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"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": "2026-06-17T20:17:10.982Z", "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"}, {"entity": "account", "iuid": "eaba3ceb6c484b64be969a9c1f11fb21", "timestamp": "2026-06-17T20:17:10.982Z", "links": {"self": {"href": "https://publications.scilifelab.se/account/tomas.axelsson%40medsci.uu.se.json"}, "display": {"href": 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{"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"}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Carmagnini", "given": "Alberto", "initials": "A"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"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"}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M"}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Barnett", "given": "Ross", "initials": "R"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Yamaguchi", "given": "Nobuyuki", "initials": "N"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Frantz", "given": "Laurent", "initials": "L"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}], "type": "journal article", "published": "2026-06-03", "journal": {"title": "Cell", "issn": "1097-4172", "issn-l": "0092-8674"}, "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": "2026-06-08T18:01:11.713Z"}, {"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", "volume": "8", "issue": "2", "pages": "lqag053", "issn-l": null}, "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": "Technology development", "NGI Short read": "Technology development", "NGI Stockholm (Genomics Applications)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC13202175"}, {"db": "pii", "key": "lqag053"}], "notes": [], "created": "2026-06-08T17:20:13.126Z", "modified": "2026-06-08T17:20:13.152Z"}, {"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"}, {"family": "Brugel", "given": "Sonia", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT"}, {"family": "Karlson", "given": "Bengt", "initials": "B"}, {"family": "Latz", "given": "Meike A C", "initials": "MAC"}, {"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": "2026-06-08T17:17:40.517Z"}, {"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": "2026-06-08T17:42:04.152Z"}, {"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 \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"}, {"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"}, {"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"}, {"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"}, {"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", "initials": "R", "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": "2026-05-09", "journal": {"title": "Gigascience", "issn": "2047-217X", "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 (B10K) 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 QV 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"}], "notes": [], "created": "2026-06-08T17:18:43.899Z", "modified": "2026-06-08T17:18:48.101Z"}, {"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": "2026-06-08T19:20:13.544Z"}, {"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"}, {"family": "Sorini", "given": "Chiara", "initials": "C"}, {"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"}, {"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"}, {"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"}], "type": "journal article", "published": "2026-05-06", "journal": {"title": "Immunity", "issn": "1097-4180", "issn-l": "1074-7613"}, "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": "2026-05-11T11:50:48.717Z"}, {"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"}, {"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"}, {"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"}, {"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"}], "type": "journal article", "published": "2026-05-06", "journal": {"title": "Brain", "issn": "1460-2156", "issn-l": "0006-8950"}, "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": "2026-05-11T12:23:19.728Z"}, {"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": "2026-05-01", "journal": {"title": "Am. J. Physiol., Cell Physiol.", "issn": "1522-1563", "issn-l": "0363-6143"}, "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 traumatic tibial fracture patients 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.", "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": "2026-05-11T12:28:53.459Z"}, {"entity": "publication", "iuid": "9e4daf0046b8477fbc62333829667614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614"}}, "title": "Epigenetic changes as regulatory mechanism for the expression of life history stages in Zonotrichia capensis inhabiting an aseasonal environment", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Gonzalez\u2010 Gomez", "given": "Paulina L", "initials": "PL", "orcid": "0000-0002-1219-8881", "researcher": {"href": "https://publications.scilifelab.se/researcher/636c42cfcc1f46c4bc83ffaa6f99c597.json"}}, {"family": "Wingfield", "given": "John C", "initials": "JC"}, {"family": "Guerrero\u2010Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal-article", "published": "2026-05-00", "journal": {"title": "Journal of Avian