1837468a384a4d009a692da1db915f18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1837468a384a4d009a692da1db915f18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1837468a384a4d009a692da1db915f18"}}, "title": "Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).", "authors": [{"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "Sundstr\u00f6m", "given": "G\u00f6rel", "initials": "G"}, {"family": "Zamani", "given": "Neda", "initials": "N"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lin", "given": "Yao-Cheng", "initials": "YC"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "H\u00f6ppner", "given": "Marc P", "initials": "MP"}, {"family": "Jern", "given": "Patric", "initials": "P"}, {"family": "Van de Peer", "given": "Yves", "initials": "Y"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Grabherr", "given": "Manfred G", "initials": "MG"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal article", "published": "2015-09-28", "journal": {"volume": "10", "issn": "1932-6203", "issue": "9", "pages": "e0139080", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.", "doi": "10.1371/journal.pone.0139080", "pmid": "26413905", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "PONE-D-15-34536"}, {"db": "pmc", "key": "PMC4586145"}], "notes": [], "created": "2017-05-02T12:56:50.290Z", "modified": "2021-07-08T13:26:08.108Z"}, {"entity": "publication", "iuid": "abda054a1679462f8fb7b278c1b968b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abda054a1679462f8fb7b278c1b968b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abda054a1679462f8fb7b278c1b968b2"}}, "title": "Gene expression profiling of pre-eclamptic placentae by RNA sequencing.", "authors": [{"family": "Kaartokallio", "given": "Tea", "initials": "T"}, {"family": "Cervera", "given": "Alejandra", "initials": "A"}, {"family": "Kyll\u00f6nen", "given": "Anjuska", "initials": "A"}, {"family": "Laivuori", "given": "Krista", "initials": "K"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Laivuori", "given": "Hannele", "initials": "H"}, {"family": "FINNPEC Core Investigator Group", "given": null, "initials": null}], "type": "journal article", "published": "2015-09-21", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "14107", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Pre-eclampsia is a common and complex pregnancy disorder that often involves impaired placental development. In order to identify altered gene expression in pre-eclamptic placenta, we sequenced placental transcriptomes of nine pre-eclamptic and nine healthy pregnant women in pools of three. The differential gene expression was tested both by including all the pools in the analysis and by excluding some of the pools based on phenotypic characteristics. From these analyses, we identified altogether 53 differently expressed genes, a subset of which was validated by qPCR in 20 cases and 19 controls. Furthermore, we conducted pathway and functional analyses which revealed disturbed vascular function and immunological balance in pre-eclamptic placenta. Some of the genes identified in our study have been reported by numerous microarray studies (BHLHE40, FSTL3, HK2, HTRA4, LEP, PVRL4, SASH1, SIGLEC6), but many have been implicated in only few studies or have not previously been linked to pre-eclampsia (ARMS2, BTNL9, CCSAP, DIO2, FER1L4, HPSE, LOC100129345, LYN, MYO7B, NCMAP, NDRG1, NRIP1, PLIN2, SBSPON, SERPINB9, SH3BP5, TET3, TPBG, ZNF175). Several of the molecules produced by these genes may have a role in the pathogenesis of pre-eclampsia, and some could qualify as biomarkers for prediction or detection of this pregnancy complication.", "doi": "10.1038/srep14107", "pmid": "26388242", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep14107"}, {"db": "pmc", "key": "PMC4585671"}], "notes": [], "created": "2017-05-02T12:57:32.623Z", "modified": "2020-01-21T13:56:04.490Z"}, {"entity": "publication", "iuid": "9c5445086576453dbfebef79673ce50c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c5445086576453dbfebef79673ce50c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c5445086576453dbfebef79673ce50c"}}, "title": "Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.", "authors": [{"family": "Mushtaq", "given": "Mamoona", "initials": "M"}, {"family": "Manzoor", "given": "Shahid", "initials": "S"}, {"family": "Pringle", "given": "M\u00e4rit", "initials": "M"}, {"family": "Rosander", "given": "Anna", "initials": "A"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2015-09-21", "journal": {"volume": "10", "issn": "1944-3277", "issue": null, "pages": "67", "title": "Stand Genomic Sci", "issn-l": "1944-3277"}, "abstract": "'Treponema phagedenis' is considered to be a key agent in the pathogenesis of bovine digital dermatitis, an infectious foot condition of economic and animal welfare importance. We hereby report the draft sequence of 'T. phagedenis' strain V1. The draft genome assembly consists of 51 scaffolds comprising 3,129,551\u00a0bp and a GC-content of 39.9\u00a0%. Putative pathogenicity related factors have been identified in the genome that can be used in future studies to gain insight into the pathogenic mechanisms of 'T. phagedenis'.", "doi": "10.1186/s40793-015-0059-0", "pmid": "26392840", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "59"}, {"db": "pmc", "key": "PMC4576374"}], "notes": [], "created": "2017-05-02T12:58:06.130Z", "modified": "2020-01-21T13:56:04.052Z"}, {"entity": "publication", "iuid": "dc1955ed9ae2463f8a8d503bd7ab63cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc1955ed9ae2463f8a8d503bd7ab63cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc1955ed9ae2463f8a8d503bd7ab63cb"}}, "title": "PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription.", "authors": [{"family": "Zhao", "given": "Honglei", "initials": "H"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG"}, {"family": "Sumida", "given": "Noriyuki", "initials": "N"}, {"family": "Mill\u00e1n-Ari\u00f1o", "given": "Llu\u00eds", "initials": "L"}, {"family": "Scholz", "given": "Barbara A", "initials": "BA"}, {"family": "Svensson", "given": "J Peter", "initials": "JP"}, {"family": "Chen", "given": "Xingqi", "initials": "X"}, {"family": "Ronnegren", "given": "Anna L", "initials": "AL"}, {"family": "Mallet de Lima", "given": "Carolina Diettrich", "initials": "CD"}, {"family": "Varnoosfaderani", "given": "Farzaneh Shahin", "initials": "FS"}, {"family": "Shi", "given": "Chengxi", "initials": "C"}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Yammine", "given": "Samer", "initials": "S"}, {"family": "Israelsson", "given": "Maria", "initials": "M"}, {"family": "Rathje", "given": "Li-Sophie", "initials": "LS"}, {"family": "N\u00e9meti", "given": "Bal\u00e1zs", "initials": "B"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}, {"family": "Imreh", "given": "M\u00e1rta P", "initials": "MP"}, {"family": "G\u00f6nd\u00f6r", "given": "Anita", "initials": "A"}], "type": "journal article", "published": "2015-09-17", "journal": {"volume": "59", "issn": "1097-4164", "issue": "6", "pages": "984-997", "title": "Mol. Cell", "issn-l": "1097-2765"}, "abstract": "Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear compartments to maintain stable expression patterns. However, here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). The interactome is regulated by PARP1 and its co-factor CTCF. They not only mediate chromatin fiber interactions but also promote the recruitment of circadian genes to the lamina. Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Furthermore, depletion of H3K9me2/3, inhibition of PARP activity by olaparib, or downregulation of PARP1 or CTCF expression counteracts both recruitment to the envelope and circadian transcription. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity.", "doi": "10.1016/j.molcel.2015.07.019", "pmid": "26321255", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1097-2765(15)00577-8"}, {"db": "GEO", "key": "GSE26880"}, {"db": "GEO", "key": "GSE58534"}], "notes": [], "created": "2017-05-02T12:59:01.424Z", "modified": "2021-07-08T13:01:30.938Z"}, {"entity": "publication", "iuid": "843da0bb73384399840655994624f7ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/843da0bb73384399840655994624f7ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/843da0bb73384399840655994624f7ec"}}, "title": "WNT3 involvement in human bladder exstrophy and cloaca development in zebrafish.", "authors": [{"family": "Baranowska K\u00f6rberg", "given": "Izabella", "initials": "I"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Markljung", "given": "Ellen", "initials": "E"}, {"family": "Cao", "given": "Jia", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Ludwig", "given": "Michael", "initials": "M"}, {"family": "Draaken", "given": "Markus", "initials": "M"}, {"family": "Holmdahl", "given": "Gundela", "initials": "G"}, {"family": "Barker", "given": "Gillian", "initials": "G"}, {"family": "Reutter", "given": "Heiko", "initials": "H"}, {"family": "Vukojevi\u0107", "given": "Vladana", "initials": "V"}, {"family": "Clementson Kockum", "given": "Christina", "initials": "C"}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A"}], "type": "journal article", "published": "2015-09-15", "journal": {"volume": "24", "issn": "1460-2083", "issue": "18", "pages": "5069-5078", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Bladder exstrophy, a severe congenital urological malformation when a child is born with an open urinary bladder, is the most common form of bladder exstrophy-epispadias complex (BEEC) with an incidence of 1:30,000 children of Caucasian descent. Recent studies suggest that WNT genes may contribute to the etiology of bladder exstrophy. Here, we evaluated WNT-pathway genes in 20 bladder exstrophy patients using massively parallel sequencing. In total 13 variants were identified in WNT3, WNT6, WNT7A, WNT8B, WNT10A, WNT11, WNT16, FZD5, LRP1 and LRP10 genes and predicted as potentially disease causing, of which seven variants were novel. One variant, identified in a patient with a de novo nonsynonymous substitution in WNT3 (p.Cys91Arg), was further evaluated in zebrafish. Knock down of wnt3 in zebrafish showed cloaca malformations, including disorganization of the cloaca epithelium and expansion of the cloaca lumen. Our study suggests that the function of the WNT3 p.Cys91Arg variant was altered, since RNA overexpression of mutant Wnt3 RNA does not result in embryonic lethality as seen with wild-type WNT3 mRNA. Finally, we also mutation screened the WNT3 gene further in 410 DNA samples from BEEC cases and identified one additional mutation c.638G>A (p.Gly213Asp), which was paternally inherited. In aggregate our data support the involvement of WNT-pathway genes in BEEC and suggest that WNT3 in itself is a rare cause of BEEC.", "doi": "10.1093/hmg/ddv225", "pmid": "26105184", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ddv225"}], "notes": [], "created": "2017-05-02T12:56:33.716Z", "modified": "2020-01-21T13:56:03.417Z"}, {"entity": "publication", "iuid": "ec39794f74774afc83f87c1d19bdbd40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec39794f74774afc83f87c1d19bdbd40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec39794f74774afc83f87c1d19bdbd40"}}, "title": "High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases.", "authors": [{"family": "N\u00e4tt", "given": "Daniel", "initials": "D"}, {"family": "Johansson", "given": "Ingela", "initials": "I"}, {"family": "Faresj\u00f6", "given": "Tomas", "initials": "T"}, {"family": "Ludvigsson", "given": "Johnny", "initials": "J"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2015-09-04", "journal": {"volume": "7", "issn": "1868-7075", "issue": null, "pages": "91", "title": "Clin Epigenetics", "issn-l": null}, "abstract": "Childhood stress leads to increased risk of many adult diseases, such as major depression and cardiovascular disease. Studies show that adults with experienced childhood stress have specific epigenetic changes, but to understand the pathways that lead to disease, we also need to study the epigenetic link prospectively in children.\n\nHere, we studied a homogenous group of 48 5-year-old children. By combining hair cortisol measurements (a well-documented biomarker for chronic stress), with whole-genome DNA-methylation sequencing, we show that high cortisol associates with a genome-wide decrease in DNA methylation and targets short interspersed nuclear elements (SINEs; a type of retrotransposon) and genes important for calcium transport: phenomena commonly affected in stress-related diseases and in biological aging. More importantly, we identify a zinc-finger transcription factor, ZNF263, whose binding sites where highly overrepresented in regions experiencing methylation loss. This type of zinc-finger protein has previously shown to be involved in the defense against retrotransposons.\n\nOur results show that stress in preschool children leads to changes in DNA methylation similar to those seen in biological aging. We suggest that this may affect future disease susceptibility by alterations in the epigenetic mechanisms that keep retrotransposons dormant. Future treatments for stress- and age-related diseases may therefore seek to target zinc-finger proteins that epigenetically control retrotransposon reactivation, such as ZNF263.", "doi": "10.1186/s13148-015-0123-z", "pmid": "26339299", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "123"}, {"db": "pmc", "key": "PMC4559301"}], "notes": [], "created": "2017-05-02T12:58:08.987Z", "modified": "2020-01-21T13:56:05.999Z"}, {"entity": "publication", "iuid": "a037290156c84ac98879f71cfffcfeab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a037290156c84ac98879f71cfffcfeab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a037290156c84ac98879f71cfffcfeab"}}, "title": "Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.", "authors": [{"family": "St\u00f6dberg", "given": "Tommy", "initials": "T"}, {"family": "McTague", "given": "Amy", "initials": "A"}, {"family": "Ruiz", "given": "Arnaud J", "initials": "AJ"}, {"family": "Hirata", "given": "Hiromi", "initials": "H"}, {"family": "Zhen", "given": "Juan", "initials": "J"}, {"family": "Long", "given": "Philip", "initials": "P"}, {"family": "Farabella", "given": "Irene", "initials": "I"}, {"family": "Meyer", "given": "Esther", "initials": "E"}, {"family": "Kawahara", "given": "Atsuo", "initials": "A"}, {"family": "Vassallo", "given": "Grace", "initials": "G"}, {"family": "Stivaros", "given": "Stavros M", "initials": "SM"}, {"family": "Bjursell", "given": "Magnus K", "initials": "MK"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Tigerschi\u00f6ld", "given": "Stephanie", "initials": "S"}, {"family": "Persson", "given": "Bengt", "initials": "B"}, {"family": "Bangash", "given": "Iftikhar", "initials": "I"}, {"family": "Das", "given": "Krishna", "initials": "K"}, {"family": "Hughes", "given": "Deborah", "initials": "D"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Scott", "given": "Rod C", "initials": "RC"}, {"family": "Poduri", "given": "Annapurna", "initials": "A"}, {"family": "Scheffer", "given": "Ingrid E", "initials": "IE"}, {"family": "Smith", "given": "Holly", "initials": "H"}, {"family": "Gissen", "given": "Paul", "initials": "P", "orcid": "0000-0002-9712-6122", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca2717808896474eae93826d8b646e48.json"}}, {"family": "Schorge", "given": "Stephanie", "initials": "S"}, {"family": "Reith", "given": "Maarten E A", "initials": "ME"}, {"family": "Topf", "given": "Maya", "initials": "M"}, {"family": "Kullmann", "given": "Dimitri M", "initials": "DM"}, {"family": "Harvey", "given": "Robert J", "initials": "RJ"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Kurian", "given": "Manju A", "initials": "MA"}], "type": "journal article", "published": "2015-09-03", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "8038", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "The potassium-chloride co-transporter KCC2, encoded by SLC12A5, plays a fundamental role in fast synaptic inhibition by maintaining a hyperpolarizing gradient for chloride ions. KCC2 dysfunction has been implicated in human epilepsy, but to date, no monogenic KCC2-related epilepsy disorders have been described. Here we show recessive loss-of-function SLC12A5 mutations in patients with a severe infantile-onset pharmacoresistant epilepsy syndrome, epilepsy of infancy with migrating focal seizures (EIMFS). Decreased KCC2 surface expression, reduced protein glycosylation and impaired chloride extrusion contribute to loss of KCC2 activity, thereby impairing normal synaptic inhibition and promoting neuronal excitability in this early-onset epileptic encephalopathy.", "doi": "10.1038/ncomms9038", "pmid": "26333769", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Clinical Genomics Stockholm": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "ncomms9038"}, {"db": "pmc", "key": "PMC4569694"}], "notes": [], "created": "2017-05-02T12:58:41.214Z", "modified": "2021-07-08T13:26:08.263Z"}, {"entity": "publication", "iuid": "a8af4caca04448bd94bece45c2b1910a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8af4caca04448bd94bece45c2b1910a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8af4caca04448bd94bece45c2b1910a"}}, "title": "Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.", "authors": [{"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Uzunel", "given": "Mehmet", "initials": "M"}, {"family": "H\u00e5rd", "given": "Joanna L", "initials": "JL"}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Mold", "given": "Jeff E", "initials": "JE"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Mejhert", "given": "Niklas", "initials": "N"}, {"family": "Andersson", "given": "Daniel P", "initials": "DP"}, {"family": "Widlund", "given": "Yvonne", "initials": "Y"}, {"family": "Hassan", "given": "Moustapha", "initials": "M"}, {"family": "Jones", "given": "Christina V", "initials": "CV"}, {"family": "Spalding", "given": "Kirsty L", "initials": "KL"}, {"family": "Svahn", "given": "Britt-Marie", "initials": "BM"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}, {"family": "Bernard", "given": "Samuel", "initials": "S"}, {"family": "Mattsson", "given": "Jonas", "initials": "J"}, {"family": "Arner", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2015-09-01", "journal": {"volume": "22", "issn": "1932-7420", "issue": "3", "pages": "408-417", "title": "Cell Metab.", "issn-l": "1550-4131"}, "abstract": "Because human white adipocytes display a high turnover throughout adulthood, a continuous supply of precursor cells is required to maintain adipogenesis. Bone marrow (BM)-derived progenitor cells may\u00a0contribute to mammalian adipogenesis; however, results in animal models are conflicting. Here we demonstrate in 65 subjects who underwent allogeneic BM or peripheral blood stem cell (PBSC) transplantation that, over the entire lifespan, BM/PBSC-derived progenitor cells contribute \u223c10% to the subcutaneous adipocyte population. While this is independent of gender, age, and different transplantation-related parameters, body fat mass exerts a strong influence, with up to 2.5-fold increased donor cell contribution in obese individuals. Exome and whole-genome sequencing of single adipocytes suggests that BM/PBSC-derived progenitors contribute to adipose tissue via both differentiation and cell fusion. Thus, at least in the setting of transplantation, BM serves as a reservoir for adipocyte progenitors, particularly in obese subjects.", "doi": "10.1016/j.cmet.2015.06.011", "pmid": "26190649", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1550-4131(15)00278-8"}], "notes": [], "created": "2017-05-02T12:58:27.095Z", "modified": "2020-01-21T13:56:04.402Z"}, {"entity": "publication", "iuid": "6d59b408a4ad4a77b4fbc7526f93c65e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d59b408a4ad4a77b4fbc7526f93c65e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d59b408a4ad4a77b4fbc7526f93c65e"}}, "title": "Exome sequencing followed by genotyping suggests SYPL2 as a susceptibility gene for morbid obesity.", "authors": [{"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Gerdhem", "given": "Paul", "initials": "P"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "N\u00e4slund", "given": "Erik", "initials": "E"}, {"family": "Thorell", "given": "Anders", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2015-09-00", "journal": {"volume": "23", "issn": "1476-5438", "issue": "9", "pages": "1216-1222", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Recently developed high-throughput sequencing technology shows power to detect low-frequency disease-causing variants by deep sequencing of all known exons. We used exome sequencing to identify variants associated with morbid obesity. DNA from 100 morbidly obese adult subjects and 100 controls were pooled (n=10/pool), subjected to exome capture, and subsequent sequencing. At least 100 million sequencing reads were obtained from each pool. After several filtering steps and comparisons of observed frequencies of variants between obese and non-obese control pools, we systematically selected 144 obesity-enriched non-synonymous, splicing site or 5' upstream single-nucleotide variants for validation. We first genotyped 494 adult subjects with morbid obesity and 496 controls. Five obesity-associated variants (nominal P-value<0.05) were subsequently genotyped in 1425 morbidly obese and 782 controls. Out of the five variants, only rs62623713:A>G (NM_001040709:c.A296G:p.E99G) was confirmed. rs62623713 showed strong association with body mass index (beta=2.13 (1.09, 3.18), P=6.28 \u00d7 10(-5)) in a joint analysis of all 3197 genotyped subjects and had an odds ratio of 1.32 for obesity association. rs62623713 is a low-frequency (2.9% minor allele frequency) non-synonymous variant (E99G) in exon 4 of the synaptophysin-like 2 (SYPL2) gene. rs62623713 was not covered by Illumina or Affymetrix genotyping arrays used in previous genome-wide association studies. Mice lacking Sypl2 has been reported to display reduced body weight. In conclusion, using exome sequencing we identified a low-frequency coding variant in the SYPL2 gene that was associated with morbid obesity. This gene may be involved in the development of excess body fat.", "doi": "10.1038/ejhg.2014.255", "pmid": "25406998", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ejhg2014255"}, {"db": "pmc", "key": "PMC4538196"}], "notes": [], "created": "2017-05-02T12:57:26.447Z", "modified": "2020-01-21T13:56:02.860Z"}, {"entity": "publication", "iuid": "fe4b514f9ac0418ab26e270cd972d4f5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe4b514f9ac0418ab26e270cd972d4f5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe4b514f9ac0418ab26e270cd972d4f5"}}, "title": "Altered serotonin (5-HT) 1D and 2A receptor expression may contribute to defective insulin and glucagon secretion in human type 2 diabetes.", "authors": [{"family": "Bennet", "given": "H", "initials": "H"}, {"family": "Balhuizen", "given": "A", "initials": "A"}, {"family": "Medina", "given": "A", "initials": "A"}, {"family": "Dekker Nitert", "given": "M", "initials": "M"}, {"family": "Ottosson Laakso", "given": "E", "initials": "E"}, {"family": "Ess\u00e9n", "given": "S", "initials": "S"}, {"family": "Sp\u00e9gel", "given": "P", "initials": "P"}, {"family": "Storm", "given": "P", "initials": "P"}, {"family": "Krus", "given": "U", "initials": "U"}, {"family": "Wierup", "given": "N", "initials": "N"}, {"family": "Fex", "given": "M", "initials": "M"}], "type": "journal article", "published": "2015-09-00", "journal": {"volume": "71", "issn": "1873-5169", "issue": null, "pages": "113-120", "title": "Peptides", "issn-l": "0196-9781"}, "abstract": "Islet produced 5-hydroxy tryptamine (5-HT) is suggested to regulate islet hormone secretion in a paracrine and autocrine manner in rodents. Hitherto, no studies demonstrate a role for this amine in human islet function, nor is it known if 5-HT signaling is involved in the development of beta cell dysfunction in type 2 diabetes (T2D). To clarify this, we performed a complete transcriptional mapping of 5-HT receptors and processing enzymes in human islets and investigated differential expression of these genes in non-diabetic and T2D human islet donors. We show the expression of fourteen 5-HT receptors as well as processing enzymes involved in the biosynthesis of 5-HT at the mRNA level in human islets. Two 5-HT receptors (HTR1D and HTR2A) were over-expressed in T2D islet donors. Both receptors (5-HT1d and 5-HT2a) were localized to human alpha, beta and delta cells. 5-HT inhibited both insulin and glucagon secretion in non-diabetic islet donors. In islets isolated from T2D donors the amine significantly increased release of insulin in response to glucose. Our results suggest that 5-HT signaling participates in regulation of overall islet hormone secretion in non- diabetic individuals and over-expression of HTR1D and HTR2A may either contribute to islet dysfunction in T2D or arise as a consequence of an already dysfunctional islet.", "doi": "10.1016/j.peptides.2015.07.008", "pmid": "26206285", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0196-9781(15)00204-1"}], "notes": [], "created": "2017-05-02T12:56:35.098Z", "modified": "2020-01-21T13:56:06.541Z"}, {"entity": "publication", "iuid": "c4b1ba70725c46388e85498a2f5b63c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4b1ba70725c46388e85498a2f5b63c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4b1ba70725c46388e85498a2f5b63c0"}}, "title": "Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.", "authors": [{"family": "Huang", "given": "Mingtao", "initials": "M"}, {"family": "Bai", "given": "Yunpeng", "initials": "Y"}, {"family": "Sjostrom", "given": "Staffan L", "initials": "SL"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Liu", "given": "Zihe", "initials": "Z"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Joensson", "given": "Haakan N", "initials": "HN"}, {"family": "Andersson-Svahn", "given": "Helene", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2015-08-25", "journal": {"volume": "112", "issn": "1091-6490", "issue": "34", "pages": "E4689-E4696", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "There is an increasing demand for biotech-based production of recombinant proteins for use as pharmaceuticals in the food and feed industry and in industrial applications. Yeast Saccharomyces cerevisiae is among preferred cell factories for recombinant protein production, and there is increasing interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV mutagenesis. Several screening and sorting rounds resulted in the selection of eight yeast clones with significantly improved secretion of recombinant \u03b1-amylase. Efficient secretion was genetically stable in the selected clones. We performed whole-genome sequencing of the eight clones and identified 330 mutations in total. Gene ontology analysis of mutated genes revealed many biological processes, including some that have not been identified before in the context of protein secretion. Mutated genes identified in this study can be potentially used for reverse metabolic engineering, with the objective to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could broadly facilitate design of novel cell factories.", "doi": "10.1073/pnas.1506460112", "pmid": "26261321", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1506460112"}, {"db": "pmc", "key": "PMC4553813"}], "notes": [], "created": "2017-05-02T12:57:19.915Z", "modified": "2021-07-08T13:44:33.607Z"}, {"entity": "publication", "iuid": "9d58f3908ade4e4f9c9db7643ece3ee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9d58f3908ade4e4f9c9db7643ece3ee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9d58f3908ade4e4f9c9db7643ece3ee7"}}, "title": "Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.", "authors": [{"family": "Yu", "given": "Nancy Yiu-Lin", "initials": "NY", "orcid": "0000-0001-8321-8141", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7b0ebe0de64edca6546aff2292c376.json"}}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Kawaji", "given": "Hideya", "initials": "H"}, {"family": "Carninci", "given": "Piero", "initials": "P"}, {"family": "Forrest", "given": "Alistair R R", "initials": "AR"}, {"family": "Fantom Consortium", "given": "", "initials": ""}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}], "type": "evaluation study", "published": "2015-08-18", "journal": {"volume": "43", "issn": "1362-4962", "issue": "14", "pages": "6787-6798", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and Heliscope-sequenced CAGE. Here, we report on the first large-scale complex tissue transcriptome comparison between full-length versus 5'-capped mRNA sequencing data. Overall gene expression correlation was high between the 22 corresponding tissues analyzed (R > 0.8). For genes ubiquitously expressed across all tissues, the two data sets showed high genome-wide correlation (91% agreement), with differences observed for a small number of individual genes indicating the need to update their gene models. Among the identified single-tissue enriched genes, up to 75% showed consensus of 7-fold enrichment in the same tissue in both methods, while another 17% exhibited multiple tissue enrichment and/or high expression variety in the other data set, likely dependent on the cell type proportions included in each tissue sample. Our results show that RNA-Seq and CAGE tissue transcriptome data sets are highly complementary for improving gene model annotations and highlight biological complexities within tissue transcriptomes. Furthermore, integration with image-based protein expression data is highly advantageous for understanding expression specificities for many genes.", "doi": "10.1093/nar/gkv608", "pmid": "26117540", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gkv608"}, {"db": "pmc", "key": "PMC4538815"}], "notes": [], "created": "2017-05-02T12:59:00.235Z", "modified": "2021-07-08T13:44:33.475Z"}, {"entity": "publication", "iuid": "fe25951df53b4e368d667506817b4d85", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe25951df53b4e368d667506817b4d85.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe25951df53b4e368d667506817b4d85"}}, "title": "Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain.", "authors": [{"family": "Zhang", "given": "Yiming", "initials": "Y"}, {"family": "Liu", "given": "Guodong", "initials": "G"}, {"family": "Engqvist", "given": "Martin K M", "initials": "MK"}, {"family": "Krivoruchko", "given": "Anastasia", "initials": "A"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Chen", "given": "Yun", "initials": "Y"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2015-08-08", "journal": {"volume": "14", "issn": "1475-2859", "issue": null, "pages": "116", "title": "Microb. Cell Fact.", "issn-l": "1475-2859"}, "abstract": "A Saccharomyces cerevisiae strain carrying deletions in all three pyruvate decarboxylase (PDC) genes (also called Pdc negative yeast) represents a non-ethanol producing platform strain for the production of pyruvate derived biochemicals. However, it cannot grow on glucose as the sole carbon source, and requires supplementation of C2 compounds to the medium in order to meet the requirement for cytosolic acetyl-CoA for biosynthesis of fatty acids and ergosterol.\n\nIn this study, a Pdc negative strain was adaptively evolved for improved growth in glucose medium via serial transfer, resulting in three independently evolved strains, which were able to grow in minimal medium containing glucose as the sole carbon source at the maximum specific rates of 0.138, 0.148, 0.141 h(-1), respectively. Several genetic changes were identified in the evolved Pdc negative strains by genomic DNA sequencing. Among these genetic changes, 4 genes were found to carry point mutations in at least two of the evolved strains: MTH1 encoding a negative regulator of the glucose-sensing signal transduction pathway, HXT2 encoding a hexose transporter, CIT1 encoding a mitochondrial citrate synthase, and RPD3 encoding a histone deacetylase. Reverse engineering of the non-evolved Pdc negative strain through introduction of the MTH1 (81D) allele restored its growth on glucose at a maximum specific rate of 0.053 h(-1) in minimal medium with 2% glucose, and the CIT1 deletion in the reverse engineered strain further increased the maximum specific growth rate to 0.069 h(-1).\n\nIn this study, possible evolving mechanisms of Pdc negative strains on glucose were investigated by genome sequencing and reverse engineering. The non-synonymous mutations in MTH1 alleviated the glucose repression by repressing expression of several hexose transporter genes. The non-synonymous mutations in HXT2 and CIT1 may function in the presence of mutated MTH1 alleles and could be related to an altered central carbon metabolism in order to ensure production of cytosolic acetyl-CoA in the Pdc negative strain.", "doi": "10.1186/s12934-015-0305-6", "pmid": "26253003", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s12934-015-0305-6"}, {"db": "pmc", "key": "PMC4529725"}], "notes": [], "created": "2017-05-02T12:59:00.828Z", "modified": "2021-07-05T13:05:37.825Z"}, {"entity": "publication", "iuid": "91a6bb5b23ff4461beda7601b16e61fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/91a6bb5b23ff4461beda7601b16e61fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/91a6bb5b23ff4461beda7601b16e61fb"}}, "title": "Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation.", "authors": [{"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Karlsson", "given": "Fredrik", "initials": "F"}, {"family": "Werling", "given": "Malin", "initials": "M"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Kovatcheva-Datchary", "given": "Petia", "initials": "P"}, {"family": "Olbers", "given": "Torsten", "initials": "T"}, {"family": "F\u00e4ndriks", "given": "Lars", "initials": "L"}, {"family": "le Roux", "given": "Carel W", "initials": "CW"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-08-04", "journal": {"volume": "22", "issn": "1932-7420", "issue": "2", "pages": "228-238", "title": "Cell Metab.", "issn-l": "1550-4131"}, "abstract": "Bariatric surgery is currently the most effective procedure for the treatment of obesity. Given the role of the gut microbiota in regulating host metabolism and adiposity, we investigated the long-term effects of bariatric surgery on the microbiome of patients randomized to Roux-en-Y gastric bypass or vertical banded gastroplasty and matched for weight and fat mass loss. The two surgical procedures induced similar and durable changes on the gut microbiome that were not dependent on body mass index and resulted in altered levels of fecal and circulating metabolites compared with obese controls. By colonizing germ-free mice with stools from the patients, we demonstrated that the surgically altered microbiota promoted reduced fat deposition in recipient mice. These mice also had a lower respiratory quotient, indicating decreased utilization of carbohydrates as fuel. Our results suggest that the gut microbiota may play a direct role in the reduction of adiposity observed after bariatric surgery.", "doi": "10.1016/j.cmet.2015.07.009", "pmid": "26244932", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1550-4131(15)00338-1"}, {"db": "pmc", "key": "PMC4537510"}], "notes": [], "created": "2017-05-02T12:58:47.108Z", "modified": "2021-07-05T13:05:37.690Z"}, {"entity": "publication", "iuid": "7f6daf16367a42c2abaa8ea957e3d8c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f6daf16367a42c2abaa8ea957e3d8c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f6daf16367a42c2abaa8ea957e3d8c3"}}, "title": "Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.", "authors": [{"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P"}, {"family": "Abdullayev", "given": "Ilgar", "initials": "I"}, {"family": "Ramsk\u00f6ld", "given": "Daniel", "initials": "D"}, {"family": "Matskova", "given": "Liudmila", "initials": "L"}, {"family": "Rilakovic", "given": "Nemanja", "initials": "N"}, {"family": "L\u00f6tstedt", "given": "Britta", "initials": "B"}, {"family": "Albert", "given": "Thomas J", "initials": "TJ"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}], "type": "journal article", "published": "2015-08-03", "journal": {"volume": "16", "issn": "1474-760X", "issue": null, "pages": "156", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Although the locations of promoters and enhancers have been identified in several cell types, we still have limited information on their connectivity. We developed HiCap, which combines a 4-cutter restriction enzyme Hi-C with sequence capture of promoter regions. Applying the method to mouse embryonic stem cells, we identified promoter-anchored interactions involving 15,905 promoters and 71,984 distal regions. The distal regions were enriched for enhancer marks and transcription, and had a mean fragment size of only 699 bp--close to single-enhancer resolution. High-resolution maps of promoter-anchored interactions with HiCap will be important for detailed characterizations of chromatin interaction landscapes.", "doi": "10.1186/s13059-015-0727-9", "pmid": "26313521", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s13059-015-0727-9"}, {"db": "pmc", "key": "PMC4557751"}, {"db": "GEO", "key": "GSE60495"}, {"db": "SRA", "key": "SRP045579"}, {"db": "SRA", "key": "SRP045580"}], "notes": [], "created": "2017-05-02T12:58:28.799Z", "modified": "2021-07-08T13:26:08.224Z"}, {"entity": "publication", "iuid": "a9ab16991ce84822a4ab77925fc8528c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a9ab16991ce84822a4ab77925fc8528c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a9ab16991ce84822a4ab77925fc8528c"}}, "title": "Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.", "authors": [{"family": "O'Hurley", "given": "Gillian", "initials": "G"}, {"family": "Busch", "given": "Christer", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Tolf", "given": "Anna", "initials": "A"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-08-03", "journal": {"volume": "10", "issn": "1932-6203", "issue": "8", "pages": "e0133449", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "To better understand prostate function and disease, it is important to define and explore the molecular constituents that signify the prostate gland. The aim of this study was to define the prostate specific transcriptome and proteome, in comparison to 26 other human tissues. Deep sequencing of mRNA (RNA-seq) and immunohistochemistry-based protein profiling were combined to identify prostate specific gene expression patterns and to explore tissue biomarkers for potential clinical use in prostate cancer diagnostics. We identified 203 genes with elevated expression in the prostate, 22 of which showed more than five-fold higher expression levels compared to all other tissue types. In addition to previously well-known proteins we identified two poorly characterized proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. In conclusion, we have applied a genome-wide analysis to identify the prostate specific proteome using transcriptomics and antibody-based protein profiling to identify genes with elevated expression in the prostate. Our data provides a starting point for further functional studies to explore the molecular repertoire of normal and diseased prostate including potential prostate cancer markers such as TMEM79 and ACOXL.", "doi": "10.1371/journal.pone.0133449", "pmid": "26237329", "labels": {"NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "Spatial Proteomics": null, "Affinity Proteomics Stockholm": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-13741"}, {"db": "pmc", "key": "PMC4523174"}], "notes": [], "created": "2017-05-02T12:57:06.092Z", "modified": "2021-07-08T13:44:33.508Z"}, {"entity": "publication", "iuid": "405838ef41ef4368a1824276419165fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/405838ef41ef4368a1824276419165fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/405838ef41ef4368a1824276419165fa"}}, "title": "Whole-exome sequencing of Ethiopian patients with ichthyosis vulgaris and atopic dermatitis.", "authors": [{"family": "Taylan", "given": "Fulya", "initials": "F"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Asad", "given": "Samina", "initials": "S"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Wahlgren", "given": "Carl-Fredrik", "initials": "CF"}, {"family": "Winge", "given": "M\u00e5rten C G", "initials": "MC"}, {"family": "Bilcha", "given": "Kassahun Desalegn", "initials": "KD"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Bradley", "given": "Maria", "initials": "M"}], "type": "letter", "published": "2015-08-00", "journal": {"volume": "136", "issn": "1097-6825", "issue": "2", "pages": "507-9.e19", "title": "J. Allergy Clin. Immunol.", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2015.02.010", "pmid": "25819062", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0091-6749(15)00231-6"}], "notes": [], "created": "2017-05-02T12:58:44.436Z", "modified": "2020-01-21T13:56:01.849Z"}, {"entity": "publication", "iuid": "86fedb7c05fd4642974675c6b85c2e35", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86fedb7c05fd4642974675c6b85c2e35.