Biology", "issn": "0908-8857", "volume": "2026", "issue": "3", "issn-l": null}, "abstract": null, "doi": "10.1002/jav.03516", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:10:53.812Z", "modified": "2026-06-01T11:10:54.000Z"}, {"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"}, {"family": "Turkez", "given": "Hasan", "initials": "H"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J"}, {"family": "Zhang", "given": "Cheng", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2026-04-30", "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": "2026-05-11T11:43:55.359Z"}, {"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"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Nouri", "given": "Mehrnaz", "initials": "M"}, {"family": "Valfridsson", "given": "Christine", "initials": "C"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"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": "2026-04-29", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038"}, "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 coding sequence, 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": "pii", "key": "8664598"}], "notes": [], "created": "2026-05-11T11:52:59.250Z", "modified": "2026-05-11T11:52:59.327Z"}, {"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": "46c0df4f63584b799ce7923246580642", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46c0df4f63584b799ce7923246580642.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46c0df4f63584b799ce7923246580642"}}, "title": "Unique sex chromosome translocations and evolutionary strata in two Sylvioidea songbird families.", "authors": [{"family": "Brown", "given": "Thomas J", "initials": "TJ", "orcid": "0000-0002-4235-0856", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f23ec5a35d142de898840b16172fdfb.json"}}, {"family": "Ellerstrand", "given": "Simon J", "initials": "SJ", "orcid": "0000-0003-2674-6997", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed13c7732674cc992f2356848b97a7b.json"}}, {"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Melo", "given": "Martim", "initials": "M", "orcid": "0000-0003-1394-4361", "researcher": {"href": "https://publications.scilifelab.se/researcher/a42199d6eca542c48290db65ae34d940.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2026-04-20", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "issn-l": "1471-2164"}, "abstract": "Avian genomes are typically stable, yet instances of chromosome fissions, fusions and translocations are known across various lineages. For example, multiple sex chromosome translocations have been described in the superfamily Sylvioidea. In this study, we examine the sex chromosomes in two Sylvioidea families, Nicatoridae and Cisticolidae, using whole-genome data. We found sex-linkage of chromosomes Z and 4A, consistent with findings in other Sylvioidea species. We also identify sex-linkage of parts of chromosome 4, marking a novel discovery for Nicatoridae and a previously documented feature in Cisticolidae. These families are non-sister taxa, and the size of the translocated region of chromosome 4 differs between them, supporting independent translocation events. We uncover variation in recombination suppression and evolutionary strata on chromosome 4 between families, as well as between two genera within Cisticolidae. This study reveals both recurrent and independent trajectories in sex chromosome evolution, deepening our understanding of complex genomes.\n\nThe online version contains supplementary material available at 10.1186/s12864-026-12861-1.", "doi": "10.1186/s12864-026-12861-1", "pmid": "42010480", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13097842"}, {"db": "pii", "key": "10.1186/s12864-026-12861-1"}], "notes": [], "created": "2026-05-27T11:37:59.563Z", "modified": "2026-05-27T11:38:00.060Z"}, {"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": "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": "510c69c23c874b20bf9361bd6a5f1796", "links": {"self": {"href": "https://publications.scilifelab.se/publication/510c69c23c874b20bf9361bd6a5f1796.json"}, "display": {"href": "https://publications.scilifelab.se/publication/510c69c23c874b20bf9361bd6a5f1796"}}, "title": "A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies.", "authors": [{"family": "Gudenas", "given": "Brian L", "initials": "BL"}, {"family": "Ahmad", "given": "Shiekh Tanveer", "initials": "ST"}, {"family": "Englinger", "given": "Bernhard", "initials": "B"}, {"family": "Liu", "given": "Anthony P Y", "initials": "APY"}, {"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Paul", "given": "Leena", "initials": "L"}, {"family": "Hadley", "given": "Jennifer", "initials": "J"}, {"family": "Li", "given": "Yiran", "initials": "Y"}, {"family": "Batts", "given": "Melissa", "initials": "M"}, {"family": "Mittal", "given": "Priya", "initials": "P"}, {"family": "Wu", "given": "Stephanie C", "initials": "SC"}, {"family": "Lewis", "given": "Sara A", "initials": "SA"}, {"family": "Han", "given": "Katie", "initials": "K"}, {"family": "Soliman", "given": "Taha", "initials": "T"}, {"family": "Lin", "given": "Hong", "initials": "H"}, {"family": "Janke", "given": "Laure", "initials": "L"}, {"family": "Meredith", "given": "David", "initials": "D"}, {"family": "Pfaff", "given": "Elke", "initials": "E"}, {"family": "Gojo", "given": "Johannes", "initials": "J"}, {"family": "Cotter", "given": "Jennifer", "initials": "J"}, {"family": "Klimo", "given": "Paul", "initials": "P"}, {"family": "Boop", "given": "Frederick A", "initials": "FA"}, {"family": "Gajjar", "given": "Amar", "initials": "A"}, {"family": "Robinson", "given": "Giles W", "initials": "GW"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Alexandrescu", "given": "Sanda", "initials": "S"}, {"family": "Jones", "given": "David T W", "initials": "DTW"}, {"family": "Orr", "given": "Brent A", "initials": "BA"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ"}, {"family": "Filbin", "given": "Mariella G", "initials": "MG"}, {"family": "Northcott", "given": "Paul A", "initials": "PA"}], "type": "journal article", "published": "2026-04-13", "journal": {"title": "Cancer Cell", "issn": "1878-3686", "volume": "44", "issue": "4", "pages": "831-845.e10", "issn-l": "1535-6108"}, "abstract": "Pineoblastoma is a clinically aggressive childhood brain tumor composed of distinct molecular subgroups with divergent driver genes, demographics, and clinical outcomes. To identify developmental origins and mechanisms governing disease pathogenesis, we derive single-cell transcriptomes from pineal parenchymal tumors, aligning malignant cells with developmental counterparts to retrace cellular origins. Integrative computational analyses map pineoblastoma origins to transient, cycling pinealocyte progenitors during development. Lineage-specific perturbation of suspected drivers in the early pineal gland yields preclinical models representative of consensus molecular subgroups. Multi-omic characterization of patient tumors and these models uncover a tumor-associated photoreceptor signature (TAPS) common to pineoblastoma, retinoblastoma, and Group 3 medulloblastoma. Transcriptional activity of this signature within respective cellular origins establishes a developmental basis for molecular similarities between entities. Photoreceptor signature constituents are selective dependencies across these anatomically distinct central nervous system malignancies, motivating future studies evaluating developmentally encoded programs of malignancy as potential therapeutic liabilities.", "doi": "10.1016/j.ccell.2026.02.010", "pmid": "41791379", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS2149981"}, {"db": "pmc", "key": "PMC13123407"}, {"db": "pii", "key": "S1535-6108(26)00108-X"}], "notes": [], "created": "2026-06-01T11:10:55.839Z", "modified": "2026-06-01T11:10:55.858Z"}, {"entity": "publication", "iuid": "11b37392972444f5998ff8f14ca156cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11b37392972444f5998ff8f14ca156cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11b37392972444f5998ff8f14ca156cd"}}, "title": "An integrative molecular map of pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Sulyaeva", "given": "Julia", "initials": "J"}, {"family": "Gogishvili", "given": "Dea", "initials": "D"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2026-04-11", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "6", "issue": "1", "issn-l": null}, "abstract": "The molecular landscape of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) has been extensively characterized through single-modality studies. However, the interplay between molecular modalities and their collective influence on treatment response and outcomes remains poorly understood.\n\nWe integrated genomic, epigenomic, transcriptomic, and ex vivo drug response data from 1231 patients diagnosed with BCP-ALL. Using Multi-Omics Factor Analysis, we identified signatures explaining key aspects of the integrative molecular landscape, referred to as cross-modal elements (CMEs). The CME-derived signatures were introduced into pathway and intermodal network analyses, while their impact on patient outcomes was assessed through survival modeling.\n\nPathway and network analyses annotate the resulting integrative CMEs, linking them to key biological processes, including disease development, cellular regulatory processes, metabolic pathways, and drug response. By leveraging correlations between DNA methylation and ex vivo response to doxorubicin, we stratify patients with hyperdiploidy into subgroups that differ in relapse-free survival. These signatures are independent of clinical variables. Survival models incorporating CME-selected ex-vivo drug responses combined with clinical data improve risk prediction compared to clinical models alone (FDR < 0.05), demonstrating the potential of integrative multiomics in refining risk stratification.\n\nOur study highlights the importance of multimodal data integration in BCP-ALL to provide biological insights with potential relevance for precision medicine.", "doi": "10.1038/s43856-026-01568-9", "pmid": "41965886", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13079846"}, {"db": "pii", "key": "10.1038/s43856-026-01568-9"}], "notes": [], "created": "2026-06-01T11:13:50.747Z", "modified": "2026-06-01T11:13:50.765Z"}, {"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": "9bc3232d9f3b460cb3a8d08f5d9bd344", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bc3232d9f3b460cb3a8d08f5d9bd344.