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86fedb7c05fd4642974675c6b85c2e35"}}, "title": "SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts.", "authors": [{"family": "Malcovati", "given": "Luca", "initials": "L"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Papaemmanuil", "given": "Elli", "initials": "E"}, {"family": "Ambaglio", "given": "Ilaria", "initials": "I"}, {"family": "J\u00e4dersten", "given": "Martin", "initials": "M"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Elena", "given": "Chiara", "initials": "C"}, {"family": "Gall\u00ec", "given": "Anna", "initials": "A"}, {"family": "Walldin", "given": "Gunilla", "initials": "G"}, {"family": "Della Porta", "given": "Matteo G", "initials": "MG"}, {"family": "Raaschou-Jensen", "given": "Klas", "initials": "K"}, {"family": "Travaglino", "given": "Erica", "initials": "E"}, {"family": "Kallenbach", "given": "Klaus", "initials": "K"}, {"family": "Pietra", "given": "Daniela", "initials": "D"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Conte", "given": "Simona", "initials": "S"}, {"family": "Boveri", "given": "Emanuela", "initials": "E"}, {"family": "Invernizzi", "given": "Rosangela", "initials": "R"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Campbell", "given": "Peter J", "initials": "PJ"}, {"family": "Cazzola", "given": "Mario", "initials": "M"}, {"family": "Hellstr\u00f6m Lindberg", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2015-07-09", "journal": {"volume": "126", "issn": "1528-0020", "issue": "2", "pages": "233-241", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Refractory anemia with ring sideroblasts (RARS) is a myelodysplastic syndrome (MDS) characterized by isolated erythroid dysplasia and 15% or more bone marrow ring sideroblasts. Ring sideroblasts are found also in other MDS subtypes, such as refractory cytopenia with multilineage dysplasia and ring sideroblasts (RCMD-RS). A high prevalence of somatic mutations of SF3B1 was reported in these conditions. To identify mutation patterns that affect disease phenotype and clinical outcome, we performed a comprehensive mutation analysis in 293 patients with myeloid neoplasm and 1% or more ring sideroblasts. SF3B1 mutations were detected in 129 of 159 cases (81%) of RARS or RCMD-RS. Among other patients with ring sideroblasts, lower prevalence of SF3B1 mutations and higher prevalence of mutations in other splicing factor genes were observed (P < .001). In multivariable analyses, patients with SF3B1 mutations showed significantly better overall survival (hazard ratio [HR], .37; P = .003) and lower cumulative incidence of disease progression (HR = 0.31; P = .018) compared with SF3B1-unmutated cases. The independent prognostic value of SF3B1 mutation was retained in MDS without excess blasts, as well as in sideroblastic categories (RARS and RCMD-RS). Among SF3B1-mutated patients, coexisting mutations in DNA methylation genes were associated with multilineage dysplasia (P = .015) but had no effect on clinical outcome. TP53 mutations were frequently detected in patients without SF3B1 mutation, and were associated with poor outcome. Thus, SF3B1 mutation identifies a distinct MDS subtype that is unlikely to develop detrimental subclonal mutations and is characterized by indolent clinical course and favorable outcome.", "doi": "10.1182/blood-2015-03-633537", "pmid": "25957392", "labels": {"National Genomics Infrastructure": null, "Clinical Genomics Uppsala": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "blood-2015-03-633537"}, {"db": "pmc", "key": "PMC4528082"}], "notes": [], "created": "2017-05-02T12:57:57.376Z", "modified": "2020-01-21T13:56:03.442Z"}, {"entity": "publication", "iuid": "fbaede1e61f042389f09ecf64caaa22f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fbaede1e61f042389f09ecf64caaa22f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fbaede1e61f042389f09ecf64caaa22f"}}, "title": "Toward Rare Blood Cell Preservation for RNA Sequencing.", "authors": [{"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}, {"family": "Lewensohn", "given": "Rolf", "initials": "R"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2015-07-00", "journal": {"volume": "17", "issn": "1943-7811", "issue": "4", "pages": "352-359", "title": "J Mol Diagn", "issn-l": "1525-1578"}, "abstract": "Cancer is driven by various events leading to cell differentiation and disease progression. Molecular tools are powerful approaches for describing how and why these events occur. With the growing field of next-generation DNA sequencing, there is an increasing need for high-quality nucleic acids derived from human cells and tissues-a prerequisite for successful cell profiling. Although advances in RNA preservation have been made, some of the largest biobanks still do not employ RNA blood preservation as standard because of limitations in low blood-input volume and RNA stability over the whole gene body. Therefore, we have developed a robust protocol for blood preservation and long-term storage while maintaining RNA integrity. Furthermore, we explored the possibility of using the protocol for preserving rare cell samples, such as circulating tumor cells. The results of our study confirmed that gene expression was not impacted by the preservation procedure (r(2) > 0.88) or by long-term storage (r(2) = 0.95), with RNA integrity number values averaging over 8. Similarly, cell surface antigens were still available for antibody selection (r(2) = 0.95). Lastly, data mining for fusion events showed that it was possible to detect rare tumor cells among a background of other cells present in blood irrespective of fixation. Thus, the developed protocol would be suitable for rare blood cell preservation followed by RNA sequencing analysis.", "doi": "10.1016/j.jmoldx.2015.03.009", "pmid": "25989392", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1525-1578(15)00084-7"}], "notes": [], "created": "2017-05-02T12:58:50.874Z", "modified": "2021-07-08T13:26:08.434Z"}, {"entity": "publication", "iuid": "041a778c63e1426fac6e0d31557a90e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/041a778c63e1426fac6e0d31557a90e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/041a778c63e1426fac6e0d31557a90e7"}}, "title": "Polymorphisms in DCDC2 and S100B associate with developmental dyslexia.", "authors": [{"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Persson", "given": "Helena", "initials": "H"}, {"family": "Einarsdottir", "given": "Elisabet", "initials": "E"}, {"family": "Tiraboschi", "given": "Ettore", "initials": "E"}, {"family": "Nopola-Hemmi", "given": "Jaana", "initials": "J"}, {"family": "Schumacher", "given": "Johannes", "initials": "J"}, {"family": "Neuhoff", "given": "Nina", "initials": "N"}, {"family": "Warnke", "given": "Andreas", "initials": "A"}, {"family": "Lyytinen", "given": "Heikki", "initials": "H"}, {"family": "Schulte-K\u00f6rne", "given": "Gert", "initials": "G"}, {"family": "N\u00f6then", "given": "Markus M", "initials": "MM"}, {"family": "Lepp\u00e4nen", "given": "Paavo H T", "initials": "PH"}, {"family": "Peyrard-Janvid", "given": "Myriam", "initials": "M"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2015-07-00", "journal": {"volume": "60", "issn": "1435-232X", "issue": "7", "pages": "399-401", "title": "J. Hum. Genet.", "issn-l": "1434-5161"}, "abstract": "Genetic studies of complex traits have become increasingly successful as progress is made in next-generation sequencing. We aimed at discovering single nucleotide variation present in known and new candidate genes for developmental dyslexia: CYP19A1, DCDC2, DIP2A, DYX1C1, GCFC2 (also known as C2orf3), KIAA0319, MRPL19, PCNT, PRMT2, ROBO1 and S100B. We used next-generation sequencing to identify single-nucleotide polymorphisms in the exons of these 11 genes in pools of 100 DNA samples of Finnish individuals with developmental dyslexia. Subsequent individual genotyping of those 100 individuals, and additional cases and controls from the Finnish and German populations, validated 92 out of 111 different single-nucleotide variants. A nonsynonymous polymorphism in DCDC2 (corrected P = 0.002) and a noncoding variant in S100B (corrected P = 0.016) showed a significant association with spelling performance in families of German origin. No significant association was found for the variants neither in the Finnish case-control sample set nor in the Finnish family sample set. Our findings further strengthen the role of DCDC2 and implicate S100B, in the biology of reading and spelling.", "doi": "10.1038/jhg.2015.37", "pmid": "25877001", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "jhg201537"}, {"db": "pmc", "key": "PMC4521290"}], "notes": [], "created": "2017-05-02T12:58:01.491Z", "modified": "2020-01-21T13:56:00.546Z"}, {"entity": "publication", "iuid": "a0c40b72913b482b8f3fb8bb2a00f79b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0c40b72913b482b8f3fb8bb2a00f79b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0c40b72913b482b8f3fb8bb2a00f79b"}}, "title": "The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.", "authors": [{"family": "Schwelm", "given": "Arne", "initials": "A"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Knaust", "given": "Andrea", "initials": "A"}, {"family": "J\u00fclke", "given": "Sabine", "initials": "S"}, {"family": "Lilja", "given": "Tua", "initials": "T"}, {"family": "Bonilla-Rosso", "given": "German", "initials": "G"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Shevchenko", "given": "Andrej", "initials": "A"}, {"family": "Dhandapani", "given": "Vignesh", "initials": "V"}, {"family": "Choi", "given": "Su Ryun", "initials": "SR"}, {"family": "Kim", "given": "Hong Gi", "initials": "HG"}, {"family": "Park", "given": "Ju Young", "initials": "JY"}, {"family": "Lim", "given": "Yong Pyo", "initials": "YP"}, {"family": "Ludwig-M\u00fcller", "given": "Jutta", "initials": "J"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2015-06-18", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "11153", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.", "doi": "10.1038/srep11153", "pmid": "26084520", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "srep11153"}, {"db": "pmc", "key": "PMC4471660"}], "notes": [], "created": "2017-05-02T12:56:27.293Z", "modified": "2020-01-21T13:56:04.138Z"}, {"entity": "publication", "iuid": "b019e78a23ef453e9060d6188198a6c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b019e78a23ef453e9060d6188198a6c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b019e78a23ef453e9060d6188198a6c2"}}, "title": "Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.", "authors": [{"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Mitsios", "given": "Nicholas", "initials": "N"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2015-06-15", "journal": {"volume": "10", "issn": "1932-6203", "issue": "6", "pages": "e0130028", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The mammalian brain is a complex organ composed of many specialized cells, harboring sets of both common, widely distributed, as well as specialized and discretely localized proteins. Here we focus on the human brain, utilizing transcriptomics and public available Human Protein Atlas (HPA) data to analyze brain-enriched (frontal cortex) polyadenylated messenger RNA and long non-coding RNA and generate a genome-wide draft of global and cellular expression patterns of the brain. Based on transcriptomics analysis of altogether 27 tissues, we have estimated that approximately 3% (n=571) of all protein coding genes and 13% (n=87) of the long non-coding genes expressed in the human brain are enriched, having at least five times higher expression levels in brain as compared to any of the other analyzed peripheral tissues. Based on gene ontology analysis and detailed annotation using antibody-based tissue micro array analysis of the corresponding proteins, we found the majority of brain-enriched protein coding genes to be expressed in astrocytes, oligodendrocytes or in neurons with molecular properties linked to synaptic transmission and brain development. Detailed analysis of the transcripts and the genetic landscape of brain-enriched coding and non-coding genes revealed brain-enriched splice variants. Several clusters of neighboring brain-enriched genes were also identified, suggesting regulation of gene expression on the chromatin level. This multi-angle approach uncovered the brain-enriched transcriptome and linked genes to cell types and functions, providing novel insights into the molecular foundation of this highly specialized organ.", "doi": "10.1371/journal.pone.0130028", "pmid": "26076492", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-15-09576"}, {"db": "pmc", "key": "PMC4468152"}, {"db": "ArrayExpress", "description": "sequences", "key": "E-MTAB-1733"}], "notes": [], "created": "2017-05-02T12:58:34.528Z", "modified": "2021-07-08T13:44:33.530Z"}, {"entity": "publication", "iuid": "4fc3954e096f41c2822af003ff117b3d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4fc3954e096f41c2822af003ff117b3d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4fc3954e096f41c2822af003ff117b3d"}}, "title": "Phasing of single DNA molecules by massively parallel barcoding.", "authors": [{"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Redin", "given": "David", "initials": "D"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Berglund", "given": "Emelie", "initials": "E"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2015-06-09", "journal": {"volume": "6", "issn": "2041-1723", "issue": null, "pages": "7173", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.", "doi": "10.1038/ncomms8173", "pmid": "26055759", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ncomms8173"}, {"db": "pmc", "key": "PMC4468844"}, {"db": "SRA", "key": "SRA248941"}], "notes": [], "created": "2017-05-02T12:56:38.182Z", "modified": "2020-01-21T13:56:02.259Z"}, {"entity": "publication", "iuid": "e71f02893ef64fbc9b479a645b5ef45b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e71f02893ef64fbc9b479a645b5ef45b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e71f02893ef64fbc9b479a645b5ef45b"}}, "title": "Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds.", "authors": [{"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2015-06-01", "journal": {"volume": "25", "issn": "1879-0445", "issue": "11", "pages": "1515-1519", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use\u00a0the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.", "doi": "10.1016/j.cub.2015.04.019", "pmid": "26004765", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(15)00432-7"}], "notes": [], "created": "2017-05-02T12:58:35.414Z", "modified": "2021-07-07T20:31:10.941Z"}, {"entity": "publication", "iuid": "aa441f2d8f9d4684adb543306810523d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aa441f2d8f9d4684adb543306810523d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aa441f2d8f9d4684adb543306810523d"}}, "title": "Whole-genome Linkage Analysis and Sequence Analysis of Candidate Loci in Familial Breast Cancer.", "authors": [{"family": "Marikkannu", "given": "Rajeshwari", "initials": "R"}, {"family": "Aravidis", "given": "Christos", "initials": "C"}, {"family": "Rantala", "given": "Johanna", "initials": "J"}, {"family": "Picelli", "given": "Simone", "initials": "S"}, {"family": "Adamovic", "given": "Tatjana", "initials": "T"}, {"family": "Keihas", "given": "Markku", "initials": "M"}, {"family": "Liu", "given": "Tao", "initials": "T", "orcid": "0000-0002-6456-4767", "researcher": {"href": "https://publications.scilifelab.se/researcher/1deea3cff23c4ae98c971c82f013ef45.json"}}, {"family": "Kontham", "given": "Vinaykumar", "initials": "V"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}], "type": "journal article", "published": "2015-06-00", "journal": {"volume": "35", "issn": "1791-7530", "issue": "6", "pages": "3155-3165", "title": "Anticancer Res.", "issn-l": "0250-7005"}, "abstract": "Known breast cancer-predisposing genes account for fewer than 25% of all familial breast cancer cases and further studies are required to find the remaining high- and moderate-risk genes. We set-out to couple linkage analysis using microsatellite marker data and sequence analysis of linked regions in 13 non-BRCA1/2 families in order to find novel susceptibility loci and high-penetrant genes.\n\nGenotyping with 540 fluorescently-labeled microsatellite markers located on the 23 chromosomes at 7.25 cM resolution was used for primary linkage analysis and an additional 40 markers were used for fine-mapping of loci with a logarithm of odds (LOD) or heterogeneity LOD (HLOD) score greater than one. Whole-exome sequencing data of 28 members from all 13 families were used for the bioinformatics sequence analysis on the linked regions of these families.\n\nLinkage analysis identified three loci on chromosome 18q as a putative region of interest (overall LOD=1, HLOD=1.2). Sequencing analysis of the three linked regions on 18q and mutation prediction algorithms did reveal three probable damaging variants.\n\nOverall, our study identified three weakly linked loci on 18q and three probable damaging variants of interest in the 13 families with breast cancer.", "doi": null, "pmid": "26026075", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "35/6/3155"}], "notes": [], "created": "2017-05-02T12:58:00.290Z", "modified": "2025-11-17T09:37:28.507Z"}, {"entity": "publication", "iuid": "b5ab43d366b44c8aa86ea1cd05572933", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5ab43d366b44c8aa86ea1cd05572933.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5ab43d366b44c8aa86ea1cd05572933"}}, "title": "Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.", "authors": [{"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Bergman", "given": "Birgitta", "initials": "B"}, {"family": "Larsson", "given": "John", "initials": "J"}, {"family": "Ekman", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2015-06-00", "journal": {"volume": "44 Suppl 3", "issn": "1654-7209", "issue": null, "pages": "439-450", "title": "Ambio", "issn-l": "0044-7447"}, "abstract": "Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world's largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.", "doi": "10.1007/s13280-015-0663-7", "pmid": "26022326", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4447691"}], "notes": [], "created": "2017-05-02T12:57:22.620Z", "modified": "2020-01-21T13:56:04.764Z"}, {"entity": "publication", "iuid": "a5f6ae98d4924314b72535e703fd75c3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5f6ae98d4924314b72535e703fd75c3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5f6ae98d4924314b72535e703fd75c3"}}, "title": "High-throughput mutational screening adds clinically important information in myelodysplastic syndromes and secondary or therapy-related acute myeloid leukemia.", "authors": [{"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Nilsson", "given": "Christer", "initials": "C"}, {"family": "Dimitriou", "given": "Marios", "initials": "M"}, {"family": "Jansson", "given": "Monika", "initials": "M"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}], "type": "letter", "published": "2015-06-00", "journal": {"volume": "100", "issn": "1592-8721", "issue": "6", "pages": "e223-e225", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": null, "doi": "10.3324/haematol.2014.118034", "pmid": "25769547", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "haematol.2014.118034"}, {"db": "pmc", "key": "PMC4450634"}], "notes": [], "created": "2017-05-02T12:57:33.790Z", "modified": "2020-01-21T13:56:04.279Z"}, {"entity": "publication", "iuid": "ddeddf1c33434805a9b76e947f45c1e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddeddf1c33434805a9b76e947f45c1e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddeddf1c33434805a9b76e947f45c1e5"}}, "title": "Hemophagocytic lymphohistiocytosis in 2 patients with underlying IFN-\u03b3 receptor deficiency", "authors": [{"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Sieni", "given": "Elena", "initials": "E"}, {"family": "Neves", "given": "Concei\u00e7\u00e3o", "initials": "C"}, {"family": "Romano", "given": "Francesca", "initials": "F"}, {"family": "Cetica", "given": "Valentina", "initials": "V"}, {"family": "Cordeiro", "given": "Ana Isabel", "initials": "AI"}, {"family": "Chiang", "given": "Samuel", "initials": "S"}, {"family": "Schlums", "given": "Heinrich", "initials": "H", "orcid": "0000-0002-2895-7766", "researcher": {"href": "https://publications.scilifelab.se/researcher/3519af1c1eae4ffcb381a420c052ac28.json"}}, {"family": "Galli", "given": "Luisa", "initials": "L"}, {"family": "Avenali", "given": "Stefano", "initials": "S"}, {"family": "Tondo", "given": "Annalisa", "initials": "A"}, {"family": "Canessa", "given": "Clementina", "initials": "C"}, {"family": "Henter", "given": "Jan Inge", "initials": "JI", "orcid": "0000-0002-0629-2126", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1a0d663491c4665a32a612e423dff1b.json"}}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4974-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f9dec008f1b42868dd133e9a396c968.json"}}, {"family": "Hsu", "given": "Amy P", "initials": "AP"}, {"family": "Holland", "given": "Steven M", "initials": "SM", "orcid": "0000-0003-3207-5464", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a22fc2635ad4265a82ae40602c502d9.json"}}, {"family": "Neves", "given": "Jo\u00e3o F", "initials": "JF"}, {"family": "Azzari", "given": "Chiara", "initials": "C"}, {"family": "Bryceson", "given": "Yenan T", "initials": "YT", "orcid": "0000-0002-7783-9934", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce63349a03924444836215ffd201d2e3.json"}}], "type": "journal-article", "published": "2015-06-00", "journal": {"volume": "135", "issn": "1085-8725", "issue": "6", "pages": "1638-1641.e5", "title": "Journal of Allergy and Clinical Immunology", "issn-l": "0091-6749"}, "abstract": null, "doi": "10.1016/j.jaci.2014.11.030", "pmid": "25592983", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0091-6749(14)01733-3"}], "notes": [], "created": "2017-05-02T12:58:45.023Z", "modified": "2023-06-19T11:37:21.990Z"}, {"entity": "publication", "iuid": "dee962559df446d89e30cacda0d2edd5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dee962559df446d89e30cacda0d2edd5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dee962559df446d89e30cacda0d2edd5"}}, "title": "Exome sequencing of contralateral breast cancer identifies metastatic disease.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Rockberg", "given": "Julia", "initials": "J"}, {"family": "Hilliges", "given": "Camilla", "initials": "C"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Sandberg", "given": "Maria", "initials": "M"}, {"family": "Czene", "given": "Kamila", "initials": "K"}], "type": "journal article", "published": "2015-06-00", "journal": {"volume": "151", "issn": "1573-7217", "issue": "2", "pages": "319-324", "title": "Breast Cancer Res. Treat.", "issn-l": "0167-6806"}, "abstract": "Women with contralateral breast cancer (CBC) have significantly worse prognosis compared to women with unilateral cancer. A possible explanation of the poor prognosis of patients with CBC is that in a subset of patients, the second cancer is not a new primary tumor but a metastasis of the first cancer that has potentially obtained aggressive characteristics through selection of treatment. Exome and whole-genome sequencing of solid tumors has previously been used to investigate the clonal relationship between primary tumors and metastases in several diseases. In order to assess the relationship between the first and the second cancer, we performed exome sequencing to identify somatic mutations in both first and second cancers, and compared paired normal tissue of 25 patients with metachronous CBC. For three patients, we identified shared somatic mutations indicating a common clonal origin thereby demonstrating that the second tumor is a metastasis of the first cancer, rather than a new primary cancer. Accordingly, these patients all developed distant metastasis within 3 years of the second diagnosis, compared with 7 out of 22 patients with non-shared somatic profiles. Genomic profiling of both tumors help the clinicians distinguish between true CBCs and subsequent metastases.", "doi": "10.1007/s10549-015-3403-6", "pmid": "25922084", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:38.053Z", "modified": "2020-01-21T13:56:05.725Z"}, {"entity": "publication", "iuid": "9dea42643c7c49c79766af974384058a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9dea42643c7c49c79766af974384058a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9dea42643c7c49c79766af974384058a"}}, "title": "Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Lef\u00e9bure", "given": "Robert", "initials": "R"}, {"family": "Degerman", "given": "Rickard", "initials": "R"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2015-06-00", "journal": {"volume": "44 Suppl 3", "issn": "1654-7209", "issue": null, "pages": "402-412", "title": "Ambio", "issn-l": "0044-7447"}, "abstract": "Predicted increases in runoff of terrestrial dissolved organic matter (DOM) and sea surface temperatures implicate substantial changes in energy fluxes of coastal marine ecosystems. Despite marine bacteria being critical drivers of marine carbon cycling, knowledge of compositional responses within bacterioplankton communities to such disturbances is strongly limited. Using 16S rRNA gene pyrosequencing, we examined bacterioplankton population dynamics in Baltic Sea mesocosms with treatments combining terrestrial DOM enrichment and increased temperature. Among the 200 most abundant taxa, 62\u00a0% either increased or decreased in relative abundance under changed environmental conditions. For example, SAR11 and SAR86 populations proliferated in combined increased terrestrial DOM/temperature mesocosms, while the hgcI and CL500-29 clades (Actinobacteria) decreased in the same mesocosms. Bacteroidetes increased in both control mesocosms and in the combined increased terrestrial DOM/temperature mesocosms. These results indicate considerable and differential responses among distinct bacterial populations to combined climate change effects, emphasizing the potential of such effects to induce shifts in ecosystem function and carbon cycling in the future Baltic Sea.", "doi": "10.1007/s13280-015-0659-3", "pmid": "26022323", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4447689"}], "notes": [], "created": "2017-05-02T12:57:50.534Z", "modified": "2020-01-21T13:56:04.083Z"}, {"entity": "publication", "iuid": "242a899e5ba144c19d809a35fd9d24cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/242a899e5ba144c19d809a35fd9d24cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/242a899e5ba144c19d809a35fd9d24cc"}}, "title": "Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.", "authors": [{"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Mallick", "given": "Swapan", "initials": "S"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Enk", "given": "Jacob", "initials": "J"}, {"family": "Rohland", "given": "Nadin", "initials": "N"}, {"family": "Li", "given": "Heng", "initials": "H"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Poinar", "given": "Hendrik", "initials": "H"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Reich", "given": "David", "initials": "D"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2015-05-18", "journal": {"volume": "25", "issn": "1879-0445", "issue": "10", "pages": "1395-1400", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding. However, whether such genetic factors have had an impact on species prior to their extinction is unclear; examining this would require a detailed reconstruction of a species' demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage and dates to \u223c4,300 years before present, representing one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from an \u223c44,800-year-old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct.", "doi": "10.1016/j.cub.2015.04.007", "pmid": "25913407", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(15)00420-0"}, {"db": "pmc", "key": "PMC4439331"}, {"db": "mid", "key": "NIHMS678983"}], "notes": [], "created": "2017-05-02T12:58:15.555Z", "modified": "2021-07-07T20:31:10.723Z"}, {"entity": "publication", "iuid": "4b8ef72e35594e09919743f5a71ab6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b8ef72e35594e09919743f5a71ab6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b8ef72e35594e09919743f5a71ab6c4"}}, "title": "Complement inhibitor CD55 governs the integrity of membrane rafts in pancreatic beta cells, but plays no role in insulin secretion.", "authors": [{"family": "Nagaraj", "given": "Vini", "initials": "V"}, {"family": "King", "given": "Ben", "initials": "B"}, {"family": "Storm", "given": "Petter", "initials": "P"}, {"family": "Vikman", "given": "Petter", "initials": "P"}, {"family": "Ottosson-Laakso", "given": "Emilia", "initials": "E"}, {"family": "Blom", "given": "Anna M", "initials": "AM"}, {"family": "Renstr\u00f6m", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2015-05-08", "journal": {"volume": "460", "issn": "1090-2104", "issue": "3", "pages": "518-524", "title": "Biochem. Biophys. Res. Commun.", "issn-l": "0006-291X"}, "abstract": "CD55 is a glycosylphosphatidylinositol-anchored protein, which inhibits complement activation by acting on the complement C3 convertases. CD55 is widely localized in the cholesterol rich regions of the cell plasma membrane termed membrane rafts. CD55 is attached to these specialized regions via a GPI link on the outer leaflet of the plasma membrane. Membrane rafts anchor many important signaling proteins, which control several cellular functions within the cell. For example, we recently demonstrated that the membrane raft protein and complement inhibitor CD59 also controls insulin secretion by an intracellular mechanism. Therefore, we have in this study aimed at addressing the expression and function of CD55 in pancreatic beta cells. To this end, we observe that CD55 is highly expressed in INS1 832/13 beta cells as well as human pancreatic islets. Diabetic human islets show a tendency for increased expression of CD55 when compared to the healthy controls. Importantly, silencing of CD55 in INS1 832/13 cells does not affect their insulin secretory capacity. On the other hand, silencing of CD55 diminished the intensity of membrane rafts as determined by Atto-SM staining. We hence conclude that CD55 expression is affected by glycemic status in human islets and plays a critical role in maintaining the conserved structure of rafts in pancreatic islets, which is similar to that of the related complement inhibitor CD59. However CD55 does not interfere with insulin secretion in beta cells, which is in sharp contrast to the action of the complement inhibitor CD59.", "doi": "10.1016/j.bbrc.2015.03.062", "pmid": "25797618", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0006-291X(15)00508-2"}], "notes": [], "created": "2017-05-02T12:58:07.514Z", "modified": "2020-01-21T13:56:02.178Z"}, {"entity": "publication", "iuid": "3384821f465944108037de1d5f9258f1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3384821f465944108037de1d5f9258f1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3384821f465944108037de1d5f9258f1"}}, "title": "Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome.", "authors": [{"family": "Engstrand Lilja", "given": "Helene", "initials": "H"}, {"family": "Wefer", "given": "Hugo", "initials": "H"}, {"family": "Nystr\u00f6m", "given": "Niklas", "initials": "N"}, {"family": "Finkel", "given": "Yigael", "initials": "Y"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2015-05-04", "journal": {"volume": "3", "issn": "2049-2618", "issue": null, "pages": "18", "title": "Microbiome", "issn-l": "2049-2618"}, "abstract": "The composition of the intestinal microbiota seems to be an important factor in determining the clinical outcome in children with short bowel syndrome (SBS). Alterations in the microbiota may result in serious complications such as small bowel bacterial overgrowth (SBBO) and intestinal mucosal inflammation that lead to prolonged parenteral nutrition (PN) dependency with subsequently increased risk of liver failure and sepsis. To date, there are no reported mappings of the intestinal microbiome in children with SBS. Here, we present the first report on the intestinal microbial community profile in children with SBS.\n\nThe study includes children diagnosed with SBS in the neonatal period. Healthy siblings served as controls. Fecal samples were collected, and microbial profiles were analyzed by using 16S rRNA gene sequencing on the Illumina MiSeq platform. We observed a pronounced microbial dysbiosis in children with SBS on PN treatment with an increased and totally dominating relative abundance of Enterobacteriacae in four out of five children compared to children with SBS weaned from PN and healthy siblings.\n\nThe overall decreased bacterial diversity in children with SBS is consistent with intestinal microbiome mappings in inflammatory bowel diseases such as Crohn's disease and necrotizing enterocolitis in preterm infants. Our findings indicate that intestinal dysbiosis in children with SBS is associated with prolonged PN dependency.", "doi": "10.1186/s40168-015-0084-7", "pmid": "25941569", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "84"}, {"db": "pmc", "key": "PMC4418071"}], "notes": [], "created": "2017-05-02T12:57:14.230Z", "modified": "2020-01-21T13:56:01.443Z"}, {"entity": "publication", "iuid": "8006e4b86dd344b48e40fb3f55936565", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8006e4b86dd344b48e40fb3f55936565.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8006e4b86dd344b48e40fb3f55936565"}}, "title": "Tracking the origin of metastatic prostate cancer.", "authors": [{"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Kristiansen", "given": "Anna", "initials": "A"}, {"family": "Wiklund", "given": "Peter", "initials": "P"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Egevad", "given": "Lars", "initials": "L"}], "type": "letter", "published": "2015-05-00", "journal": {"volume": "67", "issn": "1873-7560", "issue": "5", "pages": "819-822", "title": "Eur. Urol.", "issn-l": "0302-2838"}, "abstract": "Metastatic prostate cancer is a monoclonal disease. We previously failed to identify a common somatic denominator between primary tumor tissue and two lymph-node metastases by exome sequencing [Lindberg J, et al. Eur Urol 2013;63:702-8]. To track the seeding clone we performed copy-number alteration analysis on 34 morphologically distinct tissue areas in one prostatectomy specimen. Using break-point regions to infer phylogenetic relationships, the clone most closely related to the metastases was found in intraductal carcinoma of the prostate. Although the majority of tumor areas harbored events also found in the metastases, three carried none. This emphasizes the importance of intraprostatic tumor heterogeneity for prediction of prognosis. These findings also support recent evidence that intraductal carcinoma is a marker of aggressive disease.\n\nWe identified the area in the prostate that gave rise to metastases by searching for metastatic-specific DNA alterations in multiple regions of the prostate. The metastasizing component grew within prostatic ducts, suggesting that intraductal cancer should be reported when found in needle biopsies. It is also important to be aware of tumor heterogeneity when assessing somatic changes linked to tumor aggressiveness.", "doi": "10.1016/j.eururo.2014.09.006", "pmid": "25246081", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0302-2838(14)00892-6"}], "notes": [], "created": "2017-05-02T12:57:49.018Z", "modified": "2020-01-21T13:56:03.335Z"}, {"entity": "publication", "iuid": "dd23902bae6b4016a2757ea2928c5499", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd23902bae6b4016a2757ea2928c5499.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd23902bae6b4016a2757ea2928c5499"}}, "title": "Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.", "authors": [{"family": "Jahan", "given": "Sultana N", "initials": "SN"}, {"family": "\u00c5sman", "given": "Anna K M", "initials": "AK"}, {"family": "Corcoran", "given": "P\u00e1draic", "initials": "P"}, {"family": "Fogelqvist", "given": "Johan", "initials": "J"}, {"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2015-05-00", "journal": {"volume": "66", "issn": "1460-2431", "issue": "9", "pages": "2785-2794", "title": "J. Exp. Bot.", "issn-l": "0022-0957"}, "abstract": "Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein \u03b2-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.", "doi": "10.1093/jxb/erv094", "pmid": "25788734", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "erv094"}, {"db": "pmc", "key": "PMC4986879"}], "notes": [], "created": "2017-05-02T12:57:24.967Z", "modified": "2020-01-21T13:56:05.653Z"}, {"entity": "publication", "iuid": "9782141e3dc04c8aab688d024c2a9fee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9782141e3dc04c8aab688d024c2a9fee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9782141e3dc04c8aab688d024c2a9fee"}}, "title": "Autosomal recessive mutations in the COL2A1 gene cause severe spondyloepiphyseal dysplasia.", "authors": [{"family": "Tham", "given": "E", "initials": "E"}, {"family": "Nishimura", "given": "G", "initials": "G"}, {"family": "Geiberger", "given": "S", "initials": "S"}, {"family": "Horemuzova", "given": "E", "initials": "E"}, {"family": "Nilsson", "given": "D", "initials": "D"}, {"family": "Lindstrand", "given": "A", "initials": "A"}, {"family": "Hammarsj\u00f6", "given": "A", "initials": "A"}, {"family": "Armenio", "given": "M", "initials": "M"}, {"family": "M\u00e4kitie", "given": "O", "initials": "O"}, {"family": "Zabel", "given": "B", "initials": "B"}, {"family": "Nordgren", "given": "A", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "M", "initials": "M"}, {"family": "Grigelioniene", "given": "G", "initials": "G"}], "type": "case reports", "published": "2015-05-00", "journal": {"volume": "87", "issn": "1399-0004", "issue": "5", "pages": "496-498", "title": "Clin. Genet.", "issn-l": "0009-9163"}, "abstract": null, "doi": "10.1111/cge.12466", "pmid": "25060605", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:58:45.911Z", "modified": "2020-01-21T13:56:03.900Z"}, {"entity": "publication", "iuid": "be4ade7e06a54bb0babd3c4b044325d4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be4ade7e06a54bb0babd3c4b044325d4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be4ade7e06a54bb0babd3c4b044325d4"}}, "title": "Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A.", "authors": [{"family": "Karrman", "given": "Kristina", "initials": "K"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Behrendtz", "given": "Mikael", "initials": "M"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Ehinger", "given": "Mats", "initials": "M"}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "journal article", "published": "2015-04-24", "journal": {"volume": "8", "issn": "1756-8722", "issue": null, "pages": "42", "title": "J Hematol Oncol", "issn-l": "1756-8722"}, "abstract": "Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that arises in a multistep fashion through acquisition of several genetic aberrations, subsequently giving rise to a malignant, clonal expansion of T-lymphoblasts. The aim of the present study was to identify additional as well as cooperative genetic events in T-ALL.\n\nA population-based pediatric T-ALL series comprising 47 cases was investigated by SNP array and deep sequencing analyses of 75 genes, in order to ascertain pathogenetically pertinent aberrations and to identify cooperative events.\n\nThe majority (92%) of cases harbored copy number aberrations/uniparental isodisomies (UPIDs), with a median of three changes (range 0-11) per case. The genes recurrently deleted comprised CDKN2A, CDKN2B, LEF1, PTEN, RBI, and STIL. No case had a whole chromosome UPID; in fact, literature data show that this is a rare phenomenon in T-ALL. However, segmental UPIDs (sUPIDs) were seen in 42% of our cases, with most being sUPID9p that always were associated with homozygous CDKN2A deletions, with a heterozygous deletion occurring prior to the sUPID9p in all instances. Among the 75 genes sequenced, 14 (19%) were mutated in 28 (72%) of 39 analyzed cases. The genes targeted are involved in signaling transduction, epigenetic regulation, and transcription. In some cases, NOTCH1 mutations were seen in minor subclones and lost at relapse; thus, such mutations can be secondary events.\n\nDeep sequencing and SNP array analyses of T-ALL revealed lack of wUPIDs, a high proportion of sUPID9p targeting CDKN2A, NOTCH1 mutations in subclones, and recurrent mutations of genes involved in signaling transduction, epigenetic regulation, and transcription.", "doi": "10.1186/s13045-015-0138-0", "pmid": "25903014", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "10.1186/s13045-015-0138-0"}, {"db": "pmc", "key": "PMC4412034"}], "notes": [], "created": "2017-05-02T12:57:35.775Z", "modified": "2021-07-06T15:41:35.335Z"}, {"entity": "publication", "iuid": "46b24a756ae146c3ae7b44a2c64c44d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46b24a756ae146c3ae7b44a2c64c44d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46b24a756ae146c3ae7b44a2c64c44d3"}}, "title": "Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.", "authors": [{"family": "Lindh", "given": "Markus V", "initials": "MV"}, {"family": "Figueroa", "given": "Daniela", "initials": "D"}, {"family": "Sj\u00f6stedt", "given": "Johanna", "initials": "J"}, {"family": "Baltar", "given": "Federico", "initials": "F"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}, {"family": "Legrand", "given": "Catherine", "initials": "C"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}], "type": "journal article", "published": "2015-04-01", "journal": {"volume": "6", "issn": "1664-302X", "issue": null, "pages": "223", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.", "doi": "10.3389/fmicb.2015.00223", "pmid": "25883589", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4381636"}], "notes": [], "created": "2017-05-02T12:57:49.939Z", "modified": "2020-01-21T13:56:02.001Z"}, {"entity": "publication", "iuid": "e6d1fc47050848cd805e2ceaa9e80441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e6d1fc47050848cd805e2ceaa9e80441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e6d1fc47050848cd805e2ceaa9e80441"}}, "title": "Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.", "authors": [{"family": "Nasrollahzadeh", "given": "Dariush", "initials": "D"}, {"family": "Malekzadeh", "given": "Reza", "initials": "R"}, {"family": "Ploner", "given": "Alexander", "initials": "A"}, {"family": "Shakeri", "given": "Ramin", "initials": "R"}, {"family": "Sotoudeh", "given": "Masoud", "initials": "M"}, {"family": "Fahimi", "given": "Saman", "initials": "S"}, {"family": "Nasseri-Moghaddam", "given": "Siavosh", "initials": "S"}, {"family": "Kamangar", "given": "Farin", "initials": "F"}, {"family": "Abnet", "given": "Christian C", "initials": "CC"}, {"family": "Winckler", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Islami", "given": "Farhad", "initials": "F"}, {"family": "Boffetta", "given": "Paolo", "initials": "P"}, {"family": "Brennan", "given": "Paul", "initials": "P"}, {"family": "Dawsey", "given": "Sanford M", "initials": "SM"}, {"family": "Ye", "given": "Weimin", "initials": "W"}], "type": "journal article", "published": "2015-03-06", "journal": {"volume": "5", "issn": "2045-2322", "issue": null, "pages": "8820", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Observational studies revealed a relationship between changes in gastric mucosa and risk of esophageal squamous cell carcinoma (ESCC) which suggested a possible role for gastric microbiota in ESCC carcinogenesis. In this study we aimed to compare pattern of gastric corpus microbiota in ESCC with normal esophagus. Cases were included subjects with early ESCC (stage I-II) and esophageal squamous dysplasia (ESD) as the cancer precursor. Control groups included age and sex-matched subjects with mid-esophagus esophagitis (diseased-control), and histologically normal esophagus (healthy-control). DNA was extracted from snap-frozen gastric corpus tissues and 16S rRNA was sequenced on GS-FLX Titanium. After noise removal, an average of 3004 reads per sample was obtained from 93 subjects. We applied principal coordinate analysis to ordinate distances from beta diversity data. Pattern of gastric microbiota using Unifrac (p = 0.004) and weighted Unifrac distances (p = 0.018) statistically varied between cases and healthy controls. Sequences were aligned to SILVA database and Clostridiales and Erysipelotrichales orders were more abundant among cases after controling for multiple testing (p = 0.011). No such difference was observed between mid-esophagitis and healthy controls. This study is the first to show that composition of gastric corpus mucosal microbiota differs in early ESCC and ESD from healthy esophagus.", "doi": "10.1038/srep08820", "pmid": "25743945", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "srep08820"}, {"db": "pmc", "key": "PMC4351546"}], "notes": [], "created": "2017-05-02T12:58:08.100Z", "modified": "2020-01-21T13:56:05.900Z"}, {"entity": "publication", "iuid": "a19bb15446334e7282610bec5dbe2b3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a19bb15446334e7282610bec5dbe2b3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a19bb15446334e7282610bec5dbe2b3e"}}, "title": "The H1-receptor antagonist cetirizine ameliorates high-fat diet-induced glucose intolerance in male C57BL/6 mice, but not diabetes outcome in female non-obese diabetic (NOD) mice.", "authors": [{"family": "Anvari", "given": "Ebrahim", "initials": "E"}, {"family": "Wang", "given": "Xuan", "initials": "X"}, {"family": "Sandler", "given": "Stellan", "initials": "S"}, {"family": "Welsh", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2015-03-00", "journal": {"volume": "120", "issn": "2000-1967", "issue": "1", "pages": "40-46", "title": "Ups. J. Med. Sci.", "issn-l": "0300-9734"}, "abstract": "It has been proposed that the histamine 1-receptor (H1-receptor) not only promotes allergic reactions, but also modulates innate immunity and autoimmune reactions. In line with this, we have recently reported that the H1-receptor antagonist cetirizine partially counteracts cytokine-induced beta-cell signaling and destruction. Therefore, the aim of this study was to determine whether cetirizine affects diabetes in NOD mice, a model for human type 1 diabetes, and glucose intolerance in high-fat diet C57BL/6 mice, a model for human glucose intolerance.\n\nFemale NOD mice were treated with cetirizine in the drinking water (25 mg/kg body weight) from 9 until 30 weeks of age during which precipitation of diabetes was followed. Male C57BL/6 mice were given a high-fat diet from 5 weeks of age. When the mice were 12 weeks of age cetirizine was given for 2 weeks in the drinking water. The effects of cetirizine were analyzed by blood glucose determinations, glucose tolerance tests, and insulin sensitivity tests.\n\nCetirizine did not affect diabetes development in NOD mice. On the other hand, cetirizine treatment for 1 week protected against high-fat diet-induced hyperglycemia. The glucose tolerance after 2 weeks of cetirizine treatment was improved in high-fat diet mice. We observed no effect of cetirizine on the insulin sensitivity of high-fat diet mice.\n\nOur results suggest a protective effect of cetirizine against high-fat diet-induced beta-cell dysfunction, but not against autoimmune beta-cell destruction.", "doi": "10.3109/03009734.2014.967422", "pmid": "25291144", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4389006"}], "notes": [], "created": "2017-05-04T14:59:01.994Z", "modified": "2020-01-21T13:56:04.160Z"}, {"entity": "publication", "iuid": "8afad26d7b4748c7afcd57b946cdeaef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8afad26d7b4748c7afcd57b946cdeaef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8afad26d7b4748c7afcd57b946cdeaef"}}, "title": "The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.", "authors": [{"family": "Steglich", "given": "Babett", "initials": "B"}, {"family": "Str\u00e5lfors", "given": "Annelie", "initials": "A"}, {"family": "Khorosjutina", "given": "Olga", "initials": "O"}, {"family": "Persson", "given": "Jenna", "initials": "J"}, {"family": "Smialowska", "given": "Agata", "initials": "A"}, {"family": "Javerzat", "given": "Jean-Paul", "initials": "JP"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2015-03-00", "journal": {"volume": "11", "issn": "1553-7404", "issue": "3", "pages": "e1005101", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3\u2206 cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and the nuclear envelope.", "doi": "10.1371/journal.pgen.1005101", "pmid": "25798942", "labels": {"National Genomics Infrastructure": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-14-01797"}, {"db": "pmc", "key": "PMC4370569"}, {"db": "GEO", "key": "GSE58013"}], "notes": [], "created": "2017-05-02T12:58:39.305Z", "modified": "2020-01-21T13:56:03.564Z"}, {"entity": "publication", "iuid": "704d62a6774d4c5f8c04ea27d6237479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/704d62a6774d4c5f8c04ea27d6237479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/704d62a6774d4c5f8c04ea27d6237479"}}, "title": "Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations.", "authors": [{"family": "Karlsson", "given": "Kasper", "initials": "K"}, {"family": "Sahlin", "given": "Ellika", "initials": "E"}, {"family": "Iwarsson", "given": "Erik", "initials": "E"}, {"family": "Westgren", "given": "Magnus", "initials": "M"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}], "type": "comparative study", "published": "2015-03-00", "journal": {"volume": "105", "issn": "1089-8646", "issue": "3", "pages": "150-158", "title": "Genomics", "issn-l": "0888-7543"}, "abstract": "Cell-free DNA has been used for fetal rhesus factor and sex determination, fetal aneuploidy screening, cancer diagnostics and monitoring, and other applications. However current methods of using cell free DNA require amplification, which leads to allelic dropout and bias especially when starting with small amounts of DNA. Here we describe an amplification-free method for sequencing of cell-free DNA, even from low levels of starting material. We evaluated this method in the context of prenatal diagnosis of fetal aneuploidy and compared it with a PCR-based library preparation method as well as a recently described method using unique molecular identifiers (UMI). All methods performed well, however coverage was increased by the amplification-free method and GC-induced bias was reduced by both the amplification-free method and the UMI method. Future diagnostic applications including whole genome sequencing of cell-free DNA will benefit from amplification-free sequencing.", "doi": "10.1016/j.ygeno.2014.12.005", "pmid": "25543032", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0888-7543(14)00278-X"}], "notes": [], "created": "2017-05-02T12:57:34.890Z", "modified": "2020-01-21T13:56:02.944Z"}, {"entity": "publication", "iuid": "fe207fc9ff3a4b668a2838994dd20492", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fe207fc9ff3a4b668a2838994dd20492.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fe207fc9ff3a4b668a2838994dd20492"}}, "title": "The composition of the gut microbiota shapes the colon mucus barrier.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Rodr\u00edguez-Pi\u00f1eiro", "given": "Ana M", "initials": "AM"}, {"family": "Sch\u00fctte", "given": "Andr\u00e9", "initials": "A"}, {"family": "Ermund", "given": "Anna", "initials": "A"}, {"family": "Boysen", "given": "Preben", "initials": "P"}, {"family": "Bemark", "given": "Mats", "initials": "M"}, {"family": "Sommer", "given": "Felix", "initials": "F"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}, {"family": "Hansson", "given": "Gunnar C", "initials": "GC"}, {"family": "Johansson", "given": "Malin E V", "initials": "ME"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "16", "issn": "1469-3178", "issue": "2", "pages": "164-177", "title": "EMBO Rep.", "issn-l": "1469-221X"}, "abstract": "Two C57BL/6 mice colonies maintained in two rooms of the same specific pathogen-free (SPF) facility were found to have different gut microbiota and a mucus phenotype that was specific for each colony. The thickness and growth of the colon mucus were similar in the two colonies. However, one colony had mucus that was impenetrable to bacteria or beads the size of bacteria-which is comparable to what we observed in free-living wild mice-whereas the other colony had an inner mucus layer penetrable to bacteria and beads. The different properties of the mucus depended on the microbiota, as they were transmissible by transfer of caecal microbiota to germ-free mice. Mice with an impenetrable mucus layer had increased amounts of Erysipelotrichi, whereas mice with a penetrable mucus layer had higher levels of Proteobacteria and TM7 bacteria in the distal colon mucus. Thus, our study shows that bacteria and their community structure affect mucus barrier properties in ways that can have implications for health and disease. It also highlights that genetically identical animals housed in the same facility can have rather distinct microbiotas and barrier structures.", "doi": "10.15252/embr.201439263", "pmid": "25525071", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "embr.201439263"}, {"db": "pmc", "key": "PMC4328744"}], "notes": [], "created": "2017-05-02T12:57:25.565Z", "modified": "2020-01-21T13:56:06.529Z"}, {"entity": "publication", "iuid": "5682a631ed244850a303f6e70f78fafb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5682a631ed244850a303f6e70f78fafb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5682a631ed244850a303f6e70f78fafb"}}, "title": "Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.", "authors": [{"family": "Leong", "given": "Su-Lin L", "initials": "SL"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Olga V", "initials": "OV"}, {"family": "Frisvad", "given": "Jens C", "initials": "JC"}, {"family": "Thrane", "given": "Ulf", "initials": "U"}, {"family": "Heipieper", "given": "Hermann J", "initials": "HJ"}, {"family": "Dijksterhuis", "given": "Jan", "initials": "J"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Schn\u00fcrer", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "17", "issn": "1462-2920", "issue": "2", "pages": "496-513", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "Xeromyces bisporus can grow on sugary substrates down to 0.61, an extremely low water activity. Its genome size is approximately 22\u2009Mb. Gene clusters encoding for secondary metabolites were conspicuously absent; secondary metabolites were not detected experimentally. Thus, in its 'dry' but nutrient-rich environment, X.\u2009bisporus appears to have relinquished abilities for combative interactions. Elements to sense/signal osmotic stress, e.g. HogA pathway, were present in X.\u2009bisporus. However, transcriptomes at optimal (\u223c\u20090.89) versus low aw (0.68) revealed differential expression of only a few stress-related genes; among these, certain (not all) steps for glycerol synthesis were upregulated. Xeromyces bisporus increased glycerol production during hypo- and hyper-osmotic stress, and much of its wet weight comprised water and rinsable solutes; leaked solutes may form a protective slime. Xeromyces bisporus and other food-borne moulds increased membrane fatty acid saturation as water activity decreased. Such modifications did not appear to be transcriptionally regulated in X.\u2009bisporus; however, genes modulating sterols, phospholipids and the cell wall were differentially expressed. Xeromyces bisporus was previously proposed to be a 'chaophile', preferring solutes that disorder biomolecular structures. Both X.\u2009bisporus and the closely related xerophile, Xerochrysium xerophilum, with low membrane unsaturation indices, could represent a phylogenetic cluster of 'chaophiles'.", "doi": "10.1111/1462-2920.12596", "pmid": "25142400", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": null, "Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:46.930Z", "modified": "2020-01-21T13:56:16.749Z"}, {"entity": "publication", "iuid": "9b379261e5574a0cbfc364715c570bfc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b379261e5574a0cbfc364715c570bfc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b379261e5574a0cbfc364715c570bfc"}}, "title": "Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Edqvist", "given": "Per-Henrik D", "initials": "PH"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "63", "issn": "1551-5044", "issue": "2", "pages": "129-141", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "To increase our understanding of skin, it is important to define the molecular constituents of the cell types and epidermal layers that signify normal skin. We have combined a genome-wide transcriptomics analysis, using deep sequencing of mRNA from skin biopsies, with immunohistochemistry-based protein profiling to characterize the landscape of gene and protein expression in normal human skin. The transcriptomics and protein expression data of skin were compared to 26 (RNA) and 44 (protein) other normal tissue types. All 20,050 putative protein-coding genes were classified into categories based on patterns of expression. We found that 417 genes showed elevated expression in skin, with 106 genes expressed at least five-fold higher than that in other tissues. The 106 genes categorized as skin enriched encoded for well-known proteins involved in epidermal differentiation and proteins with unknown functions and expression patterns in skin, including the C1orf68 protein, which showed the highest relative enrichment in skin. In conclusion, we have applied a genome-wide analysis to identify the human skin-specific proteome and map the precise localization of the corresponding proteins in different compartments of the skin, to facilitate further functional studies to explore the molecular repertoire of normal skin and to identify biomarkers related to various skin diseases.", "doi": "10.1369/0022155414562646", "pmid": "25411189", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "0022155414562646"}, {"db": "pmc", "key": "PMC4305515"}], "notes": [], "created": "2017-05-02T12:56:54.324Z", "modified": "2021-07-08T13:44:33.465Z"}, {"entity": "publication", "iuid": "63a616dd816642e590352dfab4bab68e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a616dd816642e590352dfab4bab68e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a616dd816642e590352dfab4bab68e"}}, "title": "CTNND2-a candidate gene for reading problems and mild intellectual disability.", "authors": [{"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Topa", "given": "Alexandra", "initials": "A"}, {"family": "Anderlid", "given": "Britt-Marie", "initials": "BM"}, {"family": "Darki", "given": "Fahimeh", "initials": "F"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Tapia P\u00e1ez", "given": "Isabel", "initials": "I"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}, {"family": "Samuelsson", "given": "Lena", "initials": "L"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2015-02-00", "journal": {"volume": "52", "issn": "1468-6244", "issue": "2", "pages": "111-122", "title": "J. Med. Genet.", "issn-l": "0022-2593"}, "abstract": "Cytogenetically visible chromosomal translocations are highly informative as they can pinpoint strong effect genes even in complex genetic disorders.\n\nHere, we report a mother and daughter, both with borderline intelligence and learning problems within the dyslexia spectrum, and two apparently balanced reciprocal translocations: t(1;8)(p22;q24) and t(5;18)(p15;q11). By low coverage mate-pair whole-genome sequencing, we were able to pinpoint the genomic breakpoints to 2\u2005kb intervals. By direct sequencing, we then located the chromosome 5p breakpoint to intron 9 of CTNND2. An additional case with a 163\u2005kb microdeletion exclusively involving CTNND2 was identified with genome-wide array comparative genomic hybridisation. This microdeletion at 5p15.2 is also present in mosaic state in the patient's mother but absent from the healthy siblings. We then investigated the effect of CTNND2 polymorphisms on normal variability and identified a polymorphism (rs2561622) with significant effect on phonological ability and white matter volume in the left frontal lobe, close to cortical regions previously associated with phonological processing. Finally, given the potential role of CTNND2 in neuron motility, we used morpholino knockdown in zebrafish embryos to assess its effects on neuronal migration in vivo. Analysis of the zebrafish forebrain revealed a subpopulation of neurons misplaced between the diencephalon and telencephalon.\n\nTaken together, our human genetic and in vivo data suggest that defective migration of subpopulations of neuronal cells due to haploinsufficiency of CTNND2 contribute to the cognitive dysfunction in our patients.", "doi": "10.1136/jmedgenet-2014-102757", "pmid": "25473103", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Clinical Genomics Stockholm": null, "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "jmedgenet-2014-102757"}], "notes": [], "created": "2017-05-02T12:57:17.210Z", "modified": "2023-06-19T07:51:37.778Z"}, {"entity": "publication", "iuid": "3b4640678c814b81b4501deaea6a6ee1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b4640678c814b81b4501deaea6a6ee1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b4640678c814b81b4501deaea6a6ee1"}}, "title": "Endonuclease specificity and sequence dependence of type IIS restriction enzymes.", "authors": [{"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Terje-Hegge", "given": "Finn", "initials": "F"}, {"family": "Foam", "given": "Napoleon", "initials": "N"}, {"family": "Pettersson", "given": "Erik", "initials": "E"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Lexow", "given": "Preben", "initials": "P"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2015-01-28", "journal": {"volume": "10", "issn": "1932-6203", "issue": "1", "pages": "e0117059", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. Despite this, systematic functional categorization of cleavage performance has largely been lacking. We established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. We coupled this to massively parallel sequencing in order to provide sensitive and accurate measurement. With this system 14 enzymes were assayed (AcuI, BbvI, BpmI, BpuEI, BseRI, BsgI, Eco57I, Eco57MI, EcoP15I, FauI, FokI, GsuI, MmeI and SmuI). We report significant variation of slippage ranging from 1-54%, variations in sequence context dependence, as well as variation between isoschizomers. We believe this largely overlooked property of enzymes with shifted cleavage would benefit from further large scale classification and engineering efforts seeking to improve performance. The gained insights of in-vitro performance may also aid the in-vivo understanding of these enzymes.", "doi": "10.1371/journal.pone.0117059", "pmid": "25629514", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-15706"}, {"db": "pmc", "key": "PMC4309577"}, {"db": "SRA", "key": "SRS627913"}], "notes": [], "created": "2017-05-02T12:57:53.663Z", "modified": "2023-06-19T07:51:37.768Z"}, {"entity": "publication", "iuid": "25c563a160544bb799a8736c65be1e18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25c563a160544bb799a8736c65be1e18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25c563a160544bb799a8736c65be1e18"}}, "title": "Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells.", "authors": [{"family": "Feliu", "given": "Neus", "initials": "N"}, {"family": "Kohonen", "given": "Pekka", "initials": "P"}, {"family": "Ji", "given": "Jie", "initials": "J"}, {"family": "Zhang", "given": "Yuning", "initials": "Y"}, {"family": "Karlsson", "given": "Hanna L", "initials": "HL"}, {"family": "Palmberg", "given": "Lena", "initials": "L"}, {"family": "Nystr\u00f6m", "given": "Andreas", "initials": "A"}, {"family": "Fadeel", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2015-01-27", "journal": {"volume": "9", "issn": "1936-086X", "issue": "1", "pages": "146-163", "title": "ACS Nano", "issn-l": "1936-0851"}, "abstract": "Gene expression profiling has developed rapidly in recent years with the advent of deep sequencing technologies such as RNA sequencing (RNA Seq) and could be harnessed to predict and define mechanisms of toxicity of chemicals and nanomaterials. However, the full potential of these technologies in (nano)toxicology is yet to be realized. Here, we show that systems biology approaches can uncover mechanisms underlying cellular responses to nanomaterials. Using RNA Seq and computational approaches, we found that cationic poly(amidoamine) dendrimers (PAMAM-NH2) are capable of triggering down-regulation of cell-cycle-related genes in primary human bronchial epithelial cells at doses that do not elicit acute cytotoxicity, as demonstrated using conventional cell viability assays, while gene transcription was not affected by neutral PAMAM-OH dendrimers. The PAMAMs were internalized in an active manner by lung cells and localized mainly in lysosomes; amine-terminated dendrimers were internalized more efficiently when compared to the hydroxyl-terminated dendrimers. Upstream regulator analysis implicated NF-\u03baB as a putative transcriptional regulator, and subsequent cell-based assays confirmed that PAMAM-NH2 caused NF-\u03baB-dependent cell cycle arrest. However, PAMAM-NH2 did not affect cell cycle progression in the human A549 adenocarcinoma cell line. These results demonstrate the feasibility of applying systems biology approaches to predict cellular responses to nanomaterials and highlight the importance of using relevant (primary) cell models.", "doi": "10.1021/nn5061783", "pmid": "25530437", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:56:59.638Z", "modified": "2020-01-21T13:56:01.122Z"}, {"entity": "publication", "iuid": "3777a5cd8954424fb426f5163d4d01bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3777a5cd8954424fb426f5163d4d01bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3777a5cd8954424fb426f5163d4d01bf"}}, "title": "Proteomics. Tissue-based map of the human proteome.", "authors": [{"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Olsson", "given": "IngMarie", "initials": "I"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Szigyarto", "given": "Cristina Al-Khalili", "initials": "CA"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Djureinovic", "given": "Dijana", "initials": "D"}, {"family": "Takanen", "given": "Jenny Ottosson", "initials": "JO"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Alm", "given": "Tove", "initials": "T"}, {"family": "Edqvist", "given": "Per-Henrik", "initials": "PH"}, {"family": "Berling", "given": "Holger", "initials": "H"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Hamsten", "given": "Marica", "initials": "M"}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Persson", "given": "Lukas", "initials": "L"}, {"family": "Johansson", "given": "Fredric", "initials": "F"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications.scilifelab.se/researcher/f663c0a9e9e1455cbbf8e6aea13af4a9.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-01-23", "journal": {"volume": "347", "issn": "1095-9203", "issue": "6220", "pages": "1260419", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.", "doi": "10.1126/science.1260419", "pmid": "25613900", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Technology development", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "347/6220/1260419"}], "notes": [], "created": "2017-05-02T12:58:49.180Z", "modified": "2023-11-21T16:24:57.712Z"}, {"entity": "publication", "iuid": "8eb8153ee920494d99bb060da3ba565a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8eb8153ee920494d99bb060da3ba565a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8eb8153ee920494d99bb060da3ba565a"}}, "title": "The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.", "authors": [{"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Wanders", "given": "Alkwin", "initials": "A"}, {"family": "Cedernaes", "given": "Jonathan", "initials": "J"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2015-01-00", "journal": {"volume": "50", "issn": "1435-5922", "issue": "1", "pages": "46-57", "title": "J. Gastroenterol.", "issn-l": "0944-1174"}, "abstract": "The gastrointestinal tract (GIT) is subdivided into different anatomical organs with many shared functions and characteristics, but also distinct differences. We have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to describe the gene and protein expression patterns that define the human GIT.\n\nRNA sequencing data derived from stomach, duodenum, jejunum/ileum and colon specimens were compared to gene expression levels in 23 other normal human tissues analysed with the same method. Protein profiling based on immunohistochemistry and tissue microarrays was used to sub-localize the corresponding proteins with GIT-specific expression into sub-cellular compartments and cell types.\n\nApproximately 75% of all human protein-coding genes were expressed in at least one of the GIT tissues. Only 51 genes showed enriched expression in either one of the GIT tissues and an additional 83 genes were enriched in two or more GIT tissues. The list of GIT-enriched genes with validated protein expression patterns included various well-known but also previously uncharacterised or poorly studied genes. For instance, the colon-enriched expression of NXPE family member 1 (NXPE1) was established, while NLR family, pyrin domain-containing 6 (NLRP6) expression was primarily found in the human small intestine.\n\nWe have applied a genome-wide analysis based on transcriptomics and antibody-based protein profiling to identify genes that are expressed in a specific manner within the human GIT. These genes and proteins constitute important starting points for an improved understanding of the normal function and the different states of disease associated with the GIT.", "doi": "10.1007/s00535-014-0958-7", "pmid": "24789573", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:08.698Z", "modified": "2021-07-08T13:44:33.417Z"}, {"entity": "publication", "iuid": "a670ef31b8494b6c8b05f44412358c51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a670ef31b8494b6c8b05f44412358c51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a670ef31b8494b6c8b05f44412358c51"}}, "title": "Methylated RASSF1A in malignant peripheral nerve sheath tumors identifies neurofibromatosis type 1 patients with inferior prognosis.", "authors": [{"family": "Danielsen", "given": "Stine A", "initials": "SA"}, {"family": "Lind", "given": "Guro E", "initials": "GE"}, {"family": "Kolberg", "given": "Matthias", "initials": "M"}, {"family": "H\u00f8land", "given": "Maren", "initials": "M"}, {"family": "Bjerkehagen", "given": "Bodil", "initials": "B"}, {"family": "Sundby Hall", "given": "Kirsten", "initials": "K"}, {"family": "van den Berg", "given": "Eva", "initials": "E"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}, {"family": "Smeland", "given": "Sigbj\u00f8rn", "initials": "S"}, {"family": "Picci", "given": "Piero", "initials": "P"}, {"family": "Lothe", "given": "Ragnhild A", "initials": "RA"}], "type": "journal article", "published": "2015-01-00", "journal": {"volume": "17", "issn": "1523-5866", "issue": "1", "pages": "63-69", "title": "Neuro-oncology", "issn-l": "1522-8517"}, "abstract": "Malignant peripheral nerve sheath tumor (MPNST) is a rare and highly aggressive disease with no evidence of effect from adjuvant therapy. It is further associated with the hereditary syndrome neurofibromatosis type 1 (NF1). Silencing of the tumor suppressor gene RASSF1A through DNA promoter hypermethylation is known to be involved in cancer development, but its impact in MPNSTs remains unsettled.\n\nThe RASSF1A promoter was analyzed by methylation-specific PCR in 113 specimens, including 44 NF1-associated MPNSTs, 47 sporadic MPNSTs, 21 benign neurofibromas, and 1 nonneoplastic nerve sheath control.\n\nRASSF1A methylation was found only in the malignant samples (60%) and identified a subgroup among patients with NF1-associated MPNST with a poor prognosis. These patients had a mean 5-year disease-specific survival of 27.3 months (95% CI: 17.2-37.4) versus 47.4 months (95% CI: 37.5-57.2) for NF1 patients with unmethylated promoters, P = 0.014. In multivariate Cox regression analysis, methylated RASSF1A remained an adverse prognostic factor independent of clinical risk factors, P = .013 (hazard ratio: 5.2; 95% CI: 1.4-19.4).\n\nA considerable number of MPNST samples display hypermethylation of the RASSF1A gene promoter, and for these tumors, this is the first molecular marker that if validated can characterize a subgroup of patients with inferior prognosis, restricted to individuals with NF1.", "doi": "10.1093/neuonc/nou140", "pmid": "25038505", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "nou140"}, {"db": "pmc", "key": "PMC4416132"}], "notes": [], "created": "2017-05-04T14:58:49.751Z", "modified": "2020-01-21T13:56:04.288Z"}, {"entity": "publication", "iuid": "bbad5325f0ff401b8c54f97df23d3c7f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbad5325f0ff401b8c54f97df23d3c7f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbad5325f0ff401b8c54f97df23d3c7f"}}, "title": "The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Hellwig", "given": "Birte", "initials": "B"}, {"family": "Rahnenf\u00fchrer", "given": "J\u00f6rg", "initials": "J"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Micke", "given": "Patrick", "initials": "P"}], "type": "journal article", "published": "2014-12-00", "journal": {"volume": "28", "issn": "1530-6860", "issue": "12", "pages": "5184-5196", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "The combined action of multiple cell types is essential for the physiological function of the lung, and increased awareness of the molecular constituents characterizing each cell type is likely to advance the understanding of lung biology and disease. In the current study, we used genome-wide RNA sequencing of normal lung parenchyma and 26 additional tissue types, combined with antibody-based protein profiling, to localize the expression to specific cell types. Altogether, 221 genes were found to be elevated in the lung compared with their expression in other analyzed tissues. Among the gene products were several well-known markers, but also several proteins previously not described in the context of the lung. To link the lung-specific molecular repertoire to human disease, survival associations of pneumocyte-specific genes were assessed by using transcriptomics data from 7 non-small-cell lung cancer (NSCLC) cohorts. Transcript levels of 10 genes (SFTPB, SFTPC, SFTPD, SLC34A2, LAMP3, CACNA2D2, AGER, EMP2, NKX2-1, and NAPSA) were significantly associated with survival in the adenocarcinoma subgroup, thus qualifying as promising biomarker candidates. In summary, based on an integrated omics approach, we identified genes with elevated expression in lung and localized corresponding protein expression to different cell types. As biomarker candidates, these proteins may represent intriguing starting points for further exploration in health and disease.", "doi": "10.1096/fj.14-254862", "pmid": "25169055", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": "Collaborative", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "fj.14-254862"}], "notes": [], "created": "2017-05-04T14:56:05.381Z", "modified": "2021-07-08T13:44:33.564Z"}, {"entity": "publication", "iuid": "458df4ee73f744acacec9c1c53c228e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/458df4ee73f744acacec9c1c53c228e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/458df4ee73f744acacec9c1c53c228e0"}}, "title": "Intragenic duplication--a novel causative mechanism for SATB2-associated syndrome.", "authors": [{"family": "Lied\u00e9n", "given": "Agne", "initials": "A"}, {"family": "Kvarnung", "given": "Malin", "initials": "M"}, {"family": "Nilssson", "given": "Daniel", "initials": "D"}, {"family": "Sahlin", "given": "Ellika", "initials": "E"}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES"}], "type": "case reports", "published": "2014-12-00", "journal": {"volume": "164A", "issn": "1552-4833", "issue": "12", "pages": "3083-3087", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Previous studies have shown that genetic aberrations involving the special AT-rich sequence-binding protein 2 (SATB2) gene result in a variable phenotype of syndromic intellectual disability. Although only a small number of patients have been described, there is already considerable variation in regard to the underlying molecular mechanism spanning from structural variation to point mutations. We here describe a male patient with intellectual disability, speech and language impairment, cleft palate, malformed teeth, and oligodontia. Array CGH analysis identified a small intragenic duplication in the SATB2 gene that included three coding exons. The result was confirmed by multiplex ligation-dependent probe amplification and low coverage whole genome mate pair sequencing. WGS breakpoint analysis directly confirmed the duplication as intragenic. This is the first reported patient with an intragenic duplication in SATB2 in combination with a phenotype that is highly similar to previously described patients with small deletions or point mutations of the same gene. Our findings expand the spectra of SATB2 mutations and confirm the presence of a distinct SATB2-phenotype with severe ID and speech impairment, cleft palate and/or high arched palate, and abnormalities of the teeth. For patients that present with this clinical picture, a high-resolution exon targeted array CGH and/or WGS, in addition to sequencing of SATB2, should be considered.", "doi": "10.1002/ajmg.a.36769", "pmid": "25251319", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:20.858Z", "modified": "2020-01-21T13:56:01.952Z"}, {"entity": "publication", "iuid": "5a11af22e4d444d8a889bcd3ba82960e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a11af22e4d444d8a889bcd3ba82960e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a11af22e4d444d8a889bcd3ba82960e"}}, "title": "Insights into conifer giga-genomes.", "authors": [{"family": "De La Torre", "given": "Amanda R", "initials": "AR"}, {"family": "Birol", "given": "Inanc", "initials": "I"}, {"family": "Bousquet", "given": "Jean", "initials": "J"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Jones", "given": "Steven J M", "initials": "SJ"}, {"family": "Keeling", "given": "Christopher I", "initials": "CI"}, {"family": "MacKay", "given": "John", "initials": "J"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Ritland", "given": "Kermit", "initials": "K"}, {"family": "Street", "given": "Nathaniel", "initials": "N"}, {"family": "Yanchuk", "given": "Alvin", "initials": "A"}, {"family": "Zerbe", "given": "Philipp", "initials": "P"}, {"family": "Bohlmann", "given": "J\u00f6rg", "initials": "J"}], "type": "journal article", "published": "2014-12-00", "journal": {"volume": "166", "issn": "1532-2548", "issue": "4", "pages": "1724-1732", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": "Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.", "doi": "10.1104/pp.114.248708", "pmid": "25349325", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "pp.114.248708"}, {"db": "pmc", "key": "PMC4256843"}], "notes": [], "created": "2017-05-04T14:58:52.471Z", "modified": "2020-01-21T13:56:02.449Z"}, {"entity": "publication", "iuid": "261ac269091849aea4d38ec3b5f86b13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/261ac269091849aea4d38ec3b5f86b13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/261ac269091849aea4d38ec3b5f86b13"}}, "title": "Donor or recipient origin of posttransplant lymphoproliferative disorders following solid organ transplantation.", "authors": [{"family": "Kinch", "given": "A", "initials": "A"}, {"family": "Cavelier", "given": "L", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Bengtsson", "given": "M", "initials": "M"}, {"family": "Baecklund", "given": "E", "initials": "E"}, {"family": "Enblad", "given": "G", "initials": "G"}, {"family": "Backlin", "given": "C", "initials": "C"}, {"family": "Thunberg", "given": "U", "initials": "U"}, {"family": "Sundstr\u00f6m", "given": "C", "initials": "C"}, {"family": "Pauksens", "given": "K", "initials": "K"}], "type": "comparative study", "published": "2014-12-00", "journal": {"volume": "14", "issn": "1600-6143", "issue": "12", "pages": "2838-2845", "title": "Am. J. Transplant.", "issn-l": "1600-6135"}, "abstract": "Previous studies of donor or recipient origin of posttransplant lymphoproliferative disorders (PTLDs) following solid organ transplantation (SOT) have either been small or with selected patient groups. We studied tumor origin in a population-based cohort of 93 patients with PTLD following SOT. Tumor origin of PTLD tissue was analyzed by fluorescence in situ hybridization of the sex chromosomes in cases of sex mismatch between donor and recipient (n = 41), or HLA genotyping in cases of identical sex but different HLA type (n = 52). Tumor origin of PTLD could be determined in 67 of the 93 cases. All 67 PTLDs were of recipient origin. They were found in recipients of kidney (n = 38), liver (n = 12), heart (n = 10) and lung (n = 7). The most common recipient-derived lymphomas were monomorphic B-cell PTLDs (n = 45), monomorphic T cell PTLDs (n = 9), indolent lymphomas (n = 6), and polymorphic PTLD (n = 4). Half of the recipient-derived PTLDs were Epstein-Barr virus-positive. Twelve of the recipient-derived PTLDs were located in the grafts: in four cases exclusively and in eight cases in combination with disseminated disease outside the graft. Tumor origin was indeterminable in 26 cases, probably due to low DNA quality. We conclude that the vast majority of PTLDs after SOT was of recipient origin.", "doi": "10.1111/ajt.12990", "pmid": "25307322", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:21.459Z", "modified": "2021-07-08T12:52:24.329Z"}, {"entity": "publication", "iuid": "25565c8cb6d2410bbf72e122aebc4349", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25565c8cb6d2410bbf72e122aebc4349.