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bc3232d9f3b460cb3a8d08f5d9bd344"}}, "title": "Single-cell analysis of inhibitory efferent neurons of the zebrafish lateral line.", "authors": [{"family": "Manuel", "given": "Remy", "initials": "R", "orcid": "0000-0001-6938-4864", "researcher": {"href": "https://publications.scilifelab.se/researcher/927f9373b9f44c68ab362fa91a4bb8a9.json"}}, {"family": "Ahemaiti", "given": "Aikeremu", "initials": "A"}, {"family": "Tuz-Sasik", "given": "Melek Umay", "initials": "MU", "orcid": "0000-0002-0906-7477", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf8b429a428493d8ee662e648798951.json"}}, {"family": "Boije", "given": "Henrik", "initials": "H"}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "21", "issue": "4", "pages": "e0346255", "issn-l": "1932-6203"}, "abstract": "The zebrafish lateral line system is a sensory network made up of neuromasts, which contain hair cells to detect water flow. Neuromasts signal via sensory afferent neurons and their activity is modulated by efferent neurons. Inhibitory efferent neurons consist of REN, ROLE, and RELL cells and previous work has shown that neuromasts can be innervated by multiple efferent neurons, suggesting potential functional differences. To explore this, we performed single-cell RNA sequencing on REN, ROLE, and RELL neurons in 5-day-old zebrafish larvae. GO analysis across differentially expressed genes did not reveal pathways that suggest differences in cellular function. Comparing markers for neurotransmitter phenotype showed all inhibitory efferent neurons to be cholinergic, but also expressed genes related to other neurotransmitters. Expression of selected genes related to rhombomere location, axon guidance, or gap junctions was similar across efferent neurons. Expression of genes encoding proteins related to membrane potential suggest that REN neurons might be more sensitive to glutamate and may have different action potential dynamics, although functional validation remains to be done. In addition, we assessed neuromast innervation by ROLE and RELL neurons. We found that both ROLE and RELL neurons synapse to approximately 50% of hair cells within a neuromast, compared to approximately 75% innervation by all inhibitory efferent neurons combined. In addition, we did not observe flow polarity bias by innervating efferent axons. However, we did find that RELL neurons had a lower number of synaptic boutons compared to ROLE, which may reflect differences in synaptic output capacity. Taken that our transcriptional analysis did not reveal major intrinsic molecular differences, but we did observe differences in neuromast innervation, raises the possibility that functional differences, if present, may come from upstream inputs. Future work, such as retrograde tracing, could help map these input partners and clarify how different types of efferent neurons contribute to sensory modulation.", "doi": "10.1371/journal.pone.0346255", "pmid": "41950195", "labels": {"Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13061224"}, {"db": "pii", "key": "PONE-D-25-53779"}], "notes": [], "created": "2026-04-09T11:03:25.812Z", "modified": "2026-05-27T11:38:01.833Z"}, {"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": "d28a4f21a24a4775aecb9fff4b468e8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d28a4f21a24a4775aecb9fff4b468e8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d28a4f21a24a4775aecb9fff4b468e8a"}}, "title": "Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER + /HER2- breast cancer: a randomized phase II trial.", "authors": [{"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0af6483a77d746c2b838414692f1f4ed.json"}}, {"family": "Tzoras", "given": "Evangelos", "initials": "E"}, {"family": "Sarafidis", "given": "Michail", "initials": "M"}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8506000a14a4a5286aa557ab67ef690.json"}}, {"family": "Bj\u00f6hle", "given": "Judith", "initials": "J"}, {"family": "Barnekow", "given": "Elin", "initials": "E"}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Isaksson-Friman", "given": "Erika", "initials": "E"}, {"family": "Kessler", "given": "Luisa Edman", "initials": "LE"}, {"family": "Zouzos", "given": "Athanasios", "initials": "A", "orcid": "0000-0003-2654-827X", "researcher": {"href": "https://publications.scilifelab.se/researcher/776e7ba8993b4465a27451629b509490.json"}}, {"family": "Johansson", "given": "Hemming", "initials": "H"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Gryb\u00e4ck", "given": "Per", "initials": "P", "orcid": "0000-0002-1141-6234", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b5986c379cd4d23a0b48ac328faab63.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications.scilifelab.se/researcher/826836fefcf5440ebef1c404e046a0ca.json"}}, {"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications.scilifelab.se/researcher/f786763a4a0e4b5bb865ebb199eb6ca2.json"}}, {"family": "Wang", "given": "Kang", "initials": "K", "orcid": "0000-0001-5401-1803", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bdb074014224910b0f34e893b15e660.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/da7cefda6e00463d8ba95fc63eeb8f0a.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B", "orcid": "0000-0002-0972-4633", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe428be3caf4deca0a7839d555f6c33.json"}}, {"family": "Sun", "given": "Wenwen", "initials": "W"}, {"family": "Boyaci", "given": "Ceren", "initials": "C"}, {"family": "Villacampa", "given": "Guillermo", "initials": "G"}, {"family": "Pascual", "given": "Tomas", "initials": "T", "orcid": "0000-0001-8431-3183", "researcher": {"href": "https://publications.scilifelab.se/researcher/c10a027f0fa74b6b9a667edcadf8f50e.json"}}, {"family": "Gavila", "given": "Joaquin", "initials": "J"}, {"family": "Prat", "given": "Aleix", "initials": "A", "orcid": "0000-0003-2377-540X", "researcher": {"href": "https://publications.scilifelab.se/researcher/582dfbb079214acbb35af0a0590b2fb3.json"}}, {"family": "Perou", "given": "Charles", "initials": "C"}, {"family": "Brandberg", "given": "Yvonne", "initials": "Y"}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications.scilifelab.se/researcher/7683c0280e9b4145aa54305fb08936a7.json"}}], "type": "journal article", "published": "2026-04-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "In PREDIX LumB patients with estrogen receptor positive and human epidermal growth factor receptor negative (ER + /HER2-) breast cancer > 20 mm and/or with lymph node metastasis were randomized 1:1 to receive either paclitaxel weekly for 12 weeks followed by palbociclib and endocrine therapy for 12 weeks (arm A), or the reverse sequence (arm B). Primary endpoint is objective radiologic response at 12 weeks (ORR12), and key secondary endpoints are ORR24, pathologic complete response, event-free survival, safety and correlative studies of tissue and circulating biomarkers. Whole exome sequencing and RNA sequencing were performed on baseline fresh frozen tissue samples. In total, 179 patients comprise the intention-to-treat population. There is no statistically significant difference between the two arms in ORR12 (59% vs 45%, p = 0.058). An exploratory gene expression analysis identified differentially expressed genes and gene sets between responders and non-responders at 12 weeks. A predictive signature, CDKPredX, comprising 31 genes related to proliferation, ER signaling and immune activity was developed to identify patients resistant to chemotherapy but responding to palbociclib plus endocrine therapy (pinteraction=0.03). The predictive signature was independently validated in the CORALLEEN trial (pinteraction=0.048). Clinicaltrials.gov identifier: NCT02603679.", "doi": "10.1038/s41467-026-71452-6", "pmid": "41951647", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-026-71452-6"}, {"db": "pmc", "key": "PMC13069018"}, {"db": "ClinicalTrials.gov", "key": "NCT02603679"}], "notes": [], "created": "2026-04-13T07:03:30.099Z", "modified": "2026-04-13T07:03:31.324Z"}, {"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": "85934359591344b9b9aa4bb18644744a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85934359591344b9b9aa4bb18644744a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85934359591344b9b9aa4bb18644744a"}}, "title": "Nasal gene expression shows a distinct signature in type 2-high asthma but not in type 2-low disease.", "authors": [{"family": "Karp", "given": "Tatiana", "initials": "T"}, {"family": "Merid", "given": "Simon Kebede", "initials": "SK"}, {"family": "Kermani", "given": "Nazanin Zounemat", "initials": "NZ"}, {"family": "Faiz", "given": "Alen", "initials": "A"}, {"family": "Gillett", "given": "Tessa E", "initials": "TE"}, {"family": "Bults", "given": "Rene", "initials": "R"}, {"family": "Raby", "given": "Katie L", "initials": "KL"}, {"family": "Kerstjens", "given": "Huib A M", "initials": "HAM"}, {"family": "Nawijn", "given": "Martijn C", "initials": "MC"}, {"family": "Piraino", "given": "Alessio", "initials": "A"}, {"family": "Kraft", "given": "Monica", "initials": "M"}, {"family": "Begh\u00e8", "given": "Bianca", "initials": "B"}, {"family": "Rabe", "given": "Klaus F", "initials": "KF"}, {"family": "Papi", "given": "Alberto", "initials": "A"}, {"family": "Brightling", "given": "Chris", "initials": "C"}, {"family": "Singh", "given": "Dave", "initials": "D"}, {"family": "Kocks", "given": "Janwillem H", "initials": "JH"}, {"family": "Siddiqui", "given": "Salman", "initials": "S"}, {"family": "Adcock", "given": "Ian M", "initials": "IM"}, {"family": "Chung", "given": "Kian Fan", "initials": "KF"}, {"family": "Bhavsar", "given": "Pankaj", "initials": "P"}, {"family": "Koppelman", "given": "Gerard H", "initials": "GH"}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E"}, {"family": "Guryev", "given": "Victor", "initials": "V"}, {"family": "van den Berge", "given": "Maarten", "initials": "M"}], "type": "journal article", "published": "2026-04-00", "journal": {"title": "J. Allergy Clin. Immunol.", "issn": "1097-6825", "volume": "157", "issue": "4", "pages": "879-889", "issn-l": "0091-6749"}, "abstract": "Type 2 (T2)-low asthma is defined by low levels of T2 inflammation and is associated with resistance to inhaled corticosteroids. Its molecular mechanisms are mostly unknown, and treatment options are limited. We previously showed that nasal brush transcriptomes differ between asthma and controls, reflecting disease-relevant biology.\n\nWe explored nasal gene expression related to T2-low asthma in the ATLANTIS cohort.\n\nWe compared nasal brush RNA sequencing data between 82 T2-low and 63 T2-high asthma patients and 57 controls. T2-low asthma was defined as blood eosinophil counts < 0.15 