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25565c8cb6d2410bbf72e122aebc4349"}}, "title": "Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.", "authors": [{"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Bl\u00fcher", "given": "Matthias", "initials": "M"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2014-11-07", "journal": {"volume": "13", "issn": "1535-3907", "issue": "11", "pages": "5106-5119", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "White adipose tissue (WAT) has a major role in the progression of obesity. Here, we combined data from RNA-Seq and antibody-based immunohistochemistry to describe the normal physiology of human WAT obtained from three female subjects and explored WAT-specific genes by comparing WAT to 26 other major human tissues. Using the protein evidence in WAT, we validated the content of a genome-scale metabolic model for adipocytes. We employed this high-quality model for the analysis of subcutaneous adipose tissue (SAT) gene expression data obtained from subjects included in the Swedish Obese Subjects Sib Pair study to reveal molecular differences between lean and obese individuals. We integrated SAT gene expression and plasma metabolomics data, investigated the contribution of the metabolic differences in the mitochondria of SAT to the occurrence of obesity, and eventually identified cytosolic branched-chain amino acid (BCAA) transaminase 1 as a potential target that can be used for drug development. We observed decreased glutaminolysis and alterations in the BCAAs metabolism in SAT of obese subjects compared to lean subjects. We also provided mechanistic explanations for the changes in the plasma level of BCAAs, glutamate, pyruvate, and \u03b1-ketoglutarate in obese subjects. Finally, we validated a subset of our model-based predictions in 20 SAT samples obtained from 10 lean and 10 obese male and female subjects.", "doi": "10.1021/pr500586e", "pmid": "25219818", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:07.093Z", "modified": "2021-07-08T13:44:33.100Z"}, {"entity": "publication", "iuid": "dc442da430d445dc9fb4f880fea083a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc442da430d445dc9fb4f880fea083a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc442da430d445dc9fb4f880fea083a9"}}, "title": "Parallel barcoding of antibodies for DNA-assisted proteomics.", "authors": [{"family": "Dezfouli", "given": "Mahya", "initials": "M"}, {"family": "Vickovic", "given": "Sanja", "initials": "S"}, {"family": "Iglesias", "given": "Maria Jesus", "initials": "MJ"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "21-22", "pages": "2432-2436", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "DNA-assisted proteomics technologies enable ultra-sensitive measurements in multiplex format using DNA-barcoded affinity reagents. Although numerous antibodies are available, nowadays targeting nearly the complete human proteome, the majority is not accessible at the quantity, concentration, or purity recommended for most bio-conjugation protocols. Here, we introduce a magnetic bead-assisted DNA-barcoding approach, applicable for several antibodies in parallel, as well as reducing required reagents quantities up to a thousand-fold. The success of DNA-barcoding and retained functionality of antibodies were demonstrated in sandwich immunoassays and standard quantitative Immuno-PCR assays. Specific DNA-barcoding of antibodies for multiplex applications was presented on suspension bead arrays with read-out on a massively parallel sequencing platform in a procedure denoted Immuno-Sequencing. Conclusively, human plasma samples were analyzed to indicate the functionality of barcoded antibodies in intended proteomics applications.", "doi": "10.1002/pmic.201400215", "pmid": "25263329", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:59.241Z", "modified": "2021-07-08T12:07:34.293Z"}, {"entity": "publication", "iuid": "6823566564914c799633d71fcba88e93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6823566564914c799633d71fcba88e93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6823566564914c799633d71fcba88e93"}}, "title": "Human isolates of Listeria monocytogenes in Sweden during half a century (1958-2010).", "authors": [{"family": "Lopez-Valladares", "given": "G", "initials": "G"}, {"family": "Tham", "given": "W", "initials": "W"}, {"family": "Parihar", "given": "V Singh", "initials": "VS"}, {"family": "Helmersson", "given": "S", "initials": "S"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "Ivarsson", "given": "S", "initials": "S"}, {"family": "Johansson", "given": "C", "initials": "C"}, {"family": "Ringberg", "given": "H", "initials": "H"}, {"family": "Tjernberg", "given": "I", "initials": "I"}, {"family": "Henriques-Normark", "given": "B", "initials": "B"}, {"family": "Danielsson-Tham", "given": "M-L", "initials": "ML"}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "142", "issn": "1469-4409", "issue": "11", "pages": "2251-2260", "title": "Epidemiol. Infect.", "issn-l": "0950-2688"}, "abstract": "Isolates of Listeria monocytogenes (n = 932) isolated in Sweden during 1958-2010 from human patients with invasive listeriosis were characterized by serotyping and pulsed-field gel electrophoresis (PFGE) (AscI). Of the 932 isolates, 183 different PFGE types were identified, of which 83 were each represented by only one isolate. In all, 483 serovar 1/2a isolates were distributed over 114 PFGE types; 90 serovar 1/2b isolates gave 32 PFGE types; 21 serovar 1/2c isolates gave nine PFGE types; three serovar 3b isolates gave one PFGE type; and, 335 serovar 4b isolates gave 31 PFGE types. During the 1980s in Sweden, several serovar 4b cases were associated with the consumption of European raw soft cheese. However, as cheese-production hygiene has improved, the number of 4b cases has decreased. Since 1996, serovar 1/2a has been the dominant L. monocytogenes serovar in human listeriosis in Sweden. Therefore, based on current serovars and PFGE types, an association between human cases of listeriosis and the consumption of vacuum-packed gravad and cold-smoked salmon is suggested.", "doi": "10.1017/S0950268813003385", "pmid": "24480252", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0950268813003385"}], "notes": [], "created": "2017-05-04T14:58:32.055Z", "modified": "2020-01-21T13:56:02.780Z"}, {"entity": "publication", "iuid": "1c365767e47244718692e25210b4b6a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c365767e47244718692e25210b4b6a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c365767e47244718692e25210b4b6a0"}}, "title": "Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance.", "authors": [{"family": "Kildegaard", "given": "Kanchana R", "initials": "KR"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Blicher", "given": "Thomas H", "initials": "TH"}, {"family": "Sonnenschein", "given": "Nikolaus", "initials": "N"}, {"family": "Jensen", "given": "Niels B", "initials": "NB"}, {"family": "Sherstyk", "given": "Svetlana", "initials": "S"}, {"family": "Harrison", "given": "Scott J", "initials": "SJ"}, {"family": "Maury", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Herrg\u00e5rd", "given": "Markus J", "initials": "MJ"}, {"family": "Juncker", "given": "Agnieszka S", "initials": "AS"}, {"family": "Forster", "given": "Jochen", "initials": "J"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Borodina", "given": "Irina", "initials": "I"}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "26", "issn": "1096-7184", "issue": null, "pages": "57-66", "title": "Metab. Eng.", "issn-l": "1096-7176"}, "abstract": "Biologically produced 3-hydroxypropionic acid (3 HP) is a potential source for sustainable acrylates and can also find direct use as monomer in the production of biodegradable polymers. For industrial-scale production there is a need for robust cell factories tolerant to high concentration of 3 HP, preferably at low pH. Through adaptive laboratory evolution we selected S. cerevisiae strains with improved tolerance to 3 HP at pH 3.5. Genome sequencing followed by functional analysis identified the causal mutation in SFA1 gene encoding S-(hydroxymethyl)glutathione dehydrogenase. Based on our findings, we propose that 3 HP toxicity is mediated by 3-hydroxypropionic aldehyde (reuterin) and that glutathione-dependent reactions are used for reuterin detoxification. The identified molecular response to 3 HP and reuterin may well be a general mechanism for handling resistance to organic acid and aldehydes by living cells.", "doi": "10.1016/j.ymben.2014.09.004", "pmid": "25263954", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(14)00118-9"}], "notes": [], "created": "2017-05-04T14:58:43.697Z", "modified": "2020-01-21T13:56:00.973Z"}, {"entity": "publication", "iuid": "9b8a235e5dbf47648b747e04e2210661", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b8a235e5dbf47648b747e04e2210661.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b8a235e5dbf47648b747e04e2210661"}}, "title": "Defining the human gallbladder proteome by transcriptomics and affinity proteomics.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Danielsson", "given": "Angelika", "initials": "A"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "14", "issn": "1615-9861", "issue": "21-22", "pages": "2498-2507", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics.", "doi": "10.1002/pmic.201400201", "pmid": "25175928", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:56:10.318Z", "modified": "2021-07-08T13:44:33.470Z"}, {"entity": "publication", "iuid": "240b01df3ecd41839a7f60dee2613881", "links": {"self": {"href": "https://publications.scilifelab.se/publication/240b01df3ecd41839a7f60dee2613881.json"}, "display": {"href": "https://publications.scilifelab.se/publication/240b01df3ecd41839a7f60dee2613881"}}, "title": "Bcl-2 maintains the mitochondrial membrane potential, but fails to affect production of reactive oxygen species and endoplasmic reticulum stress, in sodium palmitate-induced \u03b2-cell death.", "authors": [{"family": "Wang", "given": "Xuan", "initials": "X"}, {"family": "Welsh", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2014-11-00", "journal": {"volume": "119", "issn": "2000-1967", "issue": "4", "pages": "306-315", "title": "Ups. J. Med. Sci.", "issn-l": "0300-9734"}, "abstract": "Sodium palmitate causes apoptosis of \u03b2-cells, and the anti-apoptotic protein Bcl-2 has been shown to counteract this event. However, the exact mechanisms that underlie palmitate-induced pancreatic \u03b2-cell apoptosis and through which pathway Bcl-2 executes the protective effect are still unclear.\n\nA stable Bcl-2-overexpressing RINm5F cell clone (BMG) and its negative control (B45) were exposed to palmitate for up to 8 h, and cell viability, mitochondrial membrane potential (\u0394\u03c8m), reactive oxygen species (ROS) generation, endoplasmic reticulum (ER) stress, and NF-\u03baB activation were studied in time course experiments.\n\nPalmitate exposure for 8 h resulted in increased cell death rates, and this event was partially counteracted by Bcl-2. Bcl-2 overexpression promoted in parallel also a delayed induction of GADD153/CHOP and a weaker phosphorylation of BimEL in palmitate-exposed cells. At earlier time points (2-4 h) palmitate exposure resulted in increased generation of ROS, a decrease in mitochondrial membrane potential (\u0394\u03c8m), and a modest increase in the phosphorylation of eIF2\u03b1 and IRE1\u03b1. BMG cells produced similar amounts of ROS and displayed the same eIF2\u03b1 and IRE1\u03b1 phosphorylation rates as B45 cells. However, the palmitate-induced dissipation of \u0394\u03c8m was partially counteracted by Bcl-2. In addition, basal NF-\u03baB activity was increased in BMG cells.\n\nOur results indicate that Bcl-2 counteracts palmitate-induced \u03b2-cell death by maintaining mitochondrial membrane integrity and augmenting NF-\u03baB activity, but not by affecting ROS production and ER stress.", "doi": "10.3109/03009734.2014.962714", "pmid": "25266628", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4248070"}], "notes": [], "created": "2017-05-04T14:59:02.294Z", "modified": "2020-01-21T13:56:01.087Z"}, {"entity": "publication", "iuid": "3e73a61ab5cb4580b0781e7ae5f43ab5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e73a61ab5cb4580b0781e7ae5f43ab5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e73a61ab5cb4580b0781e7ae5f43ab5"}}, "title": "Populus tremula (European aspen) shows no evidence of sexual dimorphism.", "authors": [{"family": "Robinson", "given": "Kathryn M", "initials": "KM"}, {"family": "Delhomme", "given": "Nicolas", "initials": "N"}, {"family": "M\u00e4hler", "given": "Niklas", "initials": "N"}, {"family": "Schiffthaler", "given": "Bastian", "initials": "B"}, {"family": "Onskog", "given": "Jenny", "initials": "J"}, {"family": "Albrectsen", "given": "Benedicte R", "initials": "BR"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR"}], "type": "journal article", "published": "2014-10-16", "journal": {"volume": "14", "issn": "1471-2229", "issue": null, "pages": "276", "title": "BMC Plant Biol.", "issn-l": "1471-2229"}, "abstract": "Evolutionary theory suggests that males and females may evolve sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximise reproductive success and fitness. Such sexual dimorphism would result in sex biased gene expression patterns in non-floral organs for autosomal genes associated with the control and development of such phenotypic traits.\n\nWe examined morphological, biochemical and herbivory traits to test for sexually dimorphic resource allocation strategies within collections of sexually mature and immature Populus tremula (European aspen) trees. In addition we profiled gene expression in mature leaves of sexually mature wild trees using whole-genome oligonucleotide microarrays and RNA-Sequencing.\n\nWe found no evidence of sexual dimorphism or differential resource investment strategies between males and females in either sexually immature or mature trees. Similarly, single-gene differential expression and machine learning approaches revealed no evidence of large-scale sex biased gene expression. However, two significantly differentially expressed genes were identified from the RNA-Seq data, one of which is a robust diagnostic marker of sex in P. tremula.", "doi": "10.1186/s12870-014-0276-5", "pmid": "25318822", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "s12870-014-0276-5"}, {"db": "pmc", "key": "PMC4203875"}], "notes": [], "created": "2017-05-04T14:58:25.850Z", "modified": "2020-01-21T13:56:01.801Z"}, {"entity": "publication", "iuid": "d4e691ae21f24d34be4163a90b5205df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4e691ae21f24d34be4163a90b5205df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4e691ae21f24d34be4163a90b5205df"}}, "title": "Human genetic evidence for involvement of CD137 in atherosclerosis.", "authors": [{"family": "S\u00f6derstr\u00f6m", "given": "Leif \u00c5", "initials": "L\u00c5"}, {"family": "Gertow", "given": "Karl", "initials": "K"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Sundman", "given": "Eva", "initials": "E"}, {"family": "Sheikine", "given": "Yuri", "initials": "Y"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hansson", "given": "G\u00f6ran K", "initials": "GK"}, {"family": "Olofsson", "given": "Peder S", "initials": "PS"}], "type": "journal article", "published": "2014-10-14", "journal": {"volume": "20", "issn": "1528-3658", "issue": null, "pages": "456-465", "title": "Mol. Med.", "issn-l": "1076-1551"}, "abstract": "Atherosclerosis is an inflammatory disease and the main cause of cardiovascular disease. Inflammation promotes plaque instability and clinical disease, such as myocardial infarction, stroke and peripheral vascular disease. Subclinical atherosclerosis begins with thickening of the arterial intimal layer, and increased intima-media thickness (IMT) in the carotid artery is a widely used measurement of subclinical atherosclerosis. Activation of CD137 (tumor necrosis factor receptor super family 9) promotes inflammation and disease development in murine atherosclerosis. CD137 is expressed in human atherosclerosis, but its role is largely unknown. This study uses a genetic approach to investigate CD137 in human atherosclerotic disease. In publicly available data on genotype and gene expression from the HapMap project, the minor T allele of rs2453021, a single nucleotide polymorphism in CD137, was significantly associated with CD137 gene expression. In the PROCARDIS and Wellcome Trust Case Control Consortium (WTCCC) cohorts of 13,029 cases and controls, no significant association was detected between the minor T allele of rs2453021 and risk for coronary artery disease or myocardial infarction. However, in the IMPROVE multicenter study of 3,418 individuals, the minor T allele of rs2453021 was associated with increased IMT of the common carotid artery (CCA), as measured by ultrasonography, with presence of plaque in CCA and with increased incidence of adverse noncardiac vascular events. Taken together, this study shows that the minor T allele of rs2453021 is associated with increased IMT in the CCA and increased risk of incident noncardiac vascular events, thus providing the first human genetic evidence for involvement of CD137 in atherosclerosis.", "doi": "10.2119/molmed.2014.00004", "pmid": "25032953", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "molmed.2014.00004"}, {"db": "pmc", "key": "PMC4212009"}], "notes": [], "created": "2017-05-04T14:58:45.887Z", "modified": "2020-01-21T13:56:05.431Z"}, {"entity": "publication", "iuid": "3b9762e83afa4069aa1df0598e66bb9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b9762e83afa4069aa1df0598e66bb9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b9762e83afa4069aa1df0598e66bb9c"}}, "title": "Gene and protein expression and cellular localisation of cytochrome P450 enzymes of the 1A, 2A, 2C, 2D and 2E subfamilies in equine intestine and liver.", "authors": [{"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Tj\u00e4lve", "given": "Hans", "initials": "H"}, {"family": "Larsson", "given": "Pia", "initials": "P"}], "type": "journal article", "published": "2014-10-08", "journal": {"volume": "56", "issn": "1751-0147", "issue": null, "pages": "69", "title": "Acta Vet. Scand.", "issn-l": "0044-605X"}, "abstract": "Among the cytochrome P450 enzymes (CYP), families 1-3 constitute almost half of total CYPs in mammals and play a central role in metabolism of a wide range of pharmaceuticals. This study investigated gene and protein expression and cellular localisation of CYP1A, CYP2A, CYP2C, CYP2D and CYP2E in equine intestine and liver. Real-time polymerase chain reaction (RT-PCR) was used to analyse gene expression, western blot to examine protein expression and immunohistochemical analyses to investigate cellular localisation.\n\nCYP1A and CYP2C were the CYPs with the highest gene expression in the intestine and also showed considerable gene expression in the liver. CYP2E and CYP2A showed the highest gene expression in the liver. CYP2E showed moderate intestinal gene expression, whereas that of CYP2A was very low or undetectable. For CYP2D, rather low gene expression levels were found in both intestine and the liver. In the intestine, CYP gene expression levels, except for CYP2E, exhibited patterns resembling those of the proteins, indicating that intestinal protein expression of these CYPs is regulated at the transcriptional level. For CYP2E, the results showed that the intestinal gene expression did not correlate to any visible protein expression, indicating that intestinal protein expression of this CYP is regulated at the post-transcriptional level. Immunostaining of intestine tissue samples showed preferential CYP staining in enterocytes at the tips of intestinal villi in the small intestine. In the liver, all CYPs showed preferential localisation in the centrilobular hepatocytes.\n\nOverall, different gene expression profiles were displayed by the CYPs examined in equine intestine and liver. The CYPs present in the intestine may act in concert with those in the liver to affect the oral bioavailability and therapeutic efficiency of substrate drugs. In addition, they may play a role in first-pass metabolism of feed constituents and of herbal supplements used in equine practice.", "doi": "10.1186/s13028-014-0069-8", "pmid": "25288196", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "s13028-014-0069-8"}, {"db": "pmc", "key": "PMC4192735"}], "notes": [], "created": "2017-05-04T14:58:19.296Z", "modified": "2021-07-08T12:42:24.817Z"}, {"entity": "publication", "iuid": "e7fdd93b68014f678a50df6f5e15f1c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7fdd93b68014f678a50df6f5e15f1c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7fdd93b68014f678a50df6f5e15f1c8"}}, "title": "Biofuels. Altered sterol composition renders yeast thermotolerant.", "authors": [{"family": "Caspeta", "given": "Luis", "initials": "L"}, {"family": "Chen", "given": "Yun", "initials": "Y"}, {"family": "Ghiaci", "given": "Payam", "initials": "P"}, {"family": "Feizi", "given": "Amir", "initials": "A"}, {"family": "Buskov", "given": "Steen", "initials": "S"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Petranovic", "given": "Dina", "initials": "D"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2014-10-03", "journal": {"volume": "346", "issn": "1095-9203", "issue": "6205", "pages": "75-78", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Ethanol production for use as a biofuel is mainly achieved through simultaneous saccharification and fermentation by yeast. Operating at \u226540\u00b0C would be beneficial in terms of increasing efficiency of the process and reducing costs, but yeast does not grow efficiently at those temperatures. We used adaptive laboratory evolution to select yeast strains with improved growth and ethanol production at \u226540\u00b0C. Sequencing of the whole genome, genome-wide gene expression, and metabolic-flux analyses revealed a change in sterol composition, from ergosterol to fecosterol, caused by mutations in the C-5 sterol desaturase gene, and increased expression of genes involved in sterol biosynthesis. Additionally, large chromosome III rearrangements and mutations in genes associated with DNA damage and respiration were found, but contributed less to the thermotolerant phenotype.", "doi": "10.1126/science.1258137", "pmid": "25278608", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "346/6205/75"}], "notes": [], "created": "2017-05-04T14:59:00.281Z", "modified": "2021-07-05T13:05:37.773Z"}, {"entity": "publication", "iuid": "94d3712cade249a88d3516300c703c0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94d3712cade249a88d3516300c703c0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94d3712cade249a88d3516300c703c0b"}}, "title": "Uneven distribution of human papillomavirus 16 in cervical carcinoma in situ and squamous cell carcinoma in older females: A retrospective database study.", "authors": [{"family": "Andersson", "given": "Sonia", "initials": "S"}, {"family": "Mints", "given": "Miriam", "initials": "M"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Lindell", "given": "Monica", "initials": "M"}, {"family": "Gustavsson", "given": "Inger", "initials": "I"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Wilander", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2014-10-00", "journal": {"volume": "8", "issn": "1792-1074", "issue": "4", "pages": "1528-1532", "title": "Oncol Lett", "issn-l": null}, "abstract": "Human papillomavirus (HPV) 16 is the dominant cofactor in cervical cancer development. The present report investigated the age-specific prevalence of HPV16 in cervical carcinoma in situ (CIS) in females attending organised cervical cancer screening. A retrospective observational study was performed based on individual data from two databases. A total of 162 females aged between 20 and 65 years from Uppsala County, Sweden with CIS and an HPV test conducted between 2010 and 2011, preceding or concomitant to CIS diagnosis, were included. Females with cervical squamous cell carcinoma (SCC; n=35) were used for comparison. In total, 96% (n=156) of females with CIS were positive for high-risk HPV; HPV16 was the most prevalent (44.5%), followed by HPV33/52/58 (19.5%), HPV31 (13.1%) and HPV18/45 (9.5%). HPV16 was most frequently detected in females with CIS aged between 20 and 29 years (73.6%) and least frequently detected in those aged between 50 and 65 years (33.3%), with a statistically significant age-specific difference (P=0.001). Among the HPV16-positive females, multiple infections were most frequent in the younger age groups. The prevalence of HPV16 in females with CIS decreased with age, whereas a high prevalence of HPV16 remained in females with SCC. These results may indicate that HPV16 has increased oncogenic potential in older females.", "doi": "10.3892/ol.2014.2347", "pmid": "25202362", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ol-08-04-1528"}, {"db": "pmc", "key": "PMC4156228"}], "notes": [], "created": "2017-05-04T14:58:50.657Z", "modified": "2020-01-21T13:56:03.819Z"}, {"entity": "publication", "iuid": "7fe35d59e4924630ba693512252052c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7fe35d59e4924630ba693512252052c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7fe35d59e4924630ba693512252052c4"}}, "title": "The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters.", "authors": [{"family": "J\u00e4derkvist", "given": "K", "initials": "K"}, {"family": "Andersson", "given": "L S", "initials": "LS"}, {"family": "Johansson", "given": "A M", "initials": "AM"}, {"family": "\u00c1rnason", "given": "T", "initials": "T"}, {"family": "Mikko", "given": "S", "initials": "S"}, {"family": "Eriksson", "given": "S", "initials": "S"}, {"family": "Andersson", "given": "L", "initials": "L"}, {"family": "Lindgren", "given": "G", "initials": "G"}], "type": "journal article", "published": "2014-10-00", "journal": {"volume": "92", "issn": "1525-3163", "issue": "10", "pages": "4279-4286", "title": "J. Anim. Sci.", "issn-l": "0021-8812"}, "abstract": "In a previous study it was shown that a nonsense mutation in the DMRT3 gene alters the pattern of locomotion in horses and that this mutation has a strong positive impact on trotting performance of Standardbreds. One aim of this study was to test if racing performance and trotting technique in the Nordic (Coldblood) trotters are also influenced by the DMRT3 genotype. Another aim was to further investigate the effect of the mutation on performance in Standardbreds, by using a within-family analysis and genotype-phenotype correlations in a larger horse material than in the previous study. We genotyped 427 Nordic trotters and 621 Standardbreds for the DMRT3 nonsense mutation and a SNP in strong linkage disequilibrium with it. In Nordic trotters, we show that horses homozygous for the DMRT3 mutation (A) had significantly higher EBV for trotting performance traits than heterozygous (CA) or homozygous wild-type (CC) horses (P = 0.001). Furthermore, AA homozygotes had a higher proportion of victories and top 3 placings than horses heterozygous or homozygous wild-type, when analyzing performance data for the period 3 to 6 yr of age (P = 0.06 and P = 0.05, respectively). Another finding in the Nordic trotters was that the DMRT3 mutation influenced trotting technique (P = 2.1 \u00d7 10(-8)). Standardbred horses homozygous AA had significantly higher EBV for all traits than horses with at least 1 wild-type allele (CA and CC; P = 1.6 \u00d7 10(-16)). In a within-family analysis of Standardbreds, we found significant differences in several traits (e.g., earnings, P = 0.002; number of entered races, P = 0.004; and fraction of offspring that entered races, P = 0.002) among paternal half-sibs with genotype AA or CA sired by a CA stallion. For most traits, we found significant differences at young ages. For Nordic trotters, most of the results were significant at 3 yr of age but not for the older ages, and for the Standardbreds most of the results for the ages 3 to 5 were significant. For Nordic trotters, the proportion of victories and placings were the only traits that were significant for other ages than 3 yr.", "doi": "10.2527/jas.2014-7803", "pmid": "25085403", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "jas.2014-7803"}], "notes": [], "created": "2017-05-04T14:58:40.685Z", "modified": "2020-01-21T13:56:03.328Z"}, {"entity": "publication", "iuid": "69bb921def2c4aa6b78aa0d459151bb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69bb921def2c4aa6b78aa0d459151bb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69bb921def2c4aa6b78aa0d459151bb4"}}, "title": "Signals that regulate the oncogenic fate of neural stem cells and progenitors.", "authors": [{"family": "Swartling", "given": "Fredrik J", "initials": "FJ"}, {"family": "Bolin", "given": "Sara", "initials": "S"}, {"family": "Phillips", "given": "Joanna J", "initials": "JJ"}, {"family": "Persson", "given": "Anders I", "initials": "AI"}], "type": "journal article", "published": "2014-10-00", "journal": {"volume": "260", "issn": "1090-2430", "issue": null, "pages": "56-68", "title": "Exp. Neurol.", "issn-l": "0014-4886"}, "abstract": "Brain tumors have frequently been associated with a neural stem cell (NSC) origin and contain stem-like tumor cells, so-called brain tumor stem cells (BTSCs) that share many features with normal NSCs. A stem cell state of BTSCs confers resistance to radiotherapy and treatment with alkylating agents. It is also a hallmark of aggressive brain tumors and is maintained by transcriptional networks that are also active in embryonic stem cells. Advances in reprogramming of somatic cells into induced pluripotent stem (iPS) cells have further identified genes that drive stemness. In this review, we will highlight the possible drivers of stemness in medulloblastoma and glioma, the most frequent types of primary malignant brain cancer in children and adults, respectively. Signals that drive expansion of developmentally defined neural precursor cells are also active in corresponding brain tumors. Transcriptomal subgroups of human medulloblastoma and glioma match features of NSCs but also more restricted progenitors. Lessons from genetically-engineered mouse (GEM) models show that temporally and regionally defined NSCs can give rise to distinct subgroups of medulloblastoma and glioma. We will further discuss how acquisition of stem cell features may drive brain tumorigenesis from a non-NSC origin. Genetic alterations, signaling pathways, and therapy-induced changes in the tumor microenvironment can drive reprogramming networks and induce stemness in brain tumors. Finally, we propose a model where dysregulation of microRNAs (miRNAs) that normally provide barriers against reprogramming plays an integral role in promoting stemness in brain tumors.", "doi": "10.1016/j.expneurol.2013.01.027", "pmid": "23376224", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0014-4886(13)00040-X"}, {"db": "pmc", "key": "PMC3758390"}, {"db": "mid", "key": "NIHMS441682"}], "notes": [], "created": "2017-05-04T14:58:33.271Z", "modified": "2020-01-21T13:56:02.799Z"}, {"entity": "publication", "iuid": "d027212b436046778a1d7ebf768467f8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d027212b436046778a1d7ebf768467f8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d027212b436046778a1d7ebf768467f8"}}, "title": "The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.", "authors": [{"family": "Kutsenko", "given": "Alexey", "initials": "A"}, {"family": "Svensson", "given": "Thomas", "initials": "T", "orcid": "0000-0002-9190-2979", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc636683ece84dc4ac3e4d10df0c7a49.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Bj\u00f6rk", "given": "Petra", "initials": "P"}, {"family": "Sonnhammer", "given": "Erik", "initials": "E"}, {"family": "Giacomello", "given": "Stefania", "initials": "S"}, {"family": "Visa", "given": "Neus", "initials": "N"}, {"family": "Wieslander", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2014-09-27", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "819", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.\n\nThe genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150-250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.\n\nWe show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.", "doi": "10.1186/1471-2164-15-819", "pmid": "25261295", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-819"}, {"db": "pmc", "key": "PMC4192438"}], "notes": [], "created": "2017-05-04T14:58:24.735Z", "modified": "2021-07-08T13:26:08.361Z"}, {"entity": "publication", "iuid": "2fd7f79d375e43e2ae520bccb4d57b8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fd7f79d375e43e2ae520bccb4d57b8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fd7f79d375e43e2ae520bccb4d57b8a"}}, "title": "Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.", "authors": [{"family": "Skarin", "given": "Hanna", "initials": "H"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2014-09-25", "journal": {"volume": "9", "issn": "1932-6203", "issue": "9", "pages": "e107777", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Clostridium botulinum (group III), Clostridium novyi and Clostridium haemolyticum are well-known pathogens causing animal botulism, gas gangrene/black disease, and bacillary hemoglobinuria, respectively. A close genetic relationship exists between the species, which has resulted in the collective term C. novyi sensu lato. The pathogenic traits in these species, e.g., the botulinum neurotoxin and the novyi alpha toxin, are mainly linked to a large plasmidome consisting of plasmids and circular prophages. The plasmidome of C. novyi sensu lato has so far been poorly characterized. In this study we explored the genomic relationship of a wide range of strains of C. novyi sensu lato with a special focus on the dynamics of the plasmidome. Twenty-four genomes were sequenced from strains selected to represent as much as possible the genetic diversity in C. novyi sensu lato. Sixty-one plasmids were identified in these genomes and 28 of them were completed. The genomic comparisons revealed four separate lineages, which did not strictly correlate with the species designations. The plasmids were categorized into 13 different plasmid groups on the basis of their similarity and conservation of plasmid replication or partitioning genes. The plasmid groups, lineages and species were to a large extent entwined because plasmids and toxin genes had moved across the lineage boundaries. This dynamic process appears to be primarily driven by phages. We here present a comprehensive characterization of the complex species group C. novyi sensu lato, explaining the intermixed genetic properties. This study also provides examples how the reorganization of the botulinum toxin and the novyi alpha toxin genes within the plasmidome has affected the pathogenesis of the strains.", "doi": "10.1371/journal.pone.0107777", "pmid": "25254374", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-11225"}, {"db": "pmc", "key": "PMC4177856"}], "notes": [], "created": "2017-05-04T14:58:58.122Z", "modified": "2020-01-21T13:56:01.326Z"}, {"entity": "publication", "iuid": "f8d98b5701f9453384e18ca97f67e393", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f8d98b5701f9453384e18ca97f67e393.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f8d98b5701f9453384e18ca97f67e393"}}, "title": "Oncoprotein stabilization in brain tumors.", "authors": [{"family": "Hede", "given": "S-M", "initials": "SM"}, {"family": "Savov", "given": "V", "initials": "V"}, {"family": "Weishaupt", "given": "H", "initials": "H"}, {"family": "Sangfelt", "given": "O", "initials": "O"}, {"family": "Swartling", "given": "F J", "initials": "FJ"}], "type": "journal article", "published": "2014-09-25", "journal": {"volume": "33", "issn": "1476-5594", "issue": "39", "pages": "4709-4721", "title": "Oncogene", "issn-l": "0950-9232"}, "abstract": "Proteins involved in promoting cell proliferation and viability need to be timely expressed and carefully controlled for the proper development of the brain but also efficiently degraded in order to prevent cells from becoming brain cancer cells. A major pathway for targeted protein degradation in cells is the ubiquitin-proteasome system (UPS). Oncoproteins that drive tumor development and tumor maintenance are often deregulated and stabilized in malignant cells. This can occur when oncoproteins escape degradation by the UPS because of mutations in either the oncoprotein itself or in the UPS components responsible for recognition and ubiquitylation of the oncoprotein. As the pathogenic accumulation of an oncoprotein can lead to effectively sustained cell growth, viability and tumor progression, it is an indisputable target for cancer treatment. The most common types of malignant brain tumors in children and adults are medulloblastoma and glioma, respectively. Here, we review different ways of how deregulated proteolysis of oncoproteins involved in major signaling cancer pathways contributes to medulloblastoma and glioma development. We also describe means of targeting relevant oncoproteins in brain tumors with treatments affecting their stability or therapeutic strategies directed against the UPS itself.", "doi": "10.1038/onc.2013.445", "pmid": "24166497", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "onc2013445"}], "notes": [], "created": "2017-05-04T14:58:50.357Z", "modified": "2020-01-21T13:56:06.423Z"}, {"entity": "publication", "iuid": "ec9a4e98da2445e2b76c2a3e03754045", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec9a4e98da2445e2b76c2a3e03754045.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec9a4e98da2445e2b76c2a3e03754045"}}, "title": "Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.", "authors": [{"family": "Ghoussaini", "given": "Maya", "initials": "M"}, {"family": "Edwards", "given": "Stacey L", "initials": "SL"}, {"family": "Michailidou", "given": "Kyriaki", "initials": "K"}, {"family": "Nord", "given": "Silje", "initials": "S"}, {"family": "Cowper-Sal Lari", "given": "Richard", "initials": "R"}, {"family": "Desai", "given": "Kinjal", "initials": "K"}, {"family": "Kar", "given": "Siddhartha", "initials": "S"}, {"family": "Hillman", "given": "Kristine M", "initials": "KM"}, {"family": "Kaufmann", "given": "Susanne", "initials": "S"}, {"family": "Glubb", "given": "Dylan M", "initials": "DM"}, {"family": "Beesley", "given": "Jonathan", "initials": "J"}, {"family": "Dennis", "given": "Joe", "initials": "J"}, {"family": "Bolla", "given": "Manjeet K", "initials": "MK"}, {"family": "Wang", "given": "Qin", "initials": "Q"}, {"family": "Dicks", "given": "Ed", "initials": "E"}, {"family": "Guo", "given": "Qi", "initials": "Q"}, {"family": "Schmidt", "given": "Marjanka K", "initials": "MK"}, {"family": "Shah", "given": "Mitul", "initials": "M"}, {"family": "Luben", "given": "Robert", "initials": "R"}, {"family": "Brown", "given": "Judith", "initials": "J"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Darabi", "given": "Hatef", "initials": "H"}, {"family": "Eriksson", "given": "Mikael", "initials": "M"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Bojesen", "given": "Stig E", "initials": "SE"}, {"family": "Nordestgaard", "given": "B\u00f8rge G", "initials": "BG"}, {"family": "Nielsen", "given": "Sune F", "initials": "SF"}, {"family": "Flyger", "given": "Henrik", "initials": "H"}, {"family": "Lambrechts", "given": "Diether", "initials": "D"}, {"family": "Thienpont", "given": "Bernard", "initials": "B"}, {"family": "Neven", "given": "Patrick", "initials": "P"}, {"family": "Wildiers", "given": "Hans", "initials": "H"}, {"family": "Broeks", "given": "Annegien", "initials": "A"}, {"family": "Van't Veer", "given": "Laura J", "initials": "LJ"}, {"family": "Th Rutgers", "given": "Emiel J", "initials": "EJ"}, {"family": "Couch", "given": "Fergus J", "initials": "FJ"}, {"family": "Olson", "given": "Janet E", "initials": "JE"}, {"family": "Hallberg", "given": "Emily", "initials": "E"}, {"family": "Vachon", "given": "Celine", "initials": "C"}, {"family": "Chang-Claude", "given": "Jenny", "initials": "J"}, {"family": "Rudolph", "given": "Anja", "initials": "A"}, {"family": "Seibold", "given": "Petra", "initials": "P"}, {"family": "Flesch-Janys", "given": "Dieter", "initials": "D"}, {"family": "Peto", "given": "Julian", "initials": "J"}, {"family": "Dos-Santos-Silva", "given": "Isabel", "initials": "I"}, {"family": "Gibson", "given": "Lorna", "initials": "L"}, {"family": "Nevanlinna", "given": "Heli", "initials": "H"}, {"family": "Muranen", "given": "Taru A", "initials": "TA"}, {"family": "Aittom\u00e4ki", "given": "Kristiina", "initials": "K"}, {"family": "Blomqvist", "given": "Carl", "initials": "C"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Li", "given": "Jingmei", "initials": "J"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Kang", "given": "Daehee", "initials": "D"}, {"family": "Choi", "given": "Ji-Yeob", "initials": "JY"}, {"family": "Park", "given": "Sue K", "initials": "SK"}, {"family": "Noh", "given": "Dong-Young", "initials": "DY"}, {"family": "Matsuo", "given": "Keitaro", "initials": "K"}, {"family": "Ito", "given": "Hidemi", "initials": "H"}, {"family": "Iwata", "given": "Hiroji", "initials": "H"}, {"family": "Yatabe", "given": "Yasushi", "initials": "Y"}, {"family": "Gu\u00e9nel", "given": "Pascal", "initials": "P"}, {"family": "Truong", "given": "Th\u00e9r\u00e8se", "initials": "T"}, {"family": "Menegaux", "given": "Florence", "initials": "F"}, {"family": "Sanchez", "given": "Marie", "initials": "M"}, {"family": "Burwinkel", "given": "Barbara", "initials": "B"}, {"family": "Marme", "given": "Frederik", "initials": "F"}, {"family": "Schneeweiss", "given": "Andreas", "initials": "A"}, {"family": "Sohn", "given": "Christof", "initials": "C"}, {"family": "Wu", "given": "Anna H", "initials": "AH"}, {"family": "Tseng", "given": "Chiu-Chen", "initials": "CC"}, {"family": "Van Den Berg", "given": "David", "initials": "D"}, {"family": "Stram", "given": "Daniel O", "initials": "DO"}, {"family": "Benitez", "given": "Javier", "initials": "J"}, {"family": "Zamora", "given": "M Pilar", "initials": "MP"}, {"family": "Perez", "given": "Jose Ignacio Arias", "initials": "JI"}, {"family": "Men\u00e9ndez", "given": "Primitiva", "initials": "P"}, {"family": "Shu", "given": "Xiao-Ou", "initials": "XO"}, {"family": "Lu", "given": "Wei", "initials": "W"}, {"family": "Gao", "given": "Yu-Tang", "initials": "YT"}, {"family": "Cai", "given": "Qiuyin", "initials": "Q"}, {"family": "Cox", "given": "Angela", "initials": "A"}, {"family": "Cross", "given": "Simon S", "initials": "SS"}, {"family": "Reed", "given": "Malcolm W R", "initials": "MW"}, {"family": "Andrulis", "given": "Irene L", "initials": "IL"}, {"family": "Knight", "given": "Julia A", "initials": "JA"}, {"family": "Glendon", "given": "Gord", "initials": "G"}, {"family": "Tchatchou", "given": "Sandrine", "initials": "S"}, {"family": "Sawyer", "given": "Elinor J", "initials": "EJ"}, {"family": "Tomlinson", "given": "Ian", "initials": "I"}, {"family": "Kerin", "given": "Michael J", "initials": "MJ"}, {"family": "Miller", "given": "Nicola", "initials": "N"}, {"family": "Haiman", "given": "Christopher A", "initials": "CA"}, {"family": "Henderson", "given": "Brian E", "initials": "BE"}, {"family": "Schumacher", "given": "Fredrick", "initials": "F"}, {"family": "Le Marchand", "given": "Loic", "initials": "L"}, {"family": "Lindblom", "given": "Annika", "initials": "A"}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Teo", "given": "Soo Hwang", "initials": "SH"}, {"family": "Yip", "given": "Cheng Har", "initials": "CH"}, {"family": "Lee", "given": "Daphne S C", "initials": "DS"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Hooning", "given": "Maartje J", "initials": "MJ"}, {"family": "Martens", "given": "John W M", "initials": "JW"}, {"family": "Coll\u00e9e", "given": "J Margriet", "initials": "JM"}, {"family": "van Deurzen", "given": "Carolien H M", "initials": "CH"}, {"family": "Hopper", "given": "John L", "initials": "JL"}, {"family": "Southey", "given": "Melissa C", "initials": "MC"}, {"family": "Tsimiklis", "given": "Helen", "initials": "H"}, {"family": "Kapuscinski", "given": "Miroslav K", "initials": "MK"}, {"family": "Shen", "given": "Chen-Yang", "initials": "CY"}, {"family": "Wu", "given": "Pei-Ei", "initials": "PE"}, {"family": "Yu", "given": "Jyh-Cherng", "initials": "JC"}, {"family": "Chen", "given": "Shou-Tung", "initials": "ST"}, {"family": "Aln\u00e6s", "given": "Grethe Grenaker", "initials": "GG"}, {"family": "Borresen-Dale", "given": "Anne-Lise", "initials": "AL"}, {"family": "Giles", "given": "Graham G", "initials": "GG"}, {"family": "Milne", "given": "Roger L", "initials": "RL"}, {"family": "McLean", "given": "Catriona", "initials": "C"}, {"family": "Muir", "given": "Kenneth", "initials": "K"}, {"family": "Lophatananon", "given": "Artitaya", "initials": "A"}, {"family": "Stewart-Brown", "given": "Sarah", "initials": "S"}, {"family": "Siriwanarangsan", "given": "Pornthep", "initials": "P"}, {"family": "Hartman", "given": "Mikael", "initials": "M"}, {"family": "Miao", "given": "Hui", "initials": "H"}, {"family": "Buhari", "given": "Shaik Ahmad Bin Syed", "initials": "SA"}, {"family": "Teo", "given": "Yik Ying", "initials": "YY"}, {"family": "Fasching", "given": "Peter A", "initials": "PA"}, {"family": "Haeberle", "given": "Lothar", "initials": "L"}, {"family": "Ekici", "given": "Arif B", "initials": "AB"}, {"family": "Beckmann", "given": "Matthias W", "initials": "MW"}, {"family": "Brenner", "given": "Hermann", "initials": "H"}, {"family": "Dieffenbach", "given": "Aida Karina", "initials": "AK"}, {"family": "Arndt", "given": "Volker", "initials": "V"}, {"family": "Stegmaier", "given": "Christa", "initials": "C"}, {"family": "Swerdlow", "given": "Anthony", "initials": "A"}, {"family": "Ashworth", "given": "Alan", "initials": "A"}, {"family": "Orr", "given": "Nick", "initials": "N"}, {"family": "Schoemaker", "given": "Minouk J", "initials": "MJ"}, {"family": "Garc\u00eda-Closas", "given": "Montserrat", "initials": "M"}, {"family": "Figueroa", "given": "Jonine", "initials": "J"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Lissowska", "given": "Jolanta", "initials": "J"}, {"family": "Simard", "given": "Jacques", "initials": "J"}, {"family": "Goldberg", "given": "Mark S", "initials": "MS"}, {"family": "Labr\u00e8che", "given": "France", "initials": "F"}, {"family": "Dumont", "given": "Martine", "initials": "M"}, {"family": "Winqvist", "given": "Robert", "initials": "R"}, {"family": "Pylk\u00e4s", "given": "Katri", "initials": "K"}, {"family": "Jukkola-Vuorinen", "given": "Arja", "initials": "A"}, {"family": "Brauch", "given": "Hiltrud", "initials": "H"}, {"family": "Br\u00fcning", "given": "Thomas", "initials": "T"}, {"family": "Koto", "given": "Yon-Dschun", "initials": "YD"}, {"family": "Radice", "given": "Paolo", "initials": "P"}, {"family": "Peterlongo", "given": "Paolo", "initials": "P"}, {"family": "Bonanni", "given": "Bernardo", "initials": "B"}, {"family": "Volorio", "given": "Sara", "initials": "S"}, {"family": "D\u00f6rk", "given": "Thilo", "initials": "T"}, {"family": "Bogdanova", "given": "Natalia V", "initials": "NV"}, {"family": "Helbig", "given": "Sonja", "initials": "S"}, {"family": "Mannermaa", "given": "Arto", "initials": "A"}, {"family": "Kataja", "given": "Vesa", "initials": "V"}, {"family": "Kosma", "given": "Veli-Matti", "initials": "VM"}, {"family": "Hartikainen", "given": "Jaana M", "initials": "JM"}, {"family": "Devilee", "given": "Peter", "initials": "P"}, {"family": "Tollenaar", "given": "Robert A E M", "initials": "RA"}, {"family": "Seynaeve", "given": "Caroline", "initials": "C"}, {"family": "Van Asperen", "given": "Christi J", "initials": "CJ"}, {"family": "Jakubowska", "given": "Anna", "initials": "A"}, {"family": "Lubinski", "given": "Jan", "initials": "J"}, {"family": "Jaworska-Bieniek", "given": "Katarzyna", "initials": "K"}, {"family": "Durda", "given": "Katarzyna", "initials": "K"}, {"family": "Slager", "given": "Susan", "initials": "S"}, {"family": "Toland", "given": "Amanda E", "initials": "AE"}, {"family": "Ambrosone", "given": "Christine B", "initials": "CB"}, {"family": "Yannoukakos", "given": "Drakoulis", "initials": "D"}, {"family": "Sangrajrang", "given": "Suleeporn", "initials": "S"}, {"family": "Gaborieau", "given": "Valerie", "initials": "V"}, {"family": "Brennan", "given": "Paul", "initials": "P"}, {"family": "McKay", "given": "James", "initials": "J"}, {"family": "Hamann", "given": "Ute", "initials": "U"}, {"family": "Torres", "given": "Diana", "initials": "D"}, {"family": "Zheng", "given": "Wei", "initials": "W"}, {"family": "Long", "given": "Jirong", "initials": "J"}, {"family": "Anton-Culver", "given": "Hoda", "initials": "H"}, {"family": "Neuhausen", "given": "Susan L", "initials": "SL"}, {"family": "Luccarini", "given": "Craig", "initials": "C"}, {"family": "Baynes", "given": "Caroline", "initials": "C"}, {"family": "Ahmed", "given": "Shahana", "initials": "S"}, {"family": "Maranian", "given": "Mel", "initials": "M"}, {"family": "Healey", "given": "Catherine S", "initials": "CS"}, {"family": "Gonz\u00e1lez-Neira", "given": "Anna", "initials": "A"}, {"family": "Pita", "given": "Guillermo", "initials": "G"}, {"family": "Alonso", "given": "M Rosario", "initials": "MR"}, {"family": "Alvarez", "given": "Nuria", "initials": "N"}, {"family": "Herrero", "given": "Daniel", "initials": "D"}, {"family": "Tessier", "given": "Daniel C", "initials": "DC"}, {"family": "Vincent", "given": "Daniel", "initials": "D"}, {"family": "Bacot", "given": "Francois", "initials": "F"}, {"family": "de Santiago", "given": "Ines", "initials": "I"}, {"family": "Carroll", "given": "Jason", "initials": "J"}, {"family": "Caldas", "given": "Carlos", "initials": "C"}, {"family": "Brown", "given": "Melissa A", "initials": "MA"}, {"family": "Lupien", "given": "Mathieu", "initials": "M"}, {"family": "Kristensen", "given": "Vessela N", "initials": "VN"}, {"family": "Pharoah", "given": "Paul D P", "initials": "PD"}, {"family": "Chenevix-Trench", "given": "Georgia", "initials": "G"}, {"family": "French", "given": "Juliet D", "initials": "JD"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Dunning", "given": "Alison M", "initials": "AM"}, {"family": "Australian Ovarian Cancer Management Group", "given": "", "initials": ""}], "type": "journal article", "published": "2014-09-23", "journal": {"volume": "4", "issn": "2041-1723", "issue": "1", "pages": "4999", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84-0.87; P=1.7 \u00d7 10(-43)) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology.", "doi": "10.1038/ncomms5999", "pmid": "25248036", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "mid", "key": "NIHMS654459"}, {"db": "pmc", "key": "PMC4321900"}, {"db": "pii", "key": "ncomms5999"}], "notes": [], "created": "2017-05-04T14:58:46.423Z", "modified": "2023-06-19T11:18:30.504Z"}, {"entity": "publication", "iuid": "b5a67055447d44f4b95fc1a2cf92f4d5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5a67055447d44f4b95fc1a2cf92f4d5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5a67055447d44f4b95fc1a2cf92f4d5"}}, "title": "The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.", "authors": [{"family": "Sand\u00e9n", "given": "Carl", "initials": "C"}, {"family": "J\u00e4rvstr\u00e5t", "given": "Linnea", "initials": "L"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Bratt\u00e5s", "given": "Per Ludvik", "initials": "PL"}, {"family": "Nilsson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gullberg", "given": "Urban", "initials": "U"}], "type": "journal article", "published": "2014-09-12", "journal": {"volume": "13", "issn": "1476-4598", "issue": null, "pages": "215", "title": "Mol. Cancer", "issn-l": "1476-4598"}, "abstract": "The DEK gene is highly expressed in a wide range of cancer cells, and a recurrent translocation partner in acute myeloid leukemia. While DEK has been identified as one of the most abundant proteins in human chromatin, its function and binding properties are not fully understood.\n\nWe performed ChIP-seq analysis in the myeloid cell line U937 and coupled it with epigenetic and gene expression analysis to explore the genome-wide binding pattern of DEK and its role in gene regulation.\n\nWe show that DEK preferentially binds to open chromatin, with a low degree of DNA methylation and scarce in the heterochromatin marker H3K9me(3) but rich in the euchromatin marks H3K4me(2/3), H3K27ac and H3K9ac. More specifically, DEK binding is predominantly located at the transcription start sites of highly transcribed genes and a comparative analysis with previously established transcription factor binding patterns shows a similarity with that of RNA polymerase II. Further bioinformatic analysis demonstrates that DEK mainly binds to genes that are ubiquitously expressed across tissues. The functional significance of DEK binding was demonstrated by knockdown of DEK by shRNA, resulting in both significant upregulation and downregulation of DEK-bound genes.\n\nWe find that DEK binds to transcription start sites with a dual role in activation and repression of highly and ubiquitously expressed genes.", "doi": "10.1186/1476-4598-13-215", "pmid": "25216995", "labels": {"National Genomics Infrastructure": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1476-4598-13-215"}, {"db": "pmc", "key": "PMC4175287"}, {"db": "GEO", "key": "GSE60734"}], "notes": [], "created": "2017-05-04T14:58:44.303Z", "modified": "2020-01-21T13:56:04.758Z"}, {"entity": "publication", "iuid": "f230ea784e1a485b885429b851c34bf2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f230ea784e1a485b885429b851c34bf2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f230ea784e1a485b885429b851c34bf2"}}, "title": "Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway.", "authors": [{"family": "Acuna-Hidalgo", "given": "Rocio", "initials": "R"}, {"family": "Schanze", "given": "Denny", "initials": "D"}, {"family": "Kariminejad", "given": "Ariana", "initials": "A"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Kariminejad", "given": "Mohamad Hasan", "initials": "MH"}, {"family": "Conner", "given": "Peter", "initials": "P"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Wredenberg", "given": "Anna", "initials": "A"}, {"family": "Wieczorek", "given": "Dagmar", "initials": "D"}, {"family": "Gillessen-Kaesbach", "given": "Gabriele", "initials": "G"}, {"family": "Kayserili", "given": "H\u00fclya", "initials": "H"}, {"family": "Elcioglu", "given": "Nursel", "initials": "N"}, {"family": "Ghaderi-Sohi", "given": "Siavash", "initials": "S"}, {"family": "Goodarzi", "given": "Payman", "initials": "P"}, {"family": "Setayesh", "given": "Hamidreza", "initials": "H"}, {"family": "van de Vorst", "given": "Maartje", "initials": "M"}, {"family": "Steehouwer", "given": "Marloes", "initials": "M"}, {"family": "Pfundt", "given": "Rolph", "initials": "R"}, {"family": "Krabichler", "given": "Birgit", "initials": "B"}, {"family": "Curry", "given": "Cynthia", "initials": "C"}, {"family": "MacKenzie", "given": "Malcolm G", "initials": "MG"}, {"family": "Boycott", "given": "Kym M", "initials": "KM"}, {"family": "Gilissen", "given": "Christian", "initials": "C"}, {"family": "Janecke", "given": "Andreas R", "initials": "AR"}, {"family": "Hoischen", "given": "Alexander", "initials": "A"}, {"family": "Zenker", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2014-09-04", "journal": {"volume": "95", "issn": "1537-6605", "issue": "3", "pages": "285-293", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Neu-Laxova syndrome (NLS) is a rare autosomal-recessive disorder characterized by a recognizable pattern of severe malformations leading to prenatal or early postnatal lethality. Homozygous mutations in PHGDH, a gene involved in the first and limiting step in L-serine biosynthesis, were recently identified as the cause of the disease in three families. By studying a cohort of 12 unrelated families affected by NLS, we provide evidence that NLS is genetically heterogeneous and can be caused by mutations in all three genes encoding enzymes of the L-serine biosynthesis pathway. Consistent with recently reported findings, we could identify PHGDH missense mutations in three unrelated families of our cohort. Furthermore, we mapped an overlapping homozygous chromosome 9 region containing PSAT1 in four consanguineous families. This gene encodes phosphoserine aminotransferase, the enzyme for the second step in L-serine biosynthesis. We identified six families with three different missense and frameshift PSAT1 mutations fully segregating with the disease. In another family, we discovered a homozygous frameshift mutation in PSPH, the gene encoding phosphoserine phosphatase, which catalyzes the last step of L-serine biosynthesis. Interestingly, all three identified genes have been previously implicated in serine-deficiency disorders, characterized by variable neurological manifestations. Our findings expand our understanding of NLS as a disorder of the L-serine biosynthesis pathway and suggest that NLS represents the severe end of serine-deficiency disorders, demonstrating that certain complex syndromes characterized by early lethality could indeed be the extreme end of the phenotypic spectrum of already known disorders.", "doi": "10.1016/j.ajhg.2014.07.012", "pmid": "25152457", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(14)00321-8"}, {"db": "pmc", "key": "PMC4157144"}], "notes": [], "created": "2017-05-04T14:58:19.929Z", "modified": "2020-01-21T13:56:06.251Z"}, {"entity": "publication", "iuid": "5a160d6cf4a2483aa720fdf3c3a6e176", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a160d6cf4a2483aa720fdf3c3a6e176.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a160d6cf4a2483aa720fdf3c3a6e176"}}, "title": "Recurrent GATA1 mutations in Diamond-Blackfan anaemia.", "authors": [{"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Khalfallah", "given": "Ayda", "initials": "A"}, {"family": "Arzoo", "given": "Pakeeza Shaiq", "initials": "PS"}, {"family": "Gazda", "given": "Hanna T", "initials": "HT"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "letter", "published": "2014-09-00", "journal": {"volume": "166", "issn": "1365-2141", "issue": "6", "pages": "949-951", "title": "Br. J. Haematol.", "issn-l": "0007-1048"}, "abstract": null, "doi": "10.1111/bjh.12919", "pmid": "24766296", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:26.457Z", "modified": "2020-01-21T13:56:02.456Z"}, {"entity": "publication", "iuid": "e161350a6d454ed9b4604c2ab3e25535", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e161350a6d454ed9b4604c2ab3e25535.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e161350a6d454ed9b4604c2ab3e25535"}}, "title": "Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics", "authors": [{"family": "Eiler", "given": "Alexander", "initials": "A"}, {"family": "Zaremba\u2010Niedzwiedzka", "given": "Katarzyna", "initials": "K"}, {"family": "Mart\u00ednez\u2010Garc\u00eda", "given": "Manuel", "initials": "M"}, {"family": "McMahon", "given": "Katherine D", "initials": "KD"}, {"family": "Stepanauskas", "given": "Ramunas", "initials": "R"}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal-article", "published": "2014-09-00", "journal": {"volume": "16", "issn": "1462-2912", "issue": "9", "pages": "2682-2698", "title": "Environ Microbiol", "issn-l": "1462-2912"}, "abstract": "Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.", "doi": "10.1111/1462-2920.12301", "pmid": "24118837", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4253090"}], "notes": [], "created": "2017-05-04T14:58:31.534Z", "modified": "2021-06-16T15:16:30.154Z"}, {"entity": "publication", "iuid": "2d63a03ebd324e7ab758e415df5fb8b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2d63a03ebd324e7ab758e415df5fb8b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2d63a03ebd324e7ab758e415df5fb8b6"}}, "title": "Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.", "authors": [{"family": "Larsson", "given": "John", "initials": "J"}, {"family": "Celepli", "given": "Narin", "initials": "N"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Dupont", "given": "Christopher L", "initials": "CL"}, {"family": "Yooseph", "given": "Shibu", "initials": "S"}, {"family": "Bergman", "given": "Bigitta", "initials": "B"}, {"family": "Ekman", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2014-09-00", "journal": {"volume": "8", "issn": "1751-7370", "issue": "9", "pages": "1892-1903", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh- and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.", "doi": "10.1038/ismej.2014.35", "pmid": "24621524", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej201435"}, {"db": "pmc", "key": "PMC4139726"}], "notes": [], "created": "2017-05-04T14:58:40.387Z", "modified": "2020-01-21T13:56:01.286Z"}, {"entity": "publication", "iuid": "d07b8339beb344ac86f68b1e402880c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d07b8339beb344ac86f68b1e402880c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d07b8339beb344ac86f68b1e402880c9"}}, "title": "Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.", "authors": [{"family": "Laurell", "given": "Tobias", "initials": "T"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Hofmeister", "given": "Wolfgang", "initials": "W"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Ahituv", "given": "Nadav", "initials": "N"}, {"family": "Vandermeer", "given": "Julia", "initials": "J"}, {"family": "Amilon", "given": "Anders", "initials": "A"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Arner", "given": "Marianne", "initials": "M"}, {"family": "Pettersson", "given": "Maria", "initials": "M"}, {"family": "J\u00e4ntti", "given": "Nina", "initials": "N"}, {"family": "Rosberg", "given": "Hans-Eric", "initials": "HE"}, {"family": "Cattini", "given": "Peter A", "initials": "PA"}, {"family": "Nordenskj\u00f6ld", "given": "Agneta", "initials": "A"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}, {"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}], "type": "journal article", "published": "2014-09-00", "journal": {"volume": "2", "issn": "2324-9269", "issue": "5", "pages": "402-411", "title": "Mol Genet Genomic Med", "issn-l": "2324-9269"}, "abstract": "Nonsense mutations in FGF16 have recently been linked to X-linked recessive hand malformations with fusion between the fourth and the fifth metacarpals and hypoplasia of the fifth digit (MF4; MIM#309630). The purpose of this study was to perform careful clinical phenotyping and to define molecular mechanisms behind X-linked recessive MF4 in three unrelated families. We performed whole-exome sequencing, and identified three novel mutations in FGF16. The functional impact of FGF16 loss was further studied using morpholino-based suppression of fgf16 in zebrafish. In addition, clinical investigations revealed reduced penetrance and variable expressivity of the MF4 phenotype. Cardiac disorders, including myocardial infarction and atrial fibrillation followed the X-linked FGF16 mutated trait in one large family. Our findings establish that a mutation in exon 1, 2 or 3 of FGF16 results in X-linked recessive MF4 and expand the phenotypic spectrum of FGF16 mutations to include a possible correlation with heart disease.", "doi": "10.1002/mgg3.81", "pmid": "25333065", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4190875"}], "notes": [], "created": "2017-05-04T14:58:45.367Z", "modified": "2020-01-21T13:56:05.283Z"}, {"entity": "publication", "iuid": "d12271d0bd3d47928548052fd060f6e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d12271d0bd3d47928548052fd060f6e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d12271d0bd3d47928548052fd060f6e0"}}, "title": "Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli.", "authors": [{"family": "Stoco", "given": "Patr\u00edcia Hermes", "initials": "PH"}, {"family": "Wagner", "given": "Glauber", "initials": "G"}, {"family": "Talavera-Lopez", "given": "Carlos", "initials": "C"}, {"family": "Gerber", "given": "Alexandra", "initials": "A"}, {"family": "Zaha", "given": "Arnaldo", "initials": "A"}, {"family": "Thompson", "given": "Claudia Elizabeth", "initials": "CE"}, {"family": "Bartholomeu", "given": "Daniella Castanheira", "initials": "DC"}, {"family": "L\u00fcckemeyer", "given": "D\u00e9bora Denardin", "initials": "DD"}, {"family": "Bahia", "given": "Diana", "initials": "D"}, {"family": "Loreto", "given": "Elgion", "initials": "E"}, {"family": "Prestes", "given": "Elisa Beatriz", "initials": "EB"}, {"family": "Lima", "given": "F\u00e1bio Mitsuo", "initials": "FM"}, {"family": "Rodrigues-Luiz", "given": "Gabriela", "initials": "G"}, {"family": "Vallejo", "given": "Gustavo Adolfo", "initials": "GA"}, {"family": "Filho", "given": "Jos\u00e9 Franco da Silveira", "initials": "JF"}, {"family": "Schenkman", "given": "S\u00e9rgio", "initials": "S"}, {"family": "Monteiro", "given": "Karina Mariante", "initials": "KM"}, {"family": "Tyler", "given": "Kevin Morris", "initials": "KM"}, {"family": "de Almeida", "given": "Luiz Gonzaga Paula", "initials": "LG"}, {"family": "Ortiz", "given": "Mauro Freitas", "initials": "MF"}, {"family": "Chiurillo", "given": "Miguel Angel", "initials": "MA"}, {"family": "de Moraes", "given": "Milene H\u00f6ehr", "initials": "MH"}, {"family": "Cunha", "given": "Oberdan de Lima", "initials": "Ode L"}, {"family": "Mendon\u00e7a-Neto", "given": "Rondon", "initials": "R"}, {"family": "Silva", "given": "Rosane", "initials": "R"}, {"family": "Teixeira", "given": "Santuza Maria Ribeiro", "initials": "SM"}, {"family": "Murta", "given": "Silvane Maria Fonseca", "initials": "SM"}, {"family": "Sincero", "given": "Thais Cristine Marques", "initials": "TC"}, {"family": "Mendes", "given": "Tiago Antonio de Oliveira", "initials": "TA"}, {"family": "Urmenyi", "given": "Tur\u00e1n Peter", "initials": "TP"}, {"family": "Silva", "given": "Viviane Grazielle", "initials": "VG"}, {"family": "DaRocha", "given": "Wanderson Duarte", "initials": "WD"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Romanha", "given": "Alvaro Jos\u00e9", "initials": "AJ"}, {"family": "Steindel", "given": "M\u00e1rio", "initials": "M"}, {"family": "de Vasconcelos", "given": "Ana Tereza Ribeiro", "initials": "AT"}, {"family": "Grisard", "given": "Edmundo Carlos", "initials": "EC"}], "type": "journal article", "published": "2014-09-00", "journal": {"volume": "8", "issn": "1935-2735", "issue": "9", "pages": "e3176", "title": "PLoS Negl Trop Dis", "issn-l": "1935-2727"}, "abstract": "Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.\n\nThe T. rangeli haploid genome is \u223c 24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heat-shock proteins.\n\nPhylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets.", "doi": "10.1371/journal.pntd.0003176", "pmid": "25233456", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PNTD-D-13-02024"}, {"db": "pmc", "key": "PMC4169256"}], "notes": [], "created": "2017-05-04T14:58:52.776Z", "modified": "2020-01-21T13:56:05.338Z"}, {"entity": "publication", "iuid": "9b3132abbae844bc95f381f228b343ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b3132abbae844bc95f381f228b343ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b3132abbae844bc95f381f228b343ed"}}, "title": "Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?", "authors": [{"family": "Westram", "given": "A M", "initials": "AM"}, {"family": "Galindo", "given": "J", "initials": "J"}, {"family": "Alm Rosenblad", "given": "M", "initials": "M"}, {"family": "Grahame", "given": "J W", "initials": "JW"}, {"family": "Panova", "given": "M", "initials": "M"}, {"family": "Butlin", "given": "R K", "initials": "RK"}], "type": "journal article", "published": "2014-09-00", "journal": {"volume": "23", "issn": "1365-294X", "issue": "18", "pages": "4603-4616", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on F(ST) values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.", "doi": "10.1111/mec.12883", "pmid": "25113130", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pmc", "key": "PMC4285301"}, {"db": "Dryad", "key": "21PF0"}], "notes": [], "created": "2017-05-04T14:56:32.875Z", "modified": "2020-01-21T13:56:16.771Z"}, {"entity": "publication", "iuid": "0467d06507f64ac984b761e81945087b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0467d06507f64ac984b761e81945087b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0467d06507f64ac984b761e81945087b"}}, "title": "Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.", "authors": [{"family": "Carneiro", "given": "Miguel", "initials": "M"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "Di Palma", "given": "Federica", "initials": "F"}, {"family": "Albert", "given": "Frank W", "initials": "FW"}, {"family": "Alf\u00f6ldi", "given": "Jessica", "initials": "J"}, {"family": "Barrio", "given": "Alvaro Martinez", "initials": "AM"}, {"family": "Pielberg", "given": "Gerli", "initials": "G"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Turner-Maier", "given": "Jason", "initials": "J"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Afonso", "given": "Sandra", "initials": "S"}, {"family": "Aken", "given": "Bronwen", "initials": "B"}, {"family": "Alves", "given": "Joel M", "initials": "JM"}, {"family": "Barrell", "given": "Daniel", "initials": "D"}, {"family": "Bolet", "given": "Gerard", "initials": "G"}, {"family": "Boucher", "given": "Samuel", "initials": "S"}, {"family": "Burbano", "given": "Hern\u00e1n A", "initials": "HA"}, {"family": "Campos", "given": "Rita", "initials": "R"}, {"family": "Chang", "given": "Jean L", "initials": "JL"}, {"family": "Duranthon", "given": "Veronique", "initials": "V"}, {"family": "Fontanesi", "given": "Luca", "initials": "L"}, {"family": "Garreau", "given": "Herv\u00e9", "initials": "H"}, {"family": "Heiman", "given": "David", "initials": "D"}, {"family": "Johnson", "given": "Jeremy", "initials": "J"}, {"family": "Mage", "given": "Rose G", "initials": "RG"}, {"family": "Peng", "given": "Ze", "initials": "Z"}, {"family": "Queney", "given": "Guillaume", "initials": "G"}, {"family": "Rogel-Gaillard", "given": "Claire", "initials": "C"}, {"family": "Ruffier", "given": "Magali", "initials": "M"}, {"family": "Searle", "given": "Steve", "initials": "S"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Xiong", "given": "Anqi", "initials": "A"}, {"family": "Young", "given": "Sarah", "initials": "S"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K"}, {"family": "Good", "given": "Jeffrey M", "initials": "JM"}, {"family": "Lander", "given": "Eric S", "initials": "ES"}, {"family": "Ferrand", "given": "Nuno", "initials": "N"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2014-08-29", "journal": {"volume": "345", "issn": "1095-9203", "issue": "6200", "pages": "1074-1079", "title": "Science", "issn-l": "0036-8075"}, "abstract": "The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.", "doi": "10.1126/science.1253714", "pmid": "25170157", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics Support for Computational Resources": null}, "xrefs": [{"db": "pii", "key": "345/6200/1074"}, {"db": "BioProject", "key": "PRJNA221358"}, {"db": "BioProject", "key": "PRJNA242290"}, {"db": "BioProject", "key": "PRJNA78323"}, {"db": "GENBANK", "key": "AAGW02000000"}], "notes": [], "created": "2017-05-04T14:56:13.936Z", "modified": "2024-01-16T13:48:50.820Z"}, {"entity": "publication", "iuid": "8a39ed8268da427f9f955b67ecc803bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a39ed8268da427f9f955b67ecc803bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a39ed8268da427f9f955b67ecc803bf"}}, "title": "A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone.", "authors": [{"family": "Sivertsen", "given": "Audun", "initials": "A"}, {"family": "Billstr\u00f6m", "given": "Hanna", "initials": "H"}, {"family": "Melefors", "given": "\u00d6jar", "initials": "\u00d6"}, {"family": "Liljequist", "given": "Barbro Olsson", "initials": "BO"}, {"family": "Wisell", "given": "Karin Tegmark", "initials": "KT"}, {"family": "Ullberg", "given": "M\u00e5ns", "initials": "M"}, {"family": "\u00d6zenci", "given": "Volkan", "initials": "V"}, {"family": "Sundsfjord", "given": "Arnfinn", "initials": "A"}, {"family": "Hegstad", "given": "Kristin", "initials": "K"}], "type": "journal article", "published": "2014-08-25", "journal": {"volume": "9", "issn": "1932-6203", "issue": "8", "pages": "e103274", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The clonal dissemination of VanB-type vancomycin-resistant Enterococcus faecium (VREfm) strains in three Swedish hospitals between 2007 and 2011 prompted further analysis to reveal the possible origin and molecular characteristics of the outbreak strain. A representative subset of VREfm isolates (n\u200a=\u200a18) and vancomycin-susceptible E. faecium (VSEfm, n\u200a=\u200a2) reflecting the spread in time and location was approached by an array of methods including: selective whole genome sequencing (WGS; n\u200a=\u200a3), multi locus sequence typing (MLST), antimicrobial susceptibility testing, virulence gene profiling, identification of mobile genetic elements conferring glycopeptide resistance and their ability to support glycopeptide resistance transfer. In addition, a single VREfm strain with an unrelated PFGE pattern collected prior to the outbreak was examined by WGS. MLST revealed a predominance of ST192, belonging to a hospital adapted high-risk lineage harbouring several known virulence determinants (n\u226510). The VREfm outbreak strain was resistant to ampicillin, gentamicin, ciprofloxacin and vancomycin, and susceptible to teicoplanin. Consistently, a vanB2-subtype as part of Tn1549/Tn5382 with a unique genetic signature was identified in the VREfm outbreak strains. Moreover, Southern blot hybridisation analyses of PFGE separated S1 nuclease-restricted total DNAs and filter mating experiments showed that vanB2-Tn1549/Tn5382 was located in a 70-kb sized rep17/pRUM plasmid readily transferable between E. faecium. This plasmid contained an axe-txe toxin-antitoxin module associated with stable maintenance. The two clonally related VSEfm harboured a 40 kb rep17/pRUM plasmid absent of the 30 kb vanB2-Tn1549/Tn5382 gene complex. Otherwise, these two isolates were similar to the VREfm outbreak strain in virulence- and resistance profile. In conclusion, our observations support that the origin of the multicentre outbreak was caused by an introduction of vanB2-Tn1549/Tn5382 into a rep17/pRUM plasmid harboured in a pre-existing high-risk E. faecium ST192 clone. The subsequent dissemination of VREfm to other centres was primarily caused by clonal spread rather than plasmid transfer to pre-existing high-risk clones.", "doi": "10.1371/journal.pone.0103274", "pmid": "25153894", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-06782"}, {"db": "pmc", "key": "PMC4143159"}], "notes": [], "created": "2017-05-04T14:58:57.820Z", "modified": "2020-01-21T13:56:03.523Z"}, {"entity": "publication", "iuid": "5d7e79e4e57f4e7c968bc7ea2dfe7126", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d7e79e4e57f4e7c968bc7ea2dfe7126.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d7e79e4e57f4e7c968bc7ea2dfe7126"}}, "title": "Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.", "authors": [{"family": "Fu", "given": "Cheng-Jie", "initials": "CJ"}, {"family": "Sheikh", "given": "Sanea", "initials": "S"}, {"family": "Miao", "given": "Wei", "initials": "W"}, {"family": "Andersson", "given": "Siv G E", "initials": "SG"}, {"family": "Baldauf", "given": "Sandra L", "initials": "SL"}], "type": "journal article", "published": "2014-08-21", "journal": {"volume": "6", "issn": "1759-6653", "issue": "9", "pages": "2240-2257", "title": "Genome Biol Evol", "issn-l": "1759-6653"}, "abstract": "Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs (mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.", "doi": "10.1093/gbe/evu180", "pmid": "25146648", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "evu180"}, {"db": "pmc", "key": "PMC4202320"}, {"db": "GENBANK", "key": "KJ679272"}], "notes": [], "created": "2017-05-04T14:58:37.241Z", "modified": "2021-06-16T15:16:43.365Z"}, {"entity": "publication", "iuid": "a961c66fdf4c4640b3ac3ee5e898fb77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a961c66fdf4c4640b3ac3ee5e898fb77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a961c66fdf4c4640b3ac3ee5e898fb77"}}, "title": "Winter bloom of a rare betaproteobacterium in the Arctic Ocean.", "authors": [{"family": "Alonso-S\u00e1ez", "given": "Laura", "initials": "L"}, {"family": "Zeder", "given": "Michael", "initials": "M"}, {"family": "Harding", "given": "Tommy", "initials": "T"}, {"family": "Pernthaler", "given": "Jakob", "initials": "J"}, {"family": "Lovejoy", "given": "Connie", "initials": "C"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Pedr\u00f3s-Ali\u00f3", "given": "Carlos", "initials": "C"}], "type": "journal article", "published": "2014-08-20", "journal": {"volume": "5", "issn": "1664-302X", "issue": null, "pages": "425", "title": "Front Microbiol", "issn-l": "1664-302X"}, "abstract": "Extremely low abundance microorganisms (members of the \"rare biosphere\") are believed to include dormant taxa, which can sporadically become abundant following environmental triggers. Yet, microbial transitions from rare to abundant have seldom been captured in situ, and it is uncertain how widespread these transitions are. A bloom of a single ribotype (\u226599% similarity in the 16S ribosomal RNA gene) of a widespread betaproteobacterium (Janthinobacterium sp.) occurred over 2 weeks in Arctic marine waters. The Janthinobacterium population was not detected microscopically in situ in January and early February, but suddenly appeared in the water column thereafter, eventually accounting for up to 20% of bacterial cells in mid February. During the bloom, this bacterium was detected at open water sites up to 50 km apart, being abundant down to more than 300 m. This event is one of the largest monospecific bacterial blooms reported in polar oceans. It is also remarkable because Betaproteobacteria are typically found only in low abundance in marine environments. In particular, Janthinobacterium were known from non-marine habitats and had previously been detected only in the rare biosphere of seawater samples, including the polar oceans. The Arctic Janthinobacterium formed mucilagenous monolayer aggregates after short (ca. 8 h) incubations, suggesting that biofilm formation may play a role in maintaining rare bacteria in pelagic marine environments. The spontaneous mass occurrence of this opportunistic rare taxon in polar waters during the energy-limited season extends current knowledge of how and when microbial transitions between rare and abundant occur in the ocean.", "doi": "10.3389/fmicb.2014.00425", "pmid": "25191307", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4138443"}], "notes": [], "created": "2017-05-04T14:58:35.494Z", "modified": "2020-01-21T13:56:04.430Z"}, {"entity": "publication", "iuid": "d58d90e1b5b54964b9aa5becd6d9e2d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d58d90e1b5b54964b9aa5becd6d9e2d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d58d90e1b5b54964b9aa5becd6d9e2d6"}}, "title": "Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.", "authors": [{"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Johansson", "given": "Tomas", "initials": "T"}, {"family": "Canb\u00e4ck", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Bentzer", "given": "Johan", "initials": "J"}, {"family": "Rosenblad", "given": "Magnus Alm", "initials": "MA"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}, {"family": "Tunlid", "given": "Anders", "initials": "A"}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}], "type": "journal article", "published": "2014-08-18", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "687", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying \"Crab\" and \"Wave\" ecotypes of L. saxatilis.\n\nWe could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis.\n\nThe present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.", "doi": "10.1186/1471-2164-15-687", "pmid": "25135785", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-687"}, {"db": "pmc", "key": "PMC4148934"}, {"db": "GEO", "key": "GSE59825"}], "notes": [], "created": "2017-05-04T14:56:30.407Z", "modified": "2020-01-21T13:56:16.790Z"}, {"entity": "publication", "iuid": "9594cc8981684ec38b8578013a44e451", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9594cc8981684ec38b8578013a44e451.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9594cc8981684ec38b8578013a44e451"}}, "title": "Evaluation of exome sequencing to estimate tumor burden in plasma.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Neiman", "given": "M\u00e5rten", "initials": "M"}, {"family": "Sundling", "given": "Simon", "initials": "S"}, {"family": "Eriksson", "given": "Louise", "initials": "L"}, {"family": "Darai Ramqvist", "given": "Eva", "initials": "E"}, {"family": "Celebioglu", "given": "Fuat", "initials": "F"}, {"family": "Czene", "given": "Kamila", "initials": "K"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Egevad", "given": "Lars", "initials": "L"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}], "type": "evaluation studies", "published": "2014-08-18", "journal": {"volume": "9", "issn": "1932-6203", "issue": "8", "pages": "e104417", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Accurate estimation of systemic tumor load from the blood of cancer patients has enormous potential. One avenue is to measure the presence of cell-free circulating tumor DNA in plasma. Various approaches have been investigated, predominantly covering hotspot mutations or customized, patient-specific assays. Therefore, we investigated the utility of using exome sequencing to monitor circulating tumor DNA levels through the detection of single nucleotide variants in plasma. Two technologies, claiming to offer efficient library preparation from nanogram levels of DNA, were evaluated. This allowed us to estimate the proportion of starting molecules measurable by sequence capture (<5%). As cell-free DNA is highly fragmented, we designed and provide software for efficient identification of PCR duplicates in single-end libraries with a varying size distribution. On average, this improved sequence coverage by 38% in comparison to standard tools. By exploiting the redundant information in PCR-duplicates the background noise was reduced to \u223c1/35,000. By applying our optimized analysis pipeline to a simulation analysis, we determined the current sensitivity limit to \u223c1/2400, starting with 30 ng of cell-free DNA. Subsequently, circulating tumor DNA levels were assessed in seven breast- and one prostate cancer patient. One patient carried detectable levels of circulating tumor DNA, as verified by break-point specific PCR. These results demonstrate exome sequencing on cell-free DNA to be a powerful tool for disease monitoring of metastatic cancers. To enable a broad implementation in the diagnostic settings, the efficiency limitations of sequence capture and the inherent noise levels of the Illumina sequencing technology must be further improved.", "doi": "10.1371/journal.pone.0104417", "pmid": "25133800", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-23092"}, {"db": "pmc", "key": "PMC4136786"}], "notes": [], "created": "2017-05-04T14:58:55.394Z", "modified": "2020-01-21T13:56:03.848Z"}, {"entity": "publication", "iuid": "b0e3ae5cbfbd4cf79ee65a5e792152af", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0e3ae5cbfbd4cf79ee65a5e792152af.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0e3ae5cbfbd4cf79ee65a5e792152af"}}, "title": "BESST--efficient scaffolding of large fragmented assemblies.", "authors": [{"family": "Sahlin", "given": "Kristoffer", "initials": "K"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Arvestad", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2014-08-15", "journal": {"volume": "15", "issn": "1471-2105", "issue": null, "pages": "281", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an important step in the assembly pipeline. Different algorithms have been proposed but many of them use the number of read pairs supporting a linking of two contigs as an indicator of reliability. This reasoning is intuitive, but fails to account for variation in link count due to contig features.We have also noted that published scaffolders are only evaluated on small datasets using output from only one assembler. Two issues arise from this. Firstly, some of the available tools are not well suited for complex genomes. Secondly, these evaluations provide little support for inferring a software's general performance.\n\nWe propose a new algorithm, implemented in a tool called BESST, which can scaffold genomes of all sizes and complexities and was used to scaffold the genome of P. abies (20 Gbp). We performed a comprehensive comparison of BESST against the most popular stand-alone scaffolders on a large variety of datasets. Our results confirm that some of the popular scaffolders are not practical to run on complex datasets. Furthermore, no single stand-alone scaffolder outperforms the others on all datasets. However, BESST fares favorably to the other tested scaffolders on GAGE datasets and, moreover, outperforms the other methods when library insert size distribution is wide.\n\nWe conclude from our results that information sources other than the quantity of links, as is commonly used, can provide useful information about genome structure when scaffolding.", "doi": "10.1186/1471-2105-15-281", "pmid": "25128196", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2105-15-281"}, {"db": "pmc", "key": "PMC4262078"}], "notes": [], "created": "2017-05-04T14:58:24.219Z", "modified": "2021-07-08T13:26:08.291Z"}, {"entity": "publication", "iuid": "e47cca77504141849cc4645dcbc8ddfc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e47cca77504141849cc4645dcbc8ddfc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e47cca77504141849cc4645dcbc8ddfc"}}, "title": "Common genetic determinants of lung function, subclinical atherosclerosis and risk of coronary artery disease.", "authors": [{"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Soler Artigas", "given": "Mar\u00eda", "initials": "M"}, {"family": "Baldassarre", "given": "Damiano", "initials": "D"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Veglia", "given": "Fabrizio", "initials": "F"}, {"family": "Brusselle", "given": "Guy", "initials": "G"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Engstr\u00f6m", "given": "Gunnar", "initials": "G"}, {"family": "Franco", "given": "Oscar H", "initials": "OH"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Paulsson-Berne", "given": "Gabrielle", "initials": "G"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Tremoli", "given": "Elena", "initials": "E"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2014-08-05", "journal": {"volume": "9", "issn": "1932-6203", "issue": "8", "pages": "e104082", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Chronic obstructive pulmonary disease (COPD) independently associates with an increased risk of coronary artery disease (CAD), but it has not been fully investigated whether this co-morbidity involves shared pathophysiological mechanisms. To identify potential common pathways across the two diseases, we tested all recently published single nucleotide polymorphisms (SNPs) associated with human lung function (spirometry) for association with carotid intima-media thickness (cIMT) in 3,378 subjects with multiple CAD risk factors, and for association with CAD in a case-control study of 5,775 CAD cases and 7,265 controls. SNPs rs2865531, located in the CFDP1 gene, and rs9978142, located in the KCNE2 gene, were significantly associated with CAD. In addition, SNP rs9978142 and SNP rs3995090 located in the HTR4 gene, were associated with average and maximal cIMT measures. Genetic risk scores combining the most robustly spirometry-associated SNPs from the literature were modestly associated with CAD, (odds ratio (OR) (95% confidence interval (CI95)\u200a= 1.06 (1.03, 1.09); P-value = 1.5 \u00d7 10(-4), per allele). In conclusion, our study suggests that some genetic loci implicated in determining human lung function also influence cIMT and susceptibility to CAD. The present results should help elucidate the molecular underpinnings of the co-morbidity observed across COPD and CAD.", "doi": "10.1371/journal.pone.0104082", "pmid": "25093840", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-15018"}, {"db": "pmc", "key": "PMC4122436"}], "notes": [], "created": "2017-05-04T14:58:57.203Z", "modified": "2020-01-21T13:56:05.874Z"}, {"entity": "publication", "iuid": "7db31f37719c4e0a9b5f5a5ab59263fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7db31f37719c4e0a9b5f5a5ab59263fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7db31f37719c4e0a9b5f5a5ab59263fb"}}, "title": "Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.", "authors": [{"family": "Madissoon", "given": "Elo", "initials": "E"}, {"family": "T\u00f6h\u00f6nen", "given": "Virpi", "initials": "V"}, {"family": "Vesterlund", "given": "Liselotte", "initials": "L"}, {"family": "Katayama", "given": "Shintaro", "initials": "S"}, {"family": "Unneberg", "given": "Per", "initials": "P"}, {"family": "Inzunza", "given": "Jose", "initials": "J"}, {"family": "Hovatta", "given": "Outi", "initials": "O"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2014-08-04", "journal": {"volume": "9", "issn": "1932-6203", "issue": "8", "pages": "e102949", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Infertility is a worldwide concern that can be treated with in vitro fertilization (IVF). Improvements in IVF and infertility treatment depend largely on better understanding of the molecular mechanisms for human preimplantation development. Several large-scale studies have been conducted to identify gene expression patterns for the first five days of human development, and many functional studies utilize mouse as a model system. We have identified genes of possible importance for this time period by analyzing human microarray data and available data from online databases. We selected 70 candidate genes for human preimplantation development and investigated their expression in the early mouse development from oocyte to the 8-cell stage. Maternally loaded genes expectedly decreased in expression during development both in human and mouse. We discovered that 25 significantly upregulated genes after fertilization in human included 13 genes whose orthologs in mouse behaved differently and mimicked the expression profile of maternally expressed genes. Our findings highlight many significant differences in gene expression patterns during mouse and human preimplantation development. We also describe four cancer-testis antigen families that are also highly expressed in human embryos: PRAME, SSX, GAGE and MAGEA.", "doi": "10.1371/journal.pone.0102949", "pmid": "25089626", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-08870"}, {"db": "pmc", "key": "PMC4121084"}], "notes": [], "created": "2017-05-04T14:58:56.299Z", "modified": "2020-01-21T13:56:03.262Z"}, {"entity": "publication", "iuid": "b6cafc3c2e8747d3b4253736edbab320", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6cafc3c2e8747d3b4253736edbab320.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6cafc3c2e8747d3b4253736edbab320"}}, "title": "Multifactorial analysis of changes in body mass index across the adult life course: a study with 65 years of follow-up.", "authors": [{"family": "Dahl", "given": "A K", "initials": "AK"}, {"family": "Reynolds", "given": "C A", "initials": "CA"}, {"family": "Fall", "given": "T", "initials": "T"}, {"family": "Magnusson", "given": "P K E", "initials": "PK"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "38", "issn": "1476-5497", "issue": "8", "pages": "1133-1141", "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "Although the negative consequences on health of being obese are well known, most adults gain weight across the lifespan. The general increase in body mass index (BMI) is mainly considered to originate from behavioral and environmental changes; however, few studies have evaluated the influence of these factors on change in BMI in the presence of genetic risk. We aimed to study the influence of multifactorial causes of change in BMI, over 65 years.\n\nTotally, 6130 participants from TwinGene, who had up to five assessments, and 536 from the Swedish Adoption/Twin Study of Aging, who had up to 12 assessments, ranging over 65 years were included. The influence of lifestyle factors, birth cohort, cardiometabolic diseases and an individual obesity genetic risk score (OGRS) based on 32 single nucleotide polymorphisms on change in BMI was evaluated with a growth model. For both sexes, BMI increased from early adulthood to age of 65 years, after which the increase leveled off; BMI declined after age of 80 years. A higher OGRS, birth after 1925 and cardiometabolic diseases were associated with higher average BMI and a steeper increase in BMI prior to 65 years of age. Among men, few factors were identified that influence BMI trajectories in late life, whereas for women type 2 diabetes mellitus and dementia were associated with a steeper decrease in BMI after the age of 65 years.\n\nThere are two turning points in BMI in late adulthood, one at the age of 65 years and one at the age 80 years. Factors associated with an increase in BMI in midlife were not associated with an increase in BMI after the age of 65 years. These findings indicate that the causes and consequences of change in BMI differ across the lifespan. Current health recommendations need to be adjusted accordingly.", "doi": "10.1038/ijo.2013.204", "pmid": "24193660", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ijo2013204"}, {"db": "pmc", "key": "PMC4012011"}, {"db": "mid", "key": "NIHMS534092"}], "notes": [], "created": "2017-05-04T14:57:58.478Z", "modified": "2020-01-21T13:56:04.779Z"}, {"entity": "publication", "iuid": "1eeee25224bc4ab4b3f1c46f75523720", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1eeee25224bc4ab4b3f1c46f75523720.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1eeee25224bc4ab4b3f1c46f75523720"}}, "title": "Mechanisms of mRNA export.", "authors": [{"family": "Bj\u00f6rk", "given": "Petra", "initials": "P"}, {"family": "Wieslander", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "32", "issn": "1096-3634", "issue": null, "pages": "47-54", "title": "Semin. Cell Dev. Biol.", "issn-l": "1084-9521"}, "abstract": "Release of properly processed and assembled mRNPs from the actively transcribing genes, movement of the mRNPs through the interchromatin and interaction with the Nuclear Pore Complexes, leading to cytoplasmic export, are essential steps of eukaryotic gene expression. Here, we review these intranuclear gene expression steps.", "doi": "10.1016/j.semcdb.2014.04.027", "pmid": "24813364", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1084-9521(14)00098-6"}], "notes": [], "created": "2017-05-04T14:59:00.793Z", "modified": "2020-01-21T13:56:01.003Z"}, {"entity": "publication", "iuid": "4796f3b649884ebe8b7d620cde0382ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4796f3b649884ebe8b7d620cde0382ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4796f3b649884ebe8b7d620cde0382ac"}}, "title": "High risk of tobacco-related cancers in CDKN2A mutation-positive melanoma families.", "authors": [{"family": "Helgadottir", "given": "Hildur", "initials": "H"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Borg", "given": "Ake", "initials": "A"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Hansson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "51", "issn": "1468-6244", "issue": "8", "pages": "545-552", "title": "J. Med. Genet.", "issn-l": "0022-2593"}, "abstract": "Germline mutations in the tumour suppressor gene CDKN2A occur in 5-20% of familial melanoma cases. A single founder mutation, p.Arg112dup, accounts for the majority of CDKN2A mutations in Swedish carriers. In a national program, carriers of p.Arg112dup mutation have been identified. The aim of this study was to assess cancer risks in p.Arg112dup carriers and their first degree relatives (FDRs) and second degree relatives (SDRs).\n\nIn this prospective cohort study, cancer diagnoses in carriers (n=120), non-carriers (n=111), carriers' FDRs (n=275) and SDRs (n=321) and controls (n=3976) were obtained from the Swedish Cancer Registry. Relative risks (RRs) for cancers were calculated (number of cancers/person years). Two-sided 95% CIs were calculated for all RRs.\n\nIn carriers prospective RR for non-melanoma cancers was 5.0 (95% CI 3.7 to 7.3), for pancreatic cancer 43.8 (95% CI 13.8 to 139.0), for cancers in upper digestive tissues 17.1 (95% CI 6.3 to 46.5), and in respiratory tissues 15.6 (5.4 to 46.0). In FDRs and SDRs RRs were significantly elevated for cancers in pancreas, respiratory and upper digestive tissues. In ever-smoking carriers compared with never-smoking carriers, the odds ratio (OR) of cancers in pancreas, respiratory or upper digestive tissues was 9.3 (95% CI 1.9 to 44.7).\n\nCDKN2A p.Arg112dup mutation carriers from melanoma-prone families and their FDRs and SDRs have elevated risk for pancreatic, lung, head and neck and gastro-oesophageal carcinomas. These cancers were mainly seen in ever-smoking carriers. Germline CDKN2A mutations may confer an increased sensitivity to carcinogens in tobacco smoke. CDKN2A mutation carriers should be counselled to abstain from smoking.", "doi": "10.1136/jmedgenet-2014-102320", "pmid": "24935963", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "jmedgenet-2014-102320"}, {"db": "pmc", "key": "PMC4112445"}], "notes": [], "created": "2017-05-04T14:58:42.346Z", "modified": "2020-01-21T13:56:02.071Z"}, {"entity": "publication", "iuid": "35129009e031477cb0912e1810e990e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/35129009e031477cb0912e1810e990e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/35129009e031477cb0912e1810e990e7"}}, "title": "Fusions involving protein kinase C and membrane-associated proteins in benign fibrous histiocytoma.", "authors": [{"family": "P\u0142aszczyca", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Brosj\u00f6", "given": "Otte", "initials": "O"}, {"family": "Larsson", "given": "Olle", "initials": "O"}, {"family": "Vult von Steyern", "given": "Fredrik", "initials": "F"}, {"family": "Domanski", "given": "Henryk A", "initials": "HA"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Tayebwa", "given": "Johnbosco", "initials": "J"}, {"family": "Mandahl", "given": "Nils", "initials": "N"}, {"family": "Nord", "given": "Karolin H", "initials": "KH"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "53", "issn": "1878-5875", "issue": null, "pages": "475-481", "title": "Int. J. Biochem. Cell Biol.", "issn-l": "1357-2725"}, "abstract": "Benign fibrous histiocytoma (BFH) is a mesenchymal tumor that most often occurs in the skin (so-called dermatofibroma), but may also appear in soft tissues (so-called deep BFH) and in the skeleton (so-called non-ossifying fibroma). The origin of BFH is unknown, and it has been questioned whether it is a true neoplasm. Chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, RNA sequencing, RT-PCR and quantitative real-time PCR were used to search for recurrent somatic mutations in a series of BFH. BFHs were found to harbor recurrent fusions of genes encoding membrane-associated proteins (podoplanin, CD63 and LAMTOR1) with genes encoding protein kinase C (PKC) isoforms PRKCB and PRKCD. PKCs are serine-threonine kinases that through their many phosphorylation targets are implicated in a variety of cellular processes, as well as tumor development. When inactive, the amino-terminal, regulatory domain of PKCs suppresses the activity of their catalytic domain. Upon activation, which requires several steps, they typically translocate to cell membranes, where they interact with different signaling pathways. The detected PDPN-PRKCB, CD63-PRKCD and LAMTOR1-PRKCD gene fusions are all predicted to result in chimeric proteins consisting of the membrane-binding part of PDPN, CD63 or LAMTOR1 and the entire catalytic domain of the PKC. This novel pathogenetic mechanism should result in constitutive kinase activity at an ectopic location. The results show that BFH indeed is a true neoplasm, and that distorted PKC activity is essential for tumorigenesis. The findings also provide means to differentiate BFH from other skin and soft tissue tumors. This article is part of a Directed Issue entitled: Rare cancers.", "doi": "10.1016/j.biocel.2014.03.027", "pmid": "24721208", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1357-2725(14)00110-1"}], "notes": [], "created": "2017-05-04T14:58:39.115Z", "modified": "2021-07-06T15:41:35.292Z"}, {"entity": "publication", "iuid": "12195c4c6b864b1ebfd2412dab017656", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12195c4c6b864b1ebfd2412dab017656.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12195c4c6b864b1ebfd2412dab017656"}}, "title": "Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes.", "authors": [{"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Gaidzik", "given": "Verena I", "initials": "VI"}, {"family": "Deneberg", "given": "Stefan", "initials": "S"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Bullinger", "given": "Lars", "initials": "L"}, {"family": "D\u00f6hner", "given": "Konstanze", "initials": "K"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "9", "issn": "1559-2308", "issue": "8", "pages": "1108-1119", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "The extent and role of aberrant DNA methylation in promoter CpG islands (CGIs) have been extensively studied in leukemia and other malignancies. Still, CGIs represent only a small fraction of the methylome. We aimed to characterize genome-wide differential methylation of cytogenetically normal AML (CN-AML) cells compared with normal CD34(+) bone marrow cells using the Illumina 450K methylation array. Differential methylation in CN-AML was most prominent in genomic areas far from CGIs, in so called open sea regions. Furthermore, differential methylation was specifically found in genes encoding transcription factors (TFs), with WT1 being the most differentially methylated TF. Among genetic mutations in AML, DNMT3A mutations showed the most prominent association with the DNA methylation pattern, characterized by hypomethylation of CGIs (as compared with DNMT3A wild type cases). The differential methylation in DNMT3A mutant cells vs. wild type cells was predominantly found in HOX genes, which were hypomethylated. These results were confirmed and validated in an independent CN-AML cohort. In conclusion, we show that, in CN-AML, the most pronounced changes in DNA methylation occur in non-CGI regions and that DNMT3A mutations confer a pattern of global hypomethylation that specifically targets HOX genes.", "doi": "10.4161/epi.29315", "pmid": "24866170", "labels": {"National Genomics Infrastructure": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "29315"}, {"db": "pmc", "key": "PMC4164496"}], "notes": [], "created": "2017-05-04T14:58:32.663Z", "modified": "2020-01-21T13:56:00.788Z"}, {"entity": "publication", "iuid": "e1352691e91f443f83f2e05fa911e0a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1352691e91f443f83f2e05fa911e0a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1352691e91f443f83f2e05fa911e0a2"}}, "title": "DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Wefer", "given": "Hugo A", "initials": "HA"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Lindberg", "given": "Mathilda", "initials": "M"}, {"family": "Rodin", "given": "Sandra", "initials": "S"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2014-08-00", "journal": {"volume": "80", "issn": "1098-5336", "issue": "16", "pages": "5116-5123", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571-1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.", "doi": "10.1128/AEM.01403-14", "pmid": "24928874", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "AEM.01403-14"}, {"db": "pmc", "key": "PMC4135748"}], "notes": [], "created": "2017-05-04T14:58:22.068Z", "modified": "2020-01-21T13:56:05.770Z"}, {"entity": "publication", "iuid": "5668bbc3a7b3414aadd9c76732e8773a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5668bbc3a7b3414aadd9c76732e8773a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5668bbc3a7b3414aadd9c76732e8773a"}}, "title": "Nuclease-assisted suppression of human DNA background in sepsis.", "authors": [{"family": "Song", "given": "Yajing", "initials": "Y"}, {"family": "Giske", "given": "Christian G", "initials": "CG"}, {"family": "Gille-Johnson", "given": "Patrik", "initials": "P"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Gyarmati", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2014-07-30", "journal": {"volume": "9", "issn": "1932-6203", "issue": "7", "pages": "e103610", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In order to enrich bacterial DNA, we applied the C0t effect to reduce human DNA background: a model system was set up with human and Escherichia coli (E. coli) DNA to mimic the conditions of bloodstream infections; and this system was adapted to plasma and blood samples from septic patients. As a consequence of the C0t effect, abundant DNA hybridizes faster than rare DNA. Following denaturation and re-hybridization, the amount of abundant DNA can be decreased with the application of double strand specific nucleases, leaving the non-hybridized rare DNA intact. Our experiments show that human DNA concentration can be reduced approximately 100,000-fold without affecting the E. coli DNA concentration in a model system with similarly sized amplicons. With clinical samples, the human DNA background was decreased 100-fold, as bacterial genomes are approximately 1,000-fold smaller compared to the human genome. According to our results, background suppression can be a valuable tool to enrich rare DNA in clinical samples where a high amount of background DNA can be found.", "doi": "10.1371/journal.pone.0103610", "pmid": "25076135", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-14-18983"}, {"db": "pmc", "key": "PMC4116218"}], "notes": [], "created": "2017-05-04T14:58:58.426Z", "modified": "2021-07-08T13:26:08.179Z"}, {"entity": "publication", "iuid": "f578abdd2dcc468fb3e0008446419448", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f578abdd2dcc468fb3e0008446419448.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f578abdd2dcc468fb3e0008446419448"}}, "title": "Analysis of stranded information using an automated procedure for strand specific RNA sequencing.", "authors": [{"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-07-28", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "631", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Strand specific RNA sequencing is rapidly replacing conventional cDNA sequencing as an approach for assessing information about the transcriptome. Alongside improved laboratory protocols the development of bioinformatical tools is steadily progressing. In the current procedure the Illumina TruSeq library preparation kit is used, along with additional reagents, to make stranded libraries in an automated fashion which are then sequenced on Illumina HiSeq 2000. By the use of freely available bioinformatical tools we show, through quality metrics, that the protocol is robust and reproducible. We further highlight the practicality of strand specific libraries by comparing expression of strand specific libraries to non-stranded libraries, by looking at known antisense transcription of pseudogenes and by identifying novel transcription. Furthermore, two ribosomal depletion kits, RiboMinus and RiboZero, are compared and two sequence aligners, Tophat2 and STAR, are also compared.\n\nThe, non-stranded, Illumina TruSeq kit can be adapted to generate strand specific libraries and can be used to access detailed information on the transcriptome. The RiboZero kit is very effective in removing ribosomal RNA from total RNA and the STAR aligner produces high mapping yield in a short time. Strand specific data gives more detailed and correct results than does non-stranded data as we show when estimating expression values and in assembling transcripts. Even well annotated genomes need improvements and corrections which can be achieved using strand specific data.\n\nResearchers in the field should strive to use strand specific data; it allows for more confidence in the data analysis and is less likely to lead to false conclusions. If faced with analysing non-stranded data, researchers should be well aware of the caveats of that approach.", "doi": "10.1186/1471-2164-15-631", "pmid": "25070246", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-15-631"}, {"db": "pmc", "key": "PMC4247151"}], "notes": [], "created": "2017-05-04T14:58:25.245Z", "modified": "2021-07-08T13:26:08.416Z"}, {"entity": "publication", "iuid": "a8089b7ecdce4108af9f807ec5a2cb56", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8089b7ecdce4108af9f807ec5a2cb56.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8089b7ecdce4108af9f807ec5a2cb56"}}, "title": "The archaeal legacy of eukaryotes: a phylogenomic perspective.", "authors": [{"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Saw", "given": "Jimmy H", "initials": "JH"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}], "type": "journal article", "published": "2014-07-03", "journal": {"volume": "6", "issn": "1943-0264", "issue": "10", "pages": "a016022", "title": "Cold Spring Harb Perspect Biol", "issn-l": "1943-0264"}, "abstract": "The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.", "doi": "10.1101/cshperspect.a016022", "pmid": "24993577", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4176008"}, {"db": "pii", "key": "cshperspect.a016022"}], "notes": [], "created": "2017-05-04T14:58:29.705Z", "modified": "2020-01-21T13:56:04.342Z"}, {"entity": "publication", "iuid": "1f7684007f4544b08926f588ccbd5296", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f7684007f4544b08926f588ccbd5296.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f7684007f4544b08926f588ccbd5296"}}, "title": "The human liver-specific proteome defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-07-00", "journal": {"volume": "28", "issn": "1530-6860", "issue": "7", "pages": "2901-2914", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "Human liver physiology and the genetic etiology of the liver diseases can potentially be elucidated through the identification of proteins with enriched expression in the liver. Here, we combined data from RNA sequencing (RNA-Seq) and antibody-based immunohistochemistry across all major human tissues to explore the human liver proteome with enriched expression, as well as the cell type-enriched expression in hepatocyte and bile duct cells. We identified in total 477 protein-coding genes with elevated expression in the liver: 179 genes have higher expression as compared to all the other analyzed tissues; 164 genes have elevated transcript levels in the liver shared with at least one other tissue type; and an additional 134 genes have a mild level of increased expression in the liver. We identified the precise localization of these proteins through antibody-based protein profiling and the subcellular localization of these proteins through immunofluorescent-based profiling. We also identified the biological processes and metabolic functions associated with these proteins, investigated their contribution in the occurrence of liver diseases, and identified potential targets for their treatment. Our study demonstrates the use of RNA-Seq and antibody-based immunohistochemistry for characterizing the human liver proteome, as well as the use of tissue-specific proteins in identification of novel drug targets and discovery of biomarkers.-Kampf, C., Mardinoglu, A., Fagerberg, L., Hallstr\u00f6m, B. M., Edlund, K., Lundberg, E., Pont\u00e9n, F., Nielsen, J., Uhlen, M. The human liver-specific proteome defined by transcriptomics and antibody-based profiling.", "doi": "10.1096/fj.14-250555", "pmid": "24648543", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "fj.14-250555"}], "notes": [], "created": "2017-05-04T14:55:15.921Z", "modified": "2021-07-08T13:44:33.071Z"}, {"entity": "publication", "iuid": "a8749270a8d241589d5afb9978ba5fcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8749270a8d241589d5afb9978ba5fcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8749270a8d241589d5afb9978ba5fcf"}}, "title": "Autosomal dominant brachyolmia in a large Swedish family: phenotypic spectrum and natural course.", "authors": [{"family": "Grigelioniene", "given": "Giedre", "initials": "G"}, {"family": "Geiberger", "given": "Stefan", "initials": "S"}, {"family": "Horemuzova", "given": "Eva", "initials": "E"}, {"family": "Mostr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "J\u00e4ntti", "given": "Nina", "initials": "N"}, {"family": "Neumeyer", "given": "Lo", "initials": "L"}, {"family": "\u00c5str\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O"}], "type": "case reports", "published": "2014-07-00", "journal": {"volume": "164A", "issn": "1552-4833", "issue": "7", "pages": "1635-1641", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Autosomal dominant brachyolmia (Type 3, OMIM #113500) belongs to a group of skeletal dysplasias caused by mutations in the transient receptor potential cation channel, subfamily V, member 4 (TRPV4) gene, encoding a Ca++-permeable, non-selective cation channel. The disorder is characterized by disproportionate short stature with short trunk, scoliosis and platyspondyly. The phenotypic variability and long-term natural course remain inadequately characterized. The purpose of this study was to describe a large Swedish family with brachyolmia type 3 due to a heterozygous TRPV4 mutation c.1847G>A (p.R616Q) in 11 individuals. The mutation has previously been detected in another family with autosomal dominant brachyolmia [Rock et al., 2008]. Review of hospital records and patient assessments indicated that clinical symptoms of brachyolmia became evident by school age with chronic pain in the spine and hips; radiographic changes were evident earlier. Growth was not affected during early childhood but deteriorated with age in some patients due to increasing spinal involvement. Affected individuals had a wide range of subjective symptoms with chronic pain in the extremities and the spine, and paresthesias. Our findings indicate that autosomal dominant brachyolmia may be associated with significant long-term morbidity, as seen in this family.", "doi": "10.1002/ajmg.a.36502", "pmid": "24677493", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "OMIM", "key": "113500"}], "notes": [], "created": "2017-05-04T14:58:20.553Z", "modified": "2020-01-21T13:56:04.367Z"}, {"entity": "publication", "iuid": "884c24de81744944a77486515580b3b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/884c24de81744944a77486515580b3b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/884c24de81744944a77486515580b3b2"}}, "title": "'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum.", "authors": [{"family": "Guy", "given": "Lionel", "initials": "L"}, {"family": "Spang", "given": "Anja", "initials": "A"}, {"family": "Saw", "given": "Jimmy H", "initials": "JH"}, {"family": "Ettema", "given": "Thijs J G", "initials": "TJ"}], "type": "comment", "published": "2014-07-00", "journal": {"volume": "8", "issn": "1751-7370", "issue": "7", "pages": "1353-1357", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": null, "doi": "10.1038/ismej.2014.6", "pmid": "24522265", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej20146"}, {"db": "pmc", "key": "PMC4069404"}], "notes": [], "created": "2017-05-04T14:58:40.062Z", "modified": "2020-01-21T13:56:03.468Z"}, {"entity": "publication", "iuid": "4c588940aa644ce8ac7fd1c2343376e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c588940aa644ce8ac7fd1c2343376e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c588940aa644ce8ac7fd1c2343376e3"}}, "title": "Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.", "authors": [{"family": "Woll", "given": "Petter S", "initials": "PS"}, {"family": "Kj\u00e4llquist", "given": "Una", "initials": "U"}, {"family": "Chowdhury", "given": "Onima", "initials": "O"}, {"family": "Doolittle", "given": "Helen", "initials": "H"}, {"family": "Wedge", "given": "David C", "initials": "DC"}, {"family": "Thongjuea", "given": "Supat", "initials": "S"}, {"family": "Erlandsson", "given": "Rikard", "initials": "R"}, {"family": "Ngara", "given": "Mtakai", "initials": "M"}, {"family": "Anderson", "given": "Kristina", "initials": "K"}, {"family": "Deng", "given": "Qiaolin", "initials": "Q"}, {"family": "Mead", "given": "Adam J", "initials": "AJ"}, {"family": "Stenson", "given": "Laura", "initials": "L"}, {"family": "Giustacchini", "given": "Alice", "initials": "A"}, {"family": "Duarte", "given": "Sara", "initials": "S"}, {"family": "Giannoulatou", "given": "Eleni", "initials": "E"}, {"family": "Taylor", "given": "Stephen", "initials": "S"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Scharenberg", "given": "Christian", "initials": "C"}, {"family": "Mortera-Blanco", "given": "Teresa", "initials": "T"}, {"family": "Macaulay", "given": "Iain C", "initials": "IC"}, {"family": "Clark", "given": "Sally-Ann", "initials": "SA"}, {"family": "Dybedal", "given": "Ingunn", "initials": "I"}, {"family": "Josefsen", "given": "Dag", "initials": "D"}, {"family": "Fenaux", "given": "Pierre", "initials": "P"}, {"family": "Hokland", "given": "Peter", "initials": "P"}, {"family": "Holm", "given": "Mette S", "initials": "MS"}, {"family": "Cazzola", "given": "Mario", "initials": "M"}, {"family": "Malcovati", "given": "Luca", "initials": "L"}, {"family": "Tauro", "given": "Sudhir", "initials": "S"}, {"family": "Bowen", "given": "David", "initials": "D"}, {"family": "Boultwood", "given": "Jacqueline", "initials": "J"}, {"family": "Pellagatti", "given": "Andrea", "initials": "A"}, {"family": "Pimanda", "given": "John E", "initials": "JE"}, {"family": "Unnikrishnan", "given": "Ashwin", "initials": "A"}, {"family": "Vyas", "given": "Paresh", "initials": "P"}, {"family": "G\u00f6hring", "given": "Gudrun", "initials": "G"}, {"family": "Schlegelberger", "given": "Brigitte", "initials": "B"}, {"family": "Tobiasson", "given": "Magnus", "initials": "M"}, {"family": "Kvalheim", "given": "Gunnar", "initials": "G"}, {"family": "Constantinescu", "given": "Stefan N", "initials": "SN"}, {"family": "Nerlov", "given": "Claus", "initials": "C"}, {"family": "Nilsson", "given": "Lars", "initials": "L"}, {"family": "Campbell", "given": "Peter J", "initials": "PJ"}, {"family": "Sandberg", "given": "Rickard", "initials": "R", "orcid": "0000-0001-6473-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/048c7c9b9edb4366bac7873daad461cd.json"}}, {"family": "Papaemmanuil", "given": "Elli", "initials": "E"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SE"}], "type": "journal article", "published": "2014-06-16", "journal": {"volume": "25", "issn": "1878-3686", "issue": "6", "pages": "794-808", "title": "Cancer Cell", "issn-l": "1535-6108"}, "abstract": "Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.", "doi": "10.1016/j.ccr.2014.03.036", "pmid": "24835589", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1535-6108(14)00134-2"}, {"db": "GEO", "key": "GSE55689"}, {"db": "SRA", "key": "SRP039353"}], "notes": [], "created": "2017-05-04T14:58:26.761Z", "modified": "2021-07-07T11:46:33.589Z"}, {"entity": "publication", "iuid": "68977f979c6b4bddbb7952d615314946", "links": {"self": {"href": "https://publications.scilifelab.se/publication/68977f979c6b4bddbb7952d615314946.json"}, "display": {"href": "https://publications.scilifelab.se/publication/68977f979c6b4bddbb7952d615314946"}}, "title": "Mapping-by-sequencing accelerates forward genetics in barley.", "authors": [{"family": "Mascher", "given": "Martin", "initials": "M"}, {"family": "Jost", "given": "Matthias", "initials": "M"}, {"family": "Kuon", "given": "Joel-Elias", "initials": "JE"}, {"family": "Himmelbach", "given": "Axel", "initials": "A"}, {"family": "A\u00dffalg", "given": "Axel", "initials": "A"}, {"family": "Beier", "given": "Sebastian", "initials": "S"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}, {"family": "Graner", "given": "Andreas", "initials": "A"}, {"family": "Stein", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2014-06-10", "journal": {"volume": "15", "issn": "1474-760X", "issue": "6", "pages": "R78", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "Mapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.", "doi": "10.1186/gb-2014-15-6-r78", "pmid": "24917130", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gb-2014-15-6-r78"}, {"db": "pmc", "key": "PMC4073093"}], "notes": [], "created": "2017-05-04T14:58:36.935Z", "modified": "2020-01-21T13:56:02.787Z"}, {"entity": "publication", "iuid": "062de5b535954abc89347c8dfaaaf44b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/062de5b535954abc89347c8dfaaaf44b"}}, "title": "Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.", "authors": [{"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Ye", "given": "Rosa", "initials": "R"}, {"family": "Knudsen", "given": "Bjarne", "initials": "B"}, {"family": "Simonsen", "given": "Martin", "initials": "M"}, {"family": "Turner", "given": "Benjamin", "initials": "B"}, {"family": "de Jong", "given": "Pieter", "initials": "P"}, {"family": "Wu", "given": "Cheng-Cang", "initials": "CC"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-06-06", "journal": {"volume": "15", "issn": "1471-2164", "issue": null, "pages": "439", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between sequencing costs and assembly quality.\n\nIn order to sequence the genome of Norway spruce, which is of great size and complexity, we developed and applied a new technology based on the massive production, sequencing, and assembly of Fosmid pools (FP). The spruce chromosomes were sampled with ~40,000 bp Fosmid inserts to obtain around two-fold genome coverage, in parallel with traditional whole genome shotgun sequencing (WGS) of haploid and diploid genomes. Compared to the WGS results, the contiguity and quality of the FP assemblies were high, and they allowed us to fill WGS gaps resulting from repeats, low coverage, and allelic differences. The FP contig sets were further merged with WGS data using a novel software package GAM-NGS.\n\nBy exploiting FP technology, the first published assembly of a conifer genome was sequenced entirely with massively parallel sequencing. Here we provide a comprehensive report on the different features of the approach and the optimization of the process.We have made public the input data (FASTQ format) for the set of pools used in this study:ftp://congenie.org/congenie/Nystedt_2013/Assembly/ProcessedData/FosmidPools/.(alternatively accessible via http://congenie.org/downloads).The software used for running the assembly process is available at http://research.scilifelab.se/andrej_alexeyenko/downloads/fpools/.", "doi": "10.1186/1471-2164-15-439", "pmid": "24906298", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1471-2164-15-439"}, {"db": "pmc", "key": "PMC4070561"}], "notes": [], "created": "2017-05-04T14:56:29.797Z", "modified": "2021-07-08T13:26:08.069Z"}, {"entity": "publication", "iuid": "e90a69bcc5ad4e8d9cc4fa0358ad78ae", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e90a69bcc5ad4e8d9cc4fa0358ad78ae.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e90a69bcc5ad4e8d9cc4fa0358ad78ae"}}, "title": "p53 protein expression independently predicts outcome in patients with lower-risk myelodysplastic syndromes with del(5q).", "authors": [{"family": "Saft", "given": "Leonie", "initials": "L"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Ghaderi", "given": "Mehran", "initials": "M"}, {"family": "Matolcsy", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Mufti", "given": "Ghulam J", "initials": "GJ"}, {"family": "Kulasekararaj", "given": "Austin", "initials": "A"}, {"family": "G\u00f6hring", "given": "Gudrun", "initials": "G"}, {"family": "Giagounidis", "given": "Aristoteles", "initials": "A"}, {"family": "Selleslag", "given": "Dominik", "initials": "D"}, {"family": "Muus", "given": "Petra", "initials": "P"}, {"family": "Sanz", "given": "Guillermo", "initials": "G"}, {"family": "Mittelman", "given": "Moshe", "initials": "M"}, {"family": "Bowen", "given": "David", "initials": "D"}, {"family": "Porwit", "given": "Anna", "initials": "A"}, {"family": "Fu", "given": "Tommy", "initials": "T"}, {"family": "Backstrom", "given": "Jay", "initials": "J"}, {"family": "Fenaux", "given": "Pierre", "initials": "P"}, {"family": "MacBeth", "given": "Kyle J", "initials": "KJ"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "99", "issn": "1592-8721", "issue": "6", "pages": "1041-1049", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": "Del(5q) myelodysplastic syndromes defined by the International Prognostic Scoring System as low- or intermediate-1-risk (lower-risk) are considered to have an indolent course; however, recent data have identified a subgroup of these patients with more aggressive disease and poorer outcomes. Using deep sequencing technology, we previously demonstrated that 18% of patients with lower-risk del(5q) myelodysplastic syndromes carry TP53 mutated subclones rendering them at higher risk of progression. In this study, bone marrow biopsies from 85 patients treated with lenalidomide in the MDS-004 clinical trial were retrospectively assessed for p53 expression by immunohistochemistry in association with outcome. Strong p53 expression in \u2265 1% of bone marrow progenitor cells, observed in 35% (30 of 85) of patients, was significantly associated with higher acute myeloid leukemia risk (P=0.0006), shorter overall survival (P=0.0175), and a lower cytogenetic response rate (P=0.009), but not with achievement or duration of 26-week transfusion independence response. In a multivariate analysis, p53-positive immunohistochemistry was the strongest independent predictor of transformation to acute myeloid leukemia (P=0.0035). Pyrosequencing analysis of laser-microdissected cells with strong p53 expression confirmed the TP53 mutation, whereas cells with moderate expression predominantly had wild-type p53. This study validates p53 immunohistochemistry as a strong and clinically useful predictive tool in patients with lower-risk del(5q) myelodysplastic syndromes. This study was based on data from the MDS 004 trial (clinicaltrials.gov identifier: NCT00179621).", "doi": "10.3324/haematol.2013.098103", "pmid": "24682512", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "haematol.2013.098103"}, {"db": "pmc", "key": "PMC4040908"}, {"db": "ClinicalTrials.gov", "key": "NCT00179621"}], "notes": [], "created": "2017-05-04T14:58:37.871Z", "modified": "2020-01-21T13:56:05.939Z"}, {"entity": "publication", "iuid": "a2b9b87ef49745668774781bc51b9314", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2b9b87ef49745668774781bc51b9314.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2b9b87ef49745668774781bc51b9314"}}, "title": "microRNA-34b/c on chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemia.", "authors": [{"family": "Deneberg", "given": "Stefan", "initials": "S"}, {"family": "Kanduri", "given": "Meena", "initials": "M"}, {"family": "Ali", "given": "Dina", "initials": "D"}, {"family": "Bengtzen", "given": "Sofia", "initials": "S"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Kimby", "given": "Eva", "initials": "E"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "9", "issn": "1559-2308", "issue": "6", "pages": "910-917", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "A commonly deleted region in chronic lymphocytic leukemia (CLL) is the 11q22-23 region, which encompasses the ATM gene. Evidence suggests that tumor suppressor genes other than ATM are likely to be involved in CLL with del(11q). A microRNA (miR) cluster including the miR-34b and miR-34c genes is located, among other genes, within the commonly deleted region (CDR) at 11q. Interestingly, these miRs are part of the TP53 network and have been shown to be epigenetically regulated. In this study, we investigated the expression and methylation status of these miRs in a well-characterized cohort of CLL, including cases with/without 11q-deletion. We show that the miR-34b/c promoter was aberrantly hypermethylated in a large proportion of CLL cases (48%, 25/52 cases). miR-34b/c expression correlated inversely to DNA methylation (P = 0.003), and presence of high H3K37me3 further suppressed expression regardless of methylation status. Furthermore, increased miR-34b/c methylation inversely correlated with the presence of 11q-deletion, indicating that methylation and del(11q) independently silence these miRs. Finally, 5-azacytidine and trichostatin A exposure synergistically increased the expression of miR-34b/c in CLL cells, and transfection of miR-34b or miR-34c into HG3 CLL cells significantly increased apoptosis. Altogether, our novel data suggest that miR-34b/c is a candidate tumor suppressor that is epigenetically silenced in CLL.", "doi": "10.4161/epi.28603", "pmid": "24686393", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "28603"}, {"db": "pmc", "key": "PMC4053441"}], "notes": [], "created": "2017-05-04T14:58:32.363Z", "modified": "2020-01-21T13:56:04.188Z"}, {"entity": "publication", "iuid": "78c3ad5a0d7e42e5a6a81a16e47c965f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78c3ad5a0d7e42e5a6a81a16e47c965f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78c3ad5a0d7e42e5a6a81a16e47c965f"}}, "title": "The human testis-specific proteome defined by transcriptomics and antibody-based profiling.", "authors": [{"family": "Djureinovic", "given": "D", "initials": "D"}, {"family": "Fagerberg", "given": "L", "initials": "L"}, {"family": "Hallstr\u00f6m", "given": "B", "initials": "B"}, {"family": "Danielsson", "given": "A", "initials": "A"}, {"family": "Lindskog", "given": "C", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Pont\u00e9n", "given": "F", "initials": "F"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "20", "issn": "1460-2407", "issue": "6", "pages": "476-488", "title": "Mol. Hum. Reprod.", "issn-l": "1360-9947"}, "abstract": "The testis' function is to produce haploid germ cells necessary for reproduction. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to characterize the molecular components of the testis. Deep sequencing (RNA-Seq) of normal human testicular tissue from seven individuals was performed and compared with 26 other normal human tissue types. All 20 050 putative human genes were classified into categories based on expression patterns. The analysis shows that testis is the tissue with the most tissue-specific genes by far. More than 1000 genes show a testis-enriched expression pattern in testis when compared with all other analyzed tissues. Highly testis enriched genes were further characterized with respect to protein localization within the testis, such as spermatogonia, spermatocytes, spermatids, sperm, Sertoli cells and Leydig cells. Here we present an immunohistochemistry-based analysis, showing the localization of corresponding proteins in different cell types and various stages of spermatogenesis, for 62 genes expressed at >50-fold higher levels in testis when compared with other tissues. A large fraction of these genes were unexpectedly expressed in early stages of spermatogenesis. In conclusion, we have applied a genome-wide analysis to identify the human testis-specific proteome using transcriptomics and antibody-based protein profiling, providing lists of genes expressed in a tissue-enriched manner in the testis. The majority of these genes and proteins were previously poorly characterised in terms of localization and function, and our list provides an important starting point to increase our molecular understanding of human reproductive biology and disease.", "doi": "10.1093/molehr/gau018", "pmid": "24598113", "labels": {"National Genomics Infrastructure": null, "Tissue Profiling": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "gau018"}], "notes": [], "created": "2017-05-04T14:56:08.213Z", "modified": "2021-07-08T13:44:33.374Z"}, {"entity": "publication", "iuid": "4d03b5a44169406f97833838a5ad0b42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d03b5a44169406f97833838a5ad0b42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d03b5a44169406f97833838a5ad0b42"}}, "title": "The age and genomic integrity of neurons after cortical stroke in humans.", "authors": [{"family": "Huttner", "given": "Hagen B", "initials": "HB"}, {"family": "Bergmann", "given": "Olaf", "initials": "O"}, {"family": "Salehpour", "given": "Mehran", "initials": "M"}, {"family": "R\u00e1cz", "given": "Attila", "initials": "A"}, {"family": "Tatarishvili", "given": "Jemal", "initials": "J"}, {"family": "Lindgren", "given": "Emma", "initials": "E"}, {"family": "Csonka", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Csiba", "given": "L\u00e1szl\u00f3", "initials": "L"}, {"family": "Hortob\u00e1gyi", "given": "Tibor", "initials": "T"}, {"family": "M\u00e9hes", "given": "G\u00e1bor", "initials": "G"}, {"family": "Englund", "given": "Elisabet", "initials": "E"}, {"family": "Solnestam", "given": "Beata Werne", "initials": "BW"}, {"family": "Zdunek", "given": "Sofia", "initials": "S"}, {"family": "Scharenberg", "given": "Christian", "initials": "C"}, {"family": "Str\u00f6m", "given": "Lena", "initials": "L"}, {"family": "St\u00e5hl", "given": "Patrik", "initials": "P"}, {"family": "Sigurgeirsson", "given": "Benjamin", "initials": "B"}, {"family": "Dahl", "given": "Andreas", "initials": "A"}, {"family": "Schwab", "given": "Stefan", "initials": "S"}, {"family": "Possnert", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bernard", "given": "Samuel", "initials": "S"}, {"family": "Kokaia", "given": "Zaal", "initials": "Z"}, {"family": "Lindvall", "given": "Olle", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Fris\u00e9n", "given": "Jonas", "initials": "J"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "17", "issn": "1546-1726", "issue": "6", "pages": "801-803", "title": "Nat. Neurosci.", "issn-l": "1097-6256"}, "abstract": "It has been unclear whether ischemic stroke induces neurogenesis or neuronal DNA rearrangements in the human neocortex. Using immunohistochemistry; transcriptome, genome and ploidy analyses; and determination of nuclear bomb test-derived (14)C concentration in neuronal DNA, we found neither to be the case. A large proportion of cortical neurons displayed DNA fragmentation and DNA repair a short time after stroke, whereas neurons at chronic stages after stroke showed DNA integrity, demonstrating the relevance of an intact genome for survival.", "doi": "10.1038/nn.3706", "pmid": "24747576", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "nn.3706"}, {"db": "GEO", "key": "GSE56267"}, {"db": "SRA", "key": "SRP040676"}], "notes": [], "created": "2017-05-04T14:58:49.076Z", "modified": "2021-07-08T13:26:08.173Z"}, {"entity": "publication", "iuid": "42b66ac690ee431fbf466d0f44c8ccea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42b66ac690ee431fbf466d0f44c8ccea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42b66ac690ee431fbf466d0f44c8ccea"}}, "title": "SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.", "authors": [{"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Hultin-Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "Branca", "given": "Rui M M", "initials": "RM"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "13", "issn": "1535-9484", "issue": "6", "pages": "1552-1562", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Alternative splicing is a pervasive process in eukaryotic organisms. More than 90% of human genes have alternatively spliced products, and aberrant splicing has been shown to be associated with many diseases. Current methods employed in the detection of splice variants include prediction by clustering of expressed sequence tags, exon microarray, and mRNA sequencing, all methods focusing on RNA-level information. There is a lack of tools for analyzing splice variants at the protein level. Here, we present SpliceVista, a tool for splice variant identification and visualization based on mass spectrometry proteomics data. SpliceVista retrieves gene structure and translated sequences from alternative splicing databases and maps MS-identified peptides to splice variants. The visualization module plots the exon composition of each splice variant and aligns identified peptides with transcript positions. If quantitative mass spectrometry data are used, SpliceVista plots the quantitative patterns for each peptide and provides users with the option to cluster peptides based on their quantitative patterns. SpliceVista can identify splice-variant-specific peptides, providing the possibility for variant-specific analysis. The tool was tested on two experimental datasets (PXD000065 and PXD000134). In A431 cells treated with gefitinib, 2983 splice-variant-specific peptides corresponding to 939 splice variants were identified. Through comparison of splice-variant-centric, protein-centric, and gene-centric quantification, several genes (e.g. EIF4H) were found to have differentially regulated splice variants after gefitinib treatment. The same discrepancy between protein-centric and splice-centric quantification was detected in the other dataset, in which induced pluripotent stem cells were compared with parental fibroblast and human embryotic stem cells. In addition, SpliceVista can be used to visualize novel splice variants inferred from peptide-level evidence. In summary, SpliceVista enables visualization, detection, and differential quantification of protein splice variants that are often missed in current proteomics pipelines.", "doi": "10.1074/mcp.M113.031203", "pmid": "24692640", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S1535-9476(20)33085-1"}, {"db": "pmc", "key": "PMC4047474"}], "notes": [], "created": "2017-05-04T14:58:44.841Z", "modified": "2021-07-08T11:36:15.190Z"}, {"entity": "publication", "iuid": "0ea09319631c4703bab23fa4c925977a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ea09319631c4703bab23fa4c925977a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ea09319631c4703bab23fa4c925977a"}}, "title": "Simultaneous uptake of lignocellulose-based monosaccharides by Escherichia coli.", "authors": [{"family": "Jarmander", "given": "Johan", "initials": "J"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Larsson", "given": "Gen", "initials": "G"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "111", "issn": "1097-0290", "issue": "6", "pages": "1108-1115", "title": "Biotechnol. Bioeng.", "issn-l": "0006-3592"}, "abstract": "Lignocellulosic waste is a naturally abundant biomass and is therefore an attractive material to use in second generation biorefineries. Microbial growth on the monosaccharides present in hydrolyzed lignocellulose is however associated with several obstacles whereof one is the lack of simultaneous uptake of the sugars. We have studied the aerobic growth of Escherichia coli on D-glucose, D-xylose, and L-arabinose and for simultaneous uptake to occur, both the carbon catabolite repression mechanism (CCR) and the AraC repression of xylose uptake and metabolism had to be removed. The strain AF1000 is a MC4100 derivative that is only able to assimilate arabinose after a considerable lag phase, which is unsuitable for commercial production. This strain was successfully adapted to growth on L-arabinose and this led to simultaneous uptake of arabinose and xylose in a diauxic growth mode following glucose consumption. In this strain, a deletion in the phosphoenolpyruvate:phosphotransferase system (PTS) for glucose uptake, the ptsG mutation, was introduced. The resulting strain, PPA652ara simultaneously consumed all three monosaccharides at a maximum specific growth rate of 0.59\u2009h(-1) , 55% higher than for the ptsG mutant alone. Also, no residual sugar was present in the cultivation medium. The potential of PPA652ara is further acknowledged by the performance of AF1000 during fed-batch processing on a mixture of D-glucose, D-xylose, and L-arabinose. The conclusion is that without the removal of both layers of carbon uptake control, this process results in accumulation of pentoses and leads to a reduction of the specific growth rate by 30%.", "doi": "10.1002/bit.25182", "pmid": "24382675", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:22.993Z", "modified": "2020-01-21T13:56:00.705Z"}, {"entity": "publication", "iuid": "93423dd1415c4c6ebdd0680418875c9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93423dd1415c4c6ebdd0680418875c9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93423dd1415c4c6ebdd0680418875c9f"}}, "title": "Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.", "authors": [{"family": "Goh", "given": "Gerald", "initials": "G"}, {"family": "Scholl", "given": "Ute I", "initials": "UI"}, {"family": "Healy", "given": "James M", "initials": "JM"}, {"family": "Choi", "given": "Murim", "initials": "M"}, {"family": "Prasad", "given": "Manju L", "initials": "ML"}, {"family": "Nelson-Williams", "given": "Carol", "initials": "C"}, {"family": "Kunstman", "given": "John W", "initials": "JW"}, {"family": "Kuntsman", "given": "John W", "initials": "JW"}, {"family": "Korah", "given": "Reju", "initials": "R"}, {"family": "Suttorp", "given": "Anna-Carinna", "initials": "AC"}, {"family": "Dietrich", "given": "Dimo", "initials": "D"}, {"family": "Haase", "given": "Matthias", "initials": "M"}, {"family": "Willenberg", "given": "Holger S", "initials": "HS"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Akerstr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bj\u00f6rklund", "given": "Peyman", "initials": "P"}, {"family": "Carling", "given": "Tobias", "initials": "T"}, {"family": "Lifton", "given": "Richard P", "initials": "RP"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "46", "issn": "1546-1718", "issue": "6", "pages": "613-617", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Adrenal tumors autonomously producing cortisol cause Cushing's syndrome. We performed exome sequencing of 25 tumor-normal pairs and identified 2 subgroups. Eight tumors (including three carcinomas) had many somatic copy number variants (CNVs) with frequent deletion of CDC42 and CDKN2A, amplification of 5q31.2 and protein-altering mutations in TP53 and RB1. Seventeen tumors (all adenomas) had no somatic CNVs or TP53 or RB1 mutations. Six of these had known gain-of-function mutations in CTNNB1 (\u03b2-catenin) or GNAS (G\u03b1s). Six others had somatic mutations in PRKACA (protein kinase A (PKA) catalytic subunit) resulting in a p.Leu206Arg substitution. Further sequencing identified this mutation in 13 of 63 tumors (35% of adenomas with overt Cushing's syndrome). PRKACA, GNAS and CTNNB1 mutations were mutually exclusive. Leu206 directly interacts with the regulatory subunit of PKA, PRKAR1A. Leu206Arg PRKACA loses PRKAR1A binding, increasing the phosphorylation of downstream targets. PKA activity induces cortisol production and cell proliferation, providing a mechanism for tumor development. These findings define distinct mechanisms underlying adrenal cortisol-producing tumors.", "doi": "10.1038/ng.2956", "pmid": "24747643", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ng.2956"}, {"db": "pmc", "key": "PMC4074779"}, {"db": "mid", "key": "HHMIMS577752"}, {"db": "GEO", "key": "GSE56016"}], "notes": [], "created": "2017-05-04T14:58:47.451Z", "modified": "2020-01-21T13:56:03.773Z"}, {"entity": "publication", "iuid": "6f66c32e0a7d4aad85c42f03129b7ebf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f66c32e0a7d4aad85c42f03129b7ebf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f66c32e0a7d4aad85c42f03129b7ebf"}}, "title": "Recurrent EWSR1-CREB3L1 gene fusions in sclerosing epithelioid fibrosarcoma.", "authors": [{"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Puls", "given": "Florian", "initials": "F"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Thway", "given": "Khin", "initials": "K"}, {"family": "Fisher", "given": "Cyril", "initials": "C"}, {"family": "Sumathi", "given": "Vaiyapuri P", "initials": "VP"}, {"family": "Tayebwa", "given": "Johnbosco", "initials": "J"}, {"family": "Nord", "given": "Karolin H", "initials": "KH"}, {"family": "Kindblom", "given": "Lars-Gunnar", "initials": "LG"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2014-06-00", "journal": {"volume": "38", "issn": "1532-0979", "issue": "6", "pages": "801-808", "title": "Am. J. Surg. Pathol.", "issn-l": "0147-5185"}, "abstract": "Sclerosing epithelioid fibrosarcoma (SEF) and low-grade fibromyxoid sarcoma (LGFMS) are 2 distinct types of sarcoma, with a subset of cases showing overlapping morphologic and immunohistochemical features. LGFMS is characterized by expression of the MUC4 protein, and about 90% of cases display a distinctive FUS-CREB3L2 gene fusion. In addition, SEF is often MUC4 positive, but is genetically less well studied. Fluorescence in situ hybridization (FISH) studies have shown involvement of the FUS gene in the majority of so-called hybrid LGFMS/SEF and in 10% to 25% of sarcomas with pure SEF morphology. In this study, we investigated a series of 10 primary tumors showing pure SEF morphology, 4 cases of LGFMS that at local or distant relapse showed predominant SEF morphology, and 1 primary hybrid LGFMS/SEF. All but 1 case showed diffuse expression for MUC4. Using FISH, reverse transcription polymerase chain reaction, and/or mRNA sequencing in selected cases, we found recurrent EWSR1-CREB3L1 fusion transcripts by reverse transcription polymerase chain reaction in 3/10 pure SEF cases and splits and deletions of the EWSR1 and/or CREB3L1 genes by FISH in 6 additional cases. All 5 cases of LGFMS with progression to SEF morphology or hybrid features had FUS-CREB3L2 fusion transcripts. Our results indicate that EWSR1 and CREB3L1 rearrangements are predominant over FUS and CREB3L2 rearrangements in pure SEF, highlighting that SEF and LGFMS are different tumor types, with different impacts on patient outcome.", "doi": "10.1097/PAS.0000000000000158", "pmid": "24441665", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:21.158Z", "modified": "2020-01-21T13:56:02.906Z"}, {"entity": "publication", "iuid": "5314403139f24150a946db9173cebf64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5314403139f24150a946db9173cebf64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5314403139f24150a946db9173cebf64"}}, "title": "Genetic factors may play a prominent role in the development of coronary heart disease dependent on important environmental factors.", "authors": [{"family": "Song", "given": "C", "initials": "C"}, {"family": "Chang", "given": "Z", "initials": "Z"}, {"family": "Magnusson", "given": "P K E", "initials": "PK"}, {"family": "Ingelsson", "given": "E", "initials": "E"}, {"family": "Pedersen", "given": "N L", "initials": "NL"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "275", "issn": "1365-2796", "issue": "6", "pages": "631-639", "title": "J. Intern. Med.", "issn-l": "0954-6820"}, "abstract": "The aim of the study was to examine whether various lifestyle factors modify genetic influences on coronary heart disease (CHD).\n\nThe effect of lifestyle factors [including smoking, sedentary lifestyle, alcohol intake and body mass index (BMI)] on risk of CHD was evaluated via Cox regression models in a twin study of gene-environment interaction. Using structure equation modelling, we estimated genetic variance of CHD dependent on lifestyle factors.\n\nIn total, 51\u00a0065 same-sex twins from 25\u00a0715 twin pairs born before 1958 and registered in the Swedish Twin Registry were eligible for this study. During the 40-year follow-up, 7264 incident CHD events were recorded.\n\nSmoking, sedentary lifestyle and above average BMI were significantly associated with increased CHD incidence. The heritability of CHD decreased with increasing age, as well as with increasing levels of BMI, in both men and women.\n\nThe difference in the genetic component of CHD as a function of BMI suggests that genetic factors may play a more prominent role for disease development in the absence of important environmental factors. Increased knowledge of gene-environment interactions will be important for a full understanding of the aetiology of CHD.", "doi": "10.1111/joim.12177", "pmid": "24330166", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4288985"}], "notes": [], "created": "2017-05-04T14:57:59.998Z", "modified": "2020-01-21T13:56:02.327Z"}, {"entity": "publication", "iuid": "82f246f387b649ba8c29e2ea3fd2e405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/82f246f387b649ba8c29e2ea3fd2e405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/82f246f387b649ba8c29e2ea3fd2e405"}}, "title": "Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change.", "authors": [{"family": "Osman", "given": "Omneya A", "initials": "OA"}, {"family": "Gudasz", "given": "Cristian", "initials": "C"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2014-06-00", "journal": {"volume": "88", "issn": "1574-6941", "issue": "3", "pages": "468-481", "title": "FEMS Microbiol. Ecol.", "issn-l": "0168-6496"}, "abstract": "The abundance and composition of genes involved in the catabolism of aromatic compounds provide important information on the biodegradation potential of organic pollutants and naturally occurring compounds in the environment. We studied catechol 2, 3 dioxygenase (C23O) and benzylsuccinate synthase (bssA) genes coding for key enzymes of aerobic and anaerobic degradation of aromatic compounds in experimental incubations with sediments from two contrasting lakes; humic lake Svarttj\u00e4rn and eutrophic Vallentunasj\u00f6n, respectively. Sediment cores from both lakes were incubated continuously for 5 months at constant temperatures ranging from 1.0 to 21.0 \u00b0C. The difference in C23O gene composition of the sediment analyzed at the end of the experiment was larger between lakes, than among temperature treatments within each lake. The abundance of C23O gene copies and measured respiration was positively correlated with temperature in Vallentunasj\u00f6n, whereas putative C23O genes were present in lower concentrations in Svarttj\u00e4rn sediments. Putative bssA genes were only detected in Svarttj\u00e4rn. For both lakes, the two catabolic genes were most abundant in the surface sediment. The results emphasize the important role of temperature and nutrient availability in controlling the functional potential of sediment microorganisms and reveal differences between systems with contrasting trophic status. A better understanding of catabolic pathways and enzymes will enable more accurate forecasting of the functional properties of ecosystems under various scenarios of environmental change.", "doi": "10.1111/1574-6941.12312", "pmid": "24597511", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "GENBANK", "key": "KC175607"}, {"db": "GENBANK", "key": "KC175626"}, {"db": "GENBANK", "key": "KC175627"}, {"db": "GENBANK", "key": "KC175643"}], "notes": [], "created": "2017-05-04T14:58:34.593Z", "modified": "2020-01-21T13:56:03.382Z"}, {"entity": "publication", "iuid": "69c152e0a26d4b63a13a2298e1176dc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69c152e0a26d4b63a13a2298e1176dc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69c152e0a26d4b63a13a2298e1176dc8"}}, "title": "Genetic architecture of main effect QTL for heading date in European winter wheat.", "authors": [{"family": "Zanke", "given": "Christine", "initials": "C"}, {"family": "Ling", "given": "Jie", "initials": "J"}, {"family": "Plieske", "given": "J\u00f6rg", "initials": "J"}, {"family": "Kollers", "given": "Sonja", "initials": "S"}, {"family": "Ebmeyer", "given": "Erhard", "initials": "E"}, {"family": "Korzun", "given": "Viktor", "initials": "V"}, {"family": "Argillier", "given": "Odile", "initials": "O"}, {"family": "Stiewe", "given": "Gunther", "initials": "G"}, {"family": "Hinze", "given": "Maike", "initials": "M"}, {"family": "Beier", "given": "Sebastian", "initials": "S"}, {"family": "Ganal", "given": "Martin W", "initials": "MW"}, {"family": "R\u00f6der", "given": "Marion S", "initials": "MS"}], "type": "journal article", "published": "2014-05-20", "journal": {"volume": "5", "issn": "1664-462X", "issue": null, "pages": "217", "title": "Front Plant Sci", "issn-l": "1664-462X"}, "abstract": "A genome-wide association study (GWAS) for heading date (HD) was performed with a panel of 358 European winter wheat (Triticum aestivum L.) varieties and 14 spring wheat varieties through the phenotypic evaluation of HD in field tests in eight environments. Genotyping data consisted of 770 mapped microsatellite loci and 7934 mapped SNP markers derived from the 90K iSelect wheat chip. Best linear unbiased estimations (BLUEs) were calculated across all trials and ranged from 142.5 to 159.6 days after the 1st of January with an average value of 151.4 days. Considering only associations with a -log10 (P-value) \u2265 3.0, a total of 340 SSR and 2983 SNP marker-trait associations (MTAs) were detected. After Bonferroni correction for multiple testing, a total of 72 SSR and 438 SNP marker-trait associations remained significant. Highly significant MTAs were detected for the photoperiodism gene Ppd-D1, which was genotyped in all varieties. Consistent associations were found on all chromosomes with the highest number of MTAs on chromosome 5B. Linear regression showed a clear dependence of the HD score BLUEs on the number of favorable alleles (decreasing HD) and unfavorable alleles (increasing HD) per variety meaning that genotypes with a higher number of favorable or a low number of unfavorable alleles showed lower HD and therefore flowered earlier. For the vernalization gene Vrn-A2 co-locating MTAs on chromosome 5A, as well as for the photoperiodism genes Ppd-A1 and Ppd-B1 on chromosomes 2A and 2B were detected. After the construction of an integrated map of the SSR and SNP markers and by exploiting the synteny to sequenced species, such as rice and Brachypodium distachyon, we were able to demonstrate that a marker locus on wheat chromosome 5BL with homology to the rice photoperiodism gene Hd6 played a significant role in the determination of the heading date in wheat.", "doi": "10.3389/fpls.2014.00217", "pmid": "24904613", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4033046"}], "notes": [], "created": "2017-05-04T14:58:35.795Z", "modified": "2020-01-21T13:56:02.806Z"}, {"entity": "publication", "iuid": "3df3b1fa1eaf4519ba894b5443a92791", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3df3b1fa1eaf4519ba894b5443a92791.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3df3b1fa1eaf4519ba894b5443a92791"}}, "title": "The H1-receptor antagonist cetirizine protects partially against cytokine- and hydrogen peroxide-induced \u03b2-TC6 cell death in vitro.", "authors": [{"family": "Anvari", "given": "Ebrahim", "initials": "E"}, {"family": "Fred", "given": "Rikard G", "initials": "RG"}, {"family": "Welsh", "given": "Nils", "initials": "N"}], "type": "journal article", "published": "2014-05-00", "journal": {"volume": "43", "issn": "1536-4828", "issue": "4", "pages": "624-629", "title": "Pancreas", "issn-l": "0885-3177"}, "abstract": "It has been proposed that the histamine 1 (H(1)) receptor not only promotes allergic reactions but also modulates autoimmune diseases, such as type 1 diabetes. In line with this, it has recently been reported that the H(1)-receptor antagonist cetirizine can counteract the activation of signals/factors pertinent to the pathogenesis of type 1 diabetes and cytokine-induced \u03b2-cell destruction. Therefore, the overall aim of this study was to determine whether H(1)-receptor antagonists affect cytokine-induced \u03b2-cell death and signaling in vitro.\n\nThe insulin-producing cell line \u03b2-TC6 was exposed to the proinflammatory cytokines interleukin 1\u03b2(+) interferon \u03b3, or hydrogen peroxide. The H(1)-receptor antagonists desloratadine and cetirizine were added to the cell cultures and cell viability; macrophage inhibitory factor levels, c-Jun N-terminal kinase phosphorylation, c-Jun expression, and \u03b2-catenin levels were analyzed by flow cytometry, real-time polymerase chain reaction, and immunoblotting.\n\nCetirizine protected partially against both cytokine- and hydrogen peroxide-induced cell death. This effect was paralleled by an inhibition of cytokine-induced c-Jun N-terminal kinase phosphorylation, c-Jun induction, and a restoration of macrophage inhibitory factor contents. Cetirizine also increased the \u03b2-TC6 cell contents of \u03b2-catenin at basal conditions.\n\nOur results indicate a protective effect of a specific H(1)-receptor antagonist.", "doi": "10.1097/MPA.0000000000000076", "pmid": "24717804", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "00006676-201405000-00020"}], "notes": [], "created": "2017-05-04T14:58:51.257Z", "modified": "2020-01-21T13:56:01.758Z"}, {"entity": "publication", "iuid": "d68bf4dec6be4fe38c553f53243a4465", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d68bf4dec6be4fe38c553f53243a4465.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d68bf4dec6be4fe38c553f53243a4465"}}, "title": "Single cell genomics of deep ocean bacteria", "authors": [{"family": "Zhao", "given": "Weizhou", "initials": "W"}, {"family": "Andersson", "given": "Siv G E", "initials": "SGE"}], "type": "journal-article", "published": "2014-05-00", "journal": {"volume": "22", "issn": "0966-842X", "issue": "5", "pages": "233-234", "title": "Trends Microbiol.", "issn-l": null}, "abstract": "SAR11 is one of the most abundant bacterioplanktons in the upper surface waters of the oceans. In a recent issue of The ISME Journal, Thrash and colleagues present the genomes of four single SAR11 cells isolated from the deep oceans that are enriched in genes for membrane biosynthetic functions.", "doi": "10.1016/j.tim.2014.03.002", "pmid": "24684969", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0966-842X(14)00052-3"}], "notes": [], "created": "2017-05-04T14:59:01.692Z", "modified": "2021-06-16T15:16:56.994Z"}, {"entity": "publication", "iuid": "5fe162a887c248ee8afe0cbf489a8a3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5fe162a887c248ee8afe0cbf489a8a3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5fe162a887c248ee8afe0cbf489a8a3e"}}, "title": "GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma.", "authors": [{"family": "Nord", "given": "Karolin H", "initials": "KH"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Tayebwa", "given": "Johnbosco", "initials": "J"}, {"family": "de Jong", "given": "Danielle", "initials": "D"}, {"family": "Bov\u00e9e", "given": "Judith V M G", "initials": "JV"}, {"family": "Hogendoorn", "given": "Pancras C W", "initials": "PC"}, {"family": "Szuhai", "given": "Karoly", "initials": "K"}], "type": "journal article", "published": "2014-05-00", "journal": {"volume": "46", "issn": "1546-1718", "issue": "5", "pages": "474-477", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Glutamate receptors are well-known actors in the central and peripheral nervous systems, and altered glutamate signaling is implicated in several neurological and psychiatric disorders. It is increasingly recognized that such receptors may also have a role in tumor growth. Here we provide direct evidence of aberrant glutamate signaling in the development of a locally aggressive bone tumor, chondromyxoid fibroma (CMF). We subjected a series of CMFs to whole-genome mate-pair sequencing and RNA sequencing and found that the glutamate receptor gene GRM1 recombines with several partner genes through promoter swapping and gene fusion events. The GRM1 coding region remains intact, and 18 of 20 CMFs (90%) showed a more than 100-fold and up to 1,400-fold increase in GRM1 expression levels compared to control tissues. Our findings unequivocally demonstrate that direct targeting of GRM1 is a necessary and highly specific driver event for CMF development.", "doi": "10.1038/ng.2927", "pmid": "24658000", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ng.2927"}], "notes": [], "created": "2017-05-04T14:58:48.119Z", "modified": "2020-01-21T13:56:02.599Z"}, {"entity": "publication", "iuid": "d642b0b9f53d4b819d9004c4b90247c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d642b0b9f53d4b819d9004c4b90247c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d642b0b9f53d4b819d9004c4b90247c8"}}, "title": "The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.", "authors": [{"family": "Kunze", "given": "Gotthard", "initials": "G"}, {"family": "Gaillardin", "given": "Claude", "initials": "C"}, {"family": "Czernicka", "given": "Ma\u0142gorzata", "initials": "M"}, {"family": "Durrens", "given": "Pascal", "initials": "P"}, {"family": "Martin", "given": "Tiphaine", "initials": "T"}, {"family": "B\u00f6er", "given": "Erik", "initials": "E"}, {"family": "Gabald\u00f3n", "given": "Toni", "initials": "T"}, {"family": "Cruz", "given": "Jose A", "initials": "JA"}, {"family": "Talla", "given": "Emmanuel", "initials": "E"}, {"family": "Marck", "given": "Christian", "initials": "C"}, {"family": "Goffeau", "given": "Andr\u00e9", "initials": "A"}, {"family": "Barbe", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Baret", "given": "Philippe", "initials": "P"}, {"family": "Baronian", "given": "Keith", "initials": "K"}, {"family": "Beier", "given": "Sebastian", "initials": "S"}, {"family": "Bleykasten", "given": "Claudine", "initials": "C"}, {"family": "Bode", "given": "R\u00fcdiger", "initials": "R"}, {"family": "Casaregola", "given": "Serge", "initials": "S"}, {"family": "Despons", "given": "Laurence", "initials": "L"}, {"family": "Fairhead", "given": "C\u00e9cile", "initials": "C"}, {"family": "Giersberg", "given": "Martin", "initials": "M"}, {"family": "Gierski", "given": "Przemys\u0142aw Piotr", "initials": "PP"}, {"family": "H\u00e4hnel", "given": "Urs", "initials": "U"}, {"family": "Hartmann", "given": "Anja", "initials": "A"}, {"family": "Jankowska", "given": "Dagmara", "initials": "D"}, {"family": "Jubin", "given": "Claire", "initials": "C"}, {"family": "Jung", "given": "Paul", "initials": "P"}, {"family": "Lafontaine", "given": "Ingrid", "initials": "I"}, {"family": "Leh-Louis", "given": "V\u00e9ronique", "initials": "V"}, {"family": "Lemaire", "given": "Marc", "initials": "M"}, {"family": "Marcet-Houben", "given": "Marina", "initials": "M"}, {"family": "Mascher", "given": "Martin", "initials": "M"}, {"family": "Morel", "given": "Guillaume", "initials": "G"}, {"family": "Richard", "given": "Guy-Franck", "initials": "GF"}, {"family": "Riechen", "given": "Jan", "initials": "J"}, {"family": "Sacerdot", "given": "Christine", "initials": "C"}, {"family": "Sarkar", "given": "Anasua", "initials": "A"}, {"family": "Savel", "given": "Guilhem", "initials": "G"}, {"family": "Schacherer", "given": "Joseph", "initials": "J"}, {"family": "Sherman", "given": "David J", "initials": "DJ"}, {"family": "Stein", "given": "Nils", "initials": "N"}, {"family": "Straub", "given": "Marie-Laure", "initials": "ML"}, {"family": "Thierry", "given": "Agn\u00e8s", "initials": "A"}, {"family": "Trautwein-Schult", "given": "Anke", "initials": "A"}, {"family": "Vacherie", "given": "Benoit", "initials": "B"}, {"family": "Westhof", "given": "Eric", "initials": "E"}, {"family": "Worch", "given": "Sebastian", "initials": "S"}, {"family": "Dujon", "given": "Bernard", "initials": "B"}, {"family": "Souciet", "given": "Jean-Luc", "initials": "JL"}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Scholz", "given": "Uwe", "initials": "U"}, {"family": "Neuv\u00e9glise", "given": "C\u00e9cile", "initials": "C"}], "type": "journal article", "published": "2014-04-24", "journal": {"volume": "7", "issn": "1754-6834", "issue": null, "pages": "66", "title": "Biotechnol Biofuels", "issn-l": "1754-6834"}, "abstract": "The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant.\n\nThe sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8\u00a0Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid.\n\nThe high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications.", "doi": "10.1186/1754-6834-7-66", "pmid": "24834124", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1754-6834-7-66"}, {"db": "pmc", "key": "PMC4022394"}], "notes": [], "created": "2017-05-04T14:58:23.306Z", "modified": "2020-01-21T13:56:05.481Z"}, {"entity": "publication", "iuid": "44a9d2a1fbe3426784536ffceadf1761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44a9d2a1fbe3426784536ffceadf1761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44a9d2a1fbe3426784536ffceadf1761"}}, "title": "Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.", "authors": [{"family": "R\u00f6nnerblad", "given": "Michelle", "initials": "M"}, {"family": "Andersson", "given": "Robin", "initials": "R"}, {"family": "Olofsson", "given": "Tor", "initials": "T"}, {"family": "Douagi", "given": "Iyadh", "initials": "I"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Hoof", "given": "Ilka", "initials": "I"}, {"family": "de Hoon", "given": "Michiel", "initials": "M"}, {"family": "Itoh", "given": "Masayoshi", "initials": "M"}, {"family": "Nagao-Sato", "given": "Sayaka", "initials": "S"}, {"family": "Kawaji", "given": "Hideya", "initials": "H"}, {"family": "Lassmann", "given": "Timo", "initials": "T"}, {"family": "Carninci", "given": "Piero", "initials": "P"}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y"}, {"family": "Forrest", "given": "Alistair R R", "initials": "AR"}, {"family": "Sandelin", "given": "Albin", "initials": "A"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "FANTOM consortium", "given": null, "initials": null}], "type": "journal article", "published": "2014-04-24", "journal": {"volume": "123", "issn": "1528-0020", "issue": "17", "pages": "e79-e89", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "In development, epigenetic mechanisms such as DNA methylation have been suggested to provide a cellular memory to maintain multipotency but also stabilize cell fate decisions and direct lineage restriction. In this study, we set out to characterize changes in DNA methylation and gene expression during granulopoiesis using 4 distinct cell populations ranging from the oligopotent common myeloid progenitor stage to terminally differentiated neutrophils. We observed that differentially methylated sites (DMSs) generally show decreased methylation during granulopoiesis. Methylation appears to change at specific differentiation stages and overlap with changes in transcription and activity of key hematopoietic transcription factors. DMSs were preferentially located in areas distal to CpG islands and shores. Also, DMSs were overrepresented in enhancer elements and enriched in enhancers that become active during differentiation. Overall, this study depicts in detail the epigenetic and transcriptional changes that occur during granulopoiesis and supports the role of DNA methylation as a regulatory mechanism in blood cell differentiation.", "doi": "10.1182/blood-2013-02-482893", "pmid": "24671952", "labels": {"National Genomics Infrastructure": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "blood-2013-02-482893"}], "notes": [], "created": "2017-05-04T14:58:23.914Z", "modified": "2020-01-21T13:56:01.943Z"}, {"entity": "publication", "iuid": "c3873a3b67f64ca6972379332bf09625", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3873a3b67f64ca6972379332bf09625.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3873a3b67f64ca6972379332bf09625"}}, "title": "Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.", "authors": [{"family": "Hugerth", "given": "Luisa W", "initials": "LW"}, {"family": "Muller", "given": "Emilie E L", "initials": "EE"}, {"family": "Hu", "given": "Yue O O", "initials": "YO"}, {"family": "Lebrun", "given": "Laura A M", "initials": "LA"}, {"family": "Roume", "given": "Hugo", "initials": "H"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Wilmes", "given": "Paul", "initials": "P"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2014-04-22", "journal": {"volume": "9", "issn": "1932-6203", "issue": "4", "pages": "e95567", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.", "doi": "10.1371/journal.pone.0095567", "pmid": "24755918", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-50914"}, {"db": "pmc", "key": "PMC3995771"}], "notes": [], "created": "2017-05-04T14:58:54.491Z", "modified": "2020-01-21T13:56:05.074Z"}, {"entity": "publication", "iuid": "187676e32df44a73aecd8684758a6148", "links": {"self": {"href": "https://publications.scilifelab.se/publication/187676e32df44a73aecd8684758a6148.json"}, "display": {"href": "https://publications.scilifelab.se/publication/187676e32df44a73aecd8684758a6148"}}, "title": "Elucidating the interactions between the human gut microbiota and its host through metabolic modeling.", "authors": [{"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2014-04-22", "journal": {"volume": "5", "issn": "1664-8021", "issue": null, "pages": "86", "title": "Front Genet", "issn-l": "1664-8021"}, "abstract": "Increased understanding of the interactions between the gut microbiota, diet and environmental effects may allow us to design efficient treatment strategies for addressing global health problems. Existence of symbiotic microorganisms in the human gut provides different functions for the host such as conversion of nutrients, training of the immune system, and resistance to pathogens. The gut microbiome also plays an influential role in maintaining human health, and it is a potential target for prevention and treatment of common disorders including obesity, type 2 diabetes, and atherosclerosis. Due to the extreme complexity of such disorders, it is necessary to develop mathematical models for deciphering the role of its individual elements as well as the entire system and such models may assist in better understanding of the interactions between the bacteria in the human gut and the host by use of genome-scale metabolic models (GEMs). Recently, GEMs have been employed to explore the interactions between predominant bacteria in the gut ecosystems. Additionally, these models enabled analysis of the contribution of each species to the overall metabolism of the microbiota through the integration of omics data. The outcome of these studies can be used for proposing optimal conditions for desired microbiome phenotypes. Here, we review the recent progress and challenges for elucidating the interactions between the human gut microbiota and host through metabolic modeling. We discuss how these models may provide scaffolds for analyzing high-throughput data, developing probiotics and prebiotics, evaluating the effects of probiotics and prebiotics and eventually designing clinical interventions.", "doi": "10.3389/fgene.2014.00086", "pmid": "24795748", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC4000997"}], "notes": [], "created": "2017-05-04T14:58:34.894Z", "modified": "2021-07-05T13:05:37.514Z"}, {"entity": "publication", "iuid": "afffad2d3a5648cf8f789c937e8e9a23", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afffad2d3a5648cf8f789c937e8e9a23.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afffad2d3a5648cf8f789c937e8e9a23"}}, "title": "A Drosophila immune response against Ras-induced overgrowth.", "authors": [{"family": "Hauling", "given": "Thomas", "initials": "T"}, {"family": "Krautz", "given": "Robert", "initials": "R"}, {"family": "Markus", "given": "Robert", "initials": "R"}, {"family": "Volkenhoff", "given": "Anne", "initials": "A"}, {"family": "Kucerova", "given": "Lucie", "initials": "L"}, {"family": "Theopold", "given": "Ulrich", "initials": "U"}], "type": "journal article", "published": "2014-04-15", "journal": {"volume": "3", "issn": "2046-6390", "issue": "4", "pages": "250-260", "title": "Biol Open", "issn-l": "2046-6390"}, "abstract": "Our goal is to characterize the innate immune response against the early stage of tumor development. For this, animal models where genetic changes in specific cells and tissues can be performed in a controlled way have become increasingly important, including the fruitfly Drosophila melanogaster. Many tumor mutants in Drosophila affect the germline and, as a consequence, also the immune system itself, making it difficult to ascribe their phenotype to a specific tissue. Only during the past decade, mutations have been induced systematically in somatic cells to study the control of tumorous growth by neighboring cells and by immune cells. Here we show that upon ectopic expression of a dominant-active form of the Ras oncogene (Ras(V12)), both imaginal discs and salivary glands are affected. Particularly, the glands increase in size, express metalloproteinases and display apoptotic markers. This leads to a strong cellular response, which has many hallmarks of the granuloma-like encapsulation reaction, usually mounted by the insect against larger foreign objects. RNA sequencing of the fat body reveals a characteristic humoral immune response. In addition we also identify genes that are specifically induced upon expression of Ras(V12). As a proof-of-principle, we show that one of the induced genes (santa-maria), which encodes a scavenger receptor, modulates damage to the salivary glands. The list of genes we have identified provides a rich source for further functional characterization. Our hope is that this will lead to a better understanding of the earliest stage of innate immune responses against tumors with implications for mammalian immunity.", "doi": "10.1242/bio.20146494", "pmid": "24659248", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "bio.20146494"}, {"db": "pmc", "key": "PMC3988794"}], "notes": [], "created": "2017-05-04T14:58:22.390Z", "modified": "2020-01-21T13:56:04.624Z"}, {"entity": "publication", "iuid": "4b765351569b4a00b74df1cfc6d5dc6e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b765351569b4a00b74df1cfc6d5dc6e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b765351569b4a00b74df1cfc6d5dc6e"}}, "title": "Clinical and genetic features of pediatric acute lymphoblastic leukemia in Down syndrome in the Nordic countries.", "authors": [{"family": "Lundin", "given": "Catarina", "initials": "C"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Klarskov Andersen", "given": "Mette", "initials": "M"}, {"family": "Autio", "given": "Kirsi", "initials": "K"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Golovleva", "given": "Irina", "initials": "I"}, {"family": "Heim", "given": "Sverre", "initials": "S"}, {"family": "Heinonen", "given": "Kristiina", "initials": "K"}, {"family": "Hovland", "given": "Randi", "initials": "R"}, {"family": "Johannsson", "given": "Johann H", "initials": "JH"}, {"family": "Kjeldsen", "given": "Eigil", "initials": "E"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Palmqvist", "given": "Lars", "initials": "L", "orcid": "0000-0001-9274-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e50c0057dcb47f39e085b16580806c2.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B"}, {"family": "Nordic Society of Pediatric Hematology Oncology (NOPHO)", "given": "", "initials": ""}, {"family": "Swedish Cytogenetic Leukemia Study Group (SCLSG)", "given": "", "initials": ""}, {"family": "NOPHO Leukemia Cytogenetic Study Group (NLCSG)", "given": "", "initials": ""}], "type": "journal article", "published": "2014-04-11", "journal": {"volume": "7", "issn": "1756-8722", "issue": null, "pages": "32", "title": "J Hematol Oncol", "issn-l": "1756-8722"}, "abstract": "Children with Down syndrome (DS) have an increased risk for acute lymphoblastic leukemia (ALL). Although previous studies have shown that DS-ALL differs clinically and genetically from non-DS-ALL, much remains to be elucidated as regards genetic and prognostic factors in DS-ALL.\n\nTo address clinical and genetic differences between DS-ALL and non-DS-ALL and to identify prognostic factors in DS-ALL, we ascertained and reviewed all 128 pediatric DS-ALL diagnosed in the Nordic countries between 1981 and 2010. Their clinical and genetic features were compared with those of the 4,647 B-cell precursor (BCP) ALL cases diagnosed during the same time period.\n\nAll 128 DS-ALL were BCP ALL, comprising 2.7% of all such cases. The 5-year event-free survival (EFS) and overall survival (OS) were significantly (P = 0.026 and P = 0.003, respectively) worse for DS-ALL patients with white blood cell counts \u226550 \u00d7 109/l. The age distributions varied between the DS and non-DS cases, with age peaks at 2 and 3 years, respectively; none of the DS patients had infant ALL (P = 0.029). The platelet counts were lower in the DS-ALL group (P = 0.005). Abnormal karyotypes were more common in non-DS-ALL (P < 0.0001), and there was a significant difference in the modal number distribution, with only 2% high hyperdiploid DS-ALL cases (P < 0.0001). The 5-year EFS and 5-year OS were significantly worse for DS-ALL (0.574 and 0.691, respectively) compared with non-DS-ALL (0.783 and 0.894, respectively) in the NOPHO ALL-1992/2000 protocols (P < 0.001).\n\nThe present study adds further support for genetic and clinical differences between DS-ALL and non-DS-ALL.", "doi": "10.1186/1756-8722-7-32", "pmid": "24726034", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1756-8722-7-32"}, {"db": "pmc", "key": "PMC4022076"}], "notes": [], "created": "2017-05-04T14:58:41.523Z", "modified": "2021-07-08T12:52:24.359Z"}, {"entity": "publication", "iuid": "17bfb81127154e4d930e93dd1461bbbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/17bfb81127154e4d930e93dd1461bbbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/17bfb81127154e4d930e93dd1461bbbf"}}, "title": "RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.", "authors": [{"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Sivertsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2014-04-04", "journal": {"volume": "13", "issn": "1535-3907", "issue": "4", "pages": "2019-2027", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "An important part of the Human Proteome Project is to characterize the protein complement of the genome with antibody-based profiling. Within the framework of this effort, a new version 12 of the Human Protein Atlas ( www.proteinatlas.org ) has been launched, including transcriptomics data for 27 tissues and 44 cell lines to complement the protein expression data from antibody-based profiling. Besides the extensive addition of transcriptomics data, the Human Protein Atlas now contains antibody-based protein profiles for 82% of the 20\u2009329 putative protein-coding genes. The comprehensive data resulting from RNA-seq analysis and antibody-based profiling performed within the Human Protein Atlas as well as information from UniProt were used to generate evidence summary scores for each of the 20\u2009329 genes, of which 94% now have experimental evidence at least at transcript level. The evidence scores for all individual genes are displayed with regards to both RNA- and antibody-based protein profiles, including chromosome-centric visualizations. An analysis of the human chromosome 19 shows that \u223c43% of the genes are expressed at the transcript level in all 27 tissues analyzed, suggesting a \"house-keeping\" function, while 12% of the genes show a more tissue-specific pattern with enriched expression in one of the analyzed tissues only.", "doi": "10.1021/pr401156g", "pmid": "24579871", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:16.817Z", "modified": "2021-07-08T13:44:33.044Z"}, {"entity": "publication", "iuid": "1dc720b77fdd456bb9ee0ea84bb414f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1dc720b77fdd456bb9ee0ea84bb414f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1dc720b77fdd456bb9ee0ea84bb414f0"}}, "title": "Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.", "authors": [{"family": "El-Semman", "given": "Ibrahim E", "initials": "IE"}, {"family": "Karlsson", "given": "Fredrik H", "initials": "FH"}, {"family": "Shoaie", "given": "Saeed", "initials": "S"}, {"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Soliman", "given": "Taysir H", "initials": "TH"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}], "type": "journal article", "published": "2014-04-03", "journal": {"volume": "8", "issn": "1752-0509", "issue": null, "pages": "41", "title": "BMC Syst Biol", "issn-l": "1752-0509"}, "abstract": "The gut microbiota plays an important role in human health and disease by acting as a metabolic organ. Metagenomic sequencing has shown how dysbiosis in the gut microbiota is associated with human metabolic diseases such as obesity and diabetes. Modeling may assist to gain insight into the metabolic implication of an altered microbiota. Fast and accurate reconstruction of metabolic models for members of the gut microbiota, as well as methods to simulate a community of microorganisms, are therefore needed. The Integrated Microbial Genomes (IMG) database contains functional annotation for nearly 4,650 bacterial genomes. This tremendous new genomic information adds new opportunities for systems biology to reconstruct accurate genome scale metabolic models (GEMs).\n\nHere we assembled a reaction data set containing 2,340 reactions obtained from existing genome-scale metabolic models, where each reaction is assigned with KEGG Orthology. The reaction data set was then used to reconstruct two genome scale metabolic models for gut microorganisms available in the IMG database Bifidobacterium adolescentis L2-32, which produces acetate during fermentation, and Faecalibacterium prausnitzii A2-165, which consumes acetate and produces butyrate. F. prausnitzii is less abundant in patients with Crohn's disease and has been suggested to play an anti-inflammatory role in the gut ecosystem. The B. adolescentis model, iBif452, comprises 699 reactions and 611 unique metabolites. The F. prausnitzii model, iFap484, comprises 713 reactions and 621 unique metabolites. Each model was validated with in vivo data. We used OptCom and Flux Balance Analysis to simulate how both organisms interact.\n\nThe consortium of iBif452 and iFap484 was applied to predict F. prausnitzii's demand for acetate and production of butyrate which plays an essential role in colonic homeostasis and cancer prevention. The assembled reaction set is a useful tool to generate bacterial draft models from KEGG Orthology.", "doi": "10.1186/1752-0509-8-41", "pmid": "24708835", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1752-0509-8-41"}, {"db": "pmc", "key": "PMC4108055"}], "notes": [], "created": "2017-05-04T14:58:26.151Z", "modified": "2021-07-05T13:05:37.526Z"}, {"entity": "publication", "iuid": "be4200f3e82b44bf886c89c0e8c2f362", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be4200f3e82b44bf886c89c0e8c2f362.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be4200f3e82b44bf886c89c0e8c2f362"}}, "title": "Temporal profiling of cytokine-induced genes in pancreatic \u03b2-cells by meta-analysis and network inference.", "authors": [{"family": "Lopes", "given": "Miguel", "initials": "M"}, {"family": "Kutlu", "given": "Burak", "initials": "B"}, {"family": "Miani", "given": "Michela", "initials": "M"}, {"family": "Bang-Berthelsen", "given": "Claus H", "initials": "CH"}, {"family": "St\u00f8rling", "given": "Joachim", "initials": "J"}, {"family": "Pociot", "given": "Flemming", "initials": "F"}, {"family": "Goodman", "given": "Nathan", "initials": "N"}, {"family": "Hood", "given": "Lee", "initials": "L"}, {"family": "Welsh", "given": "Nils", "initials": "N"}, {"family": "Bontempi", "given": "Gianluca", "initials": "G"}, {"family": "Eizirik", "given": "Decio L", "initials": "DL"}], "type": "journal article", "published": "2014-04-00", "journal": {"volume": "103", "issn": "1089-8646", "issue": "4", "pages": "264-275", "title": "Genomics", "issn-l": "0888-7543"}, "abstract": "Type 1 Diabetes (T1D) is an autoimmune disease where local release of cytokines such as IL-1\u03b2 and IFN-\u03b3 contributes to \u03b2-cell apoptosis. To identify relevant genes regulating this process we performed a meta-analysis of 8 datasets of \u03b2-cell gene expression after exposure to IL-1\u03b2 and IFN-\u03b3. Two of these datasets are novel and contain time-series expressions in human islet cells and rat INS-1E cells. Genes were ranked according to their differential expression within and after 24 h from exposure, and characterized by function and prior knowledge in the literature. A regulatory network was then inferred from the human time expression datasets, using a time-series extension of a network inference method. The two most differentially expressed genes previously unknown in T1D literature (RIPK2 and ELF3) were found to modulate cytokine-induced apoptosis. The inferred regulatory network is thus supported by the experimental validation, providing a proof-of-concept for the proposed statistical inference approach.", "doi": "10.1016/j.ygeno.2013.12.007", "pmid": "24462878", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0888-7543(14)00006-8"}, {"db": "GEO", "key": "GSE53453"}, {"db": "GEO", "key": "GSE53454"}], "notes": [], "created": "2017-05-04T14:58:37.546Z", "modified": "2020-01-21T13:56:04.957Z"}, {"entity": "publication", "iuid": "d1b94af4c3f840faa7090d6403a2f6c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d1b94af4c3f840faa7090d6403a2f6c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d1b94af4c3f840faa7090d6403a2f6c0"}}, "title": "A novel SERPINE1-FOSB fusion gene results in transcriptional up-regulation of FOSB in pseudomyogenic haemangioendothelioma.", "authors": [{"family": "Walther", "given": "Charles", "initials": "C"}, {"family": "Tayebwa", "given": "Johnbosco", "initials": "J"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Nilsson", "given": "Jenny", "initials": "J"}, {"family": "von Steyern", "given": "Fredrik Vult", "initials": "FV"}, {"family": "\u00d8ra", "given": "Ingrid", "initials": "I"}, {"family": "Domanski", "given": "Henryk A", "initials": "HA"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Nord", "given": "Karolin H", "initials": "KH"}, {"family": "Fletcher", "given": "Christopher D M", "initials": "CD"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "case reports", "published": "2014-04-00", "journal": {"volume": "232", "issn": "1096-9896", "issue": "5", "pages": "534-540", "title": "J. Pathol.", "issn-l": "0022-3417"}, "abstract": "Pseudomyogenic haemangioendothelioma (PHE) is an intermediate malignant vascular soft tissue tumour primarily affecting children and young adults. The molecular basis of this neoplasm is unknown. We here used chromosome banding analysis, fluorescence in situ hybridization (FISH), mRNA sequencing, RT-PCR and quantitative real-time PCR on a series of morphologically well-characterized PHEs to show that a balanced translocation, t(7;19)(q22;q13), detected as the sole cytogenetic aberration in two cases, results in fusion of the SERPINE1 and FOSB genes. This translocation has not been observed in any other bone or soft tissue tumour. Interphase FISH on sections from eight additional PHEs identified the same SERPINE1-FOSB fusion in all cases. The role of SERPINE1, which is highly expressed in vascular cells, in this gene fusion is probably to provide a strong promoter for FOSB, which was found to be expressed at higher levels in PHEs than in other soft tissue tumours. FOSB encodes a transcription factor belonging to the FOS family of proteins, which, together with members of the JUN family of transcription factors, are major components of the activating protein 1 (AP-1) complex. Further studies are needed to understand the cellular impact of the aberrant expression of the FOSB gene, but as the t(7;19) resulting in the SERPINE1-FOSB fusion seems to be pathognomonic for PHE, FISH or RT-PCR could be useful for differential diagnostic purposes.", "doi": "10.1002/path.4322", "pmid": "24374978", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:58:42.950Z", "modified": "2021-07-06T15:41:35.349Z"}, {"entity": "publication", "iuid": "9a77ab7989a14c33ada831caaf15fd9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9a77ab7989a14c33ada831caaf15fd9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9a77ab7989a14c33ada831caaf15fd9f"}}, "title": "An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.", "authors": [{"family": "Brownstein", "given": "Catherine A", "initials": "CA"}, {"family": "Beggs", "given": "Alan H", "initials": "AH"}, {"family": "Homer", "given": "Nils", "initials": "N"}, {"family": "Merriman", "given": "Barry", "initials": "B"}, {"family": "Yu", "given": "Timothy W", "initials": "TW"}, {"family": "Flannery", "given": "Katherine C", "initials": "KC"}, {"family": "DeChene", "given": "Elizabeth T", "initials": "ET"}, {"family": "Towne", "given": "Meghan C", "initials": "MC"}, {"family": "Savage", "given": "Sarah K", "initials": "SK"}, {"family": "Price", "given": "Emily N", "initials": "EN"}, {"family": "Holm", "given": "Ingrid A", "initials": "IA"}, {"family": "Luquette", "given": "Lovelace J", "initials": "LJ"}, {"family": "Lyon", "given": "Elaine", "initials": "E"}, {"family": "Majzoub", "given": "Joseph", "initials": "J"}, {"family": "Neupert", "given": "Peter", "initials": "P"}, {"family": "McCallie", "given": "David", "initials": "D"}, {"family": "Szolovits", "given": "Peter", "initials": "P"}, {"family": "Willard", "given": "Huntington F", "initials": "HF"}, {"family": "Mendelsohn", "given": "Nancy J", "initials": "NJ"}, {"family": "Temme", "given": "Renee", "initials": "R"}, {"family": "Finkel", "given": "Richard S", "initials": "RS"}, {"family": "Yum", "given": "Sabrina W", "initials": "SW"}, {"family": "Medne", "given": "Livija", "initials": "L"}, {"family": "Sunyaev", "given": "Shamil R", "initials": "SR"}, {"family": "Adzhubey", "given": "Ivan", "initials": "I"}, {"family": "Cassa", "given": "Christopher A", "initials": "CA"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PI"}, {"family": "Duzkale", "given": "Hatice", "initials": "H"}, {"family": "Dworzy\u0144ski", "given": "Piotr", "initials": "P"}, {"family": "Fairbrother", "given": "William", "initials": "W"}, {"family": "Francioli", "given": "Laurent", "initials": "L"}, {"family": "Funke", "given": "Birgit H", "initials": "BH"}, {"family": "Giovanni", "given": "Monica A", "initials": "MA"}, {"family": "Handsaker", "given": "Robert E", "initials": "RE"}, {"family": "Lage", "given": "Kasper", "initials": "K"}, {"family": "Lebo", "given": "Matthew S", "initials": "MS"}, {"family": "Lek", "given": "Monkol", "initials": "M"}, {"family": "Leshchiner", "given": "Ignaty", "initials": "I"}, {"family": "MacArthur", "given": "Daniel G", "initials": "DG"}, {"family": "McLaughlin", "given": "Heather M", "initials": "HM"}, {"family": "Murray", "given": "Michael F", "initials": "MF"}, {"family": "Pers", "given": "Tune H", "initials": "TH"}, {"family": "Polak", "given": "Paz P", "initials": "PP"}, {"family": "Raychaudhuri", "given": "Soumya", "initials": "S"}, {"family": "Rehm", "given": "Heidi L", "initials": "HL"}, {"family": "Soemedi", "given": "Rachel", "initials": "R"}, {"family": "Stitziel", "given": "Nathan O", "initials": "NO"}, {"family": "Vestecka", "given": "Sara", "initials": "S"}, {"family": "Supper", "given": "Jochen", "initials": "J"}, {"family": "Gugenmus", "given": "Claudia", "initials": "C"}, {"family": "Klocke", "given": "Bernward", "initials": "B"}, {"family": "Hahn", "given": "Alexander", "initials": "A"}, {"family": "Schubach", "given": "Max", "initials": "M"}, {"family": "Menzel", "given": "Mortiz", "initials": "M"}, {"family": "Biskup", "given": "Saskia", "initials": "S"}, {"family": "Freisinger", "given": "Peter", "initials": "P"}, {"family": "Deng", "given": "Mario", "initials": "M"}, {"family": "Braun", "given": "Martin", "initials": "M"}, {"family": "Perner", "given": "Sven", "initials": "S"}, {"family": "Smith", "given": "Richard J H", "initials": "RJ"}, {"family": "Andorf", "given": "Janeen L", "initials": "JL"}, {"family": "Huang", "given": "Jian", "initials": "J"}, {"family": "Ryckman", "given": "Kelli", "initials": "K"}, {"family": "Sheffield", "given": "Val C", "initials": "VC"}, {"family": "Stone", "given": "Edwin M", "initials": "EM"}, {"family": 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"given": "Lee", "initials": "L"}, {"family": "Richards", "given": "Daniel R", "initials": "DR"}, {"family": "San Lucas", "given": "F Anthony", "initials": "FA"}, {"family": "Gonzalez-Garay", "given": "Manuel L", "initials": "ML"}, {"family": "Caskey", "given": "C Thomas", "initials": "CT"}, {"family": "Bai", "given": "Yu", "initials": "Y"}, {"family": "Huang", "given": "Ying", "initials": "Y"}, {"family": "Fang", "given": "Fang", "initials": "F"}, {"family": "Zhang", "given": "Yan", "initials": "Y"}, {"family": "Wang", "given": "Zhengyuan", "initials": "Z"}, {"family": "Barrera", "given": "Jorge", "initials": "J"}, {"family": "Garcia-Lobo", "given": "Juan M", "initials": "JM"}, {"family": "Gonz\u00e1lez-Lamu\u00f1o", "given": "Domingo", "initials": "D"}, {"family": "Llorca", "given": "Javier", "initials": "J"}, {"family": "Rodriguez", "given": "Maria C", "initials": "MC"}, {"family": "Varela", "given": "Ignacio", "initials": "I"}, {"family": "Reese", "given": "Martin G", "initials": "MG"}, {"family": "De La Vega", "given": "Francisco M", "initials": "FM"}, {"family": "Kiruluta", "given": "Edward", "initials": "E"}, {"family": "Cargill", "given": "Michele", "initials": "M"}, {"family": "Hart", "given": "Reece K", "initials": "RK"}, {"family": "Sorenson", "given": "Jon M", "initials": "JM"}, {"family": "Lyon", "given": "Gholson J", "initials": "GJ"}, {"family": "Stevenson", "given": "David A", "initials": "DA"}, {"family": "Bray", "given": "Bruce E", "initials": "BE"}, {"family": "Moore", "given": "Barry M", "initials": "BM"}, {"family": "Eilbeck", "given": "Karen", "initials": "K"}, {"family": "Yandell", "given": "Mark", "initials": "M"}, {"family": "Zhao", "given": "Hongyu", "initials": "H"}, {"family": "Hou", "given": "Lin", "initials": "L"}, {"family": "Chen", "given": "Xiaowei", "initials": "X"}, {"family": "Yan", "given": "Xiting", "initials": "X"}, {"family": "Chen", "given": "Mengjie", "initials": "M"}, {"family": "Li", "given": "Cong", "initials": "C"}, {"family": "Yang", "given": "Can", "initials": "C"}, {"family": "Gunel", "given": "Murat", "initials": "M"}, {"family": "Li", "given": "Peining", "initials": "P"}, {"family": "Kong", "given": "Yong", "initials": "Y"}, {"family": "Alexander", "given": "Austin C", "initials": "AC"}, {"family": "Albertyn", "given": "Zayed I", "initials": "ZI"}, {"family": "Boycott", "given": "Kym M", "initials": "KM"}, {"family": "Bulman", "given": "Dennis E", "initials": "DE"}, {"family": "Gordon", "given": "Paul M K", "initials": "PM"}, {"family": "Innes", "given": "A Micheil", "initials": "AM"}, {"family": "Knoppers", "given": "Bartha M", "initials": "BM"}, {"family": "Majewski", "given": "Jacek", "initials": "J"}, {"family": "Marshall", "given": "Christian R", "initials": "CR"}, {"family": "Parboosingh", "given": "Jillian S", "initials": "JS"}, {"family": "Sawyer", "given": "Sarah L", "initials": "SL"}, {"family": "Samuels", "given": "Mark E", "initials": "ME"}, {"family": "Schwartzentruber", "given": "Jeremy", "initials": "J"}, {"family": "Kohane", "given": "Isaac S", "initials": "IS"}, {"family": "Margulies", "given": "David M", "initials": "DM"}], "type": "journal article", "published": "2014-03-25", "journal": {"volume": "15", "issn": "1474-760X", "issue": "3", "pages": "R53", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.\n\nA total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization.\n\nThe CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.", "doi": "10.1186/gb-2014-15-3-r53", "pmid": "24667040", "labels": {"National Genomics Infrastructure": null, "Bioinformatics Support, Infrastructure and Training": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support and Infrastructure": null, "NGI Stockholm (Genomics Production)": null, "Bioinformatics (NBIS)": null}, "xrefs": [{"db": "pii", "key": "gb-2014-15-3-r53"}, {"db": "pmc", "key": "PMC4073084"}], "notes": [], "created": "2017-05-04T14:56:31.024Z", "modified": "2021-07-05T12:48:16.023Z"}, {"entity": "publication", "iuid": "33f47ac0c09144e881d215be48a9f919", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f47ac0c09144e881d215be48a9f919.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f47ac0c09144e881d215be48a9f919"}}, "title": "Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.", "authors": [{"family": "Lee", "given": "Changhan", "initials": "C"}, {"family": "Peters", "given": "Verena", "initials": "V"}, {"family": "Melefors", "given": "Ojar", "initials": "O"}, {"family": "R\u00f6mling", "given": "Ute", "initials": "U"}], "type": "journal article", "published": "2014-03-20", "journal": {"volume": "2", "issn": "2169-8287", "issue": "2", "title": "Genome Announc", "issn-l": "2169-8287"}, "abstract": "Pseudomonas aeruginosa SG17M is an environmental isolate recovered from river water in the city of Mulheim, Germany. SG17M belongs to clone C, which is distributed worldwide. This is the first clone C strain whose genome sequence has been determined.", "doi": "10.1128/genomeA.00186-14", "pmid": "24652978", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "2/2/e00186-14"}, {"db": "pmc", "key": "PMC3961725"}], "notes": [], "created": "2017-05-04T14:58:36.393Z", "modified": "2020-01-21T13:56:01.470Z"}, {"entity": "publication", "iuid": "de1dbb0fab4149a8a391cf69f93db271", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de1dbb0fab4149a8a391cf69f93db271.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de1dbb0fab4149a8a391cf69f93db271"}}, "title": "Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi.", "authors": [{"family": "Geng", "given": "Peng", "initials": "P"}, {"family": "Li", "given": "Wenli", "initials": "W"}, {"family": "Lin", "given": "Lan", "initials": "L"}, {"family": "de Miranda", "given": "Joachim R", "initials": "JR"}, {"family": "Emrich", "given": "Scott", "initials": "S"}, {"family": "An", "given": "Lijia", "initials": "L"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2014-03-17", "journal": {"volume": "9", "issn": "1932-6203", "issue": "3", "pages": "e92107", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Larvae of the Chinese oak silkmoth (Antheraea pernyi) are often affected by AVD (A. pernyi vomiting disease), whose causative agent has long been suspected to be a virus. In an unrelated project we discovered a novel positive sense single-stranded RNA virus that could reproduce AVD symptoms upon injection into healthy A. pernyi larvae. The genome of this virus is 10,163 nucleotides long, has a natural poly-A tail, and contains a single, large open reading frame flanked at the 5' and 3' ends by untranslated regions containing putative structural elements for replication and translation of the virus genome. The open reading frame is predicted to encode a 3036 amino acid polyprotein with four viral structural proteins (VP1-VP4) located in the N-terminal end and the non-structural proteins, including a helicase, RNA-dependent RNA polymerase and 3C-protease, located in the C-terminal end of the polyprotein. Putative 3C-protease and autolytic cleavage sites were identified for processing the polyprotein into functional units. The genome organization, amino acid sequence and phylogenetic analyses suggest that the virus is a novel species of the genus Iflavirus, with the proposed name of Antheraea pernyi Iflavirus (ApIV).", "doi": "10.1371/journal.pone.0092107", "pmid": "24637949", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-13-51480"}, {"db": "pmc", "key": "PMC3956879"}], "notes": [], "created": "2017-05-04T14:58:53.906Z", "modified": "2020-01-21T13:56:05.708Z"}, {"entity": "publication", "iuid": "ca54ec046554446e8a24006110d15b01", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca54ec046554446e8a24006110d15b01.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca54ec046554446e8a24006110d15b01"}}, "title": "Sequencing degraded RNA addressed by 3' tag counting.", "authors": [{"family": "Sigurgeirsson", "given": "Benjam\u00edn", "initials": "B"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2014-03-14", "journal": {"volume": "9", "issn": "1932-6203", "issue": "3", "pages": "e91851", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "RNA sequencing has become widely used in gene expression profiling experiments. Prior to any RNA sequencing experiment the quality of the RNA must be measured to assess whether or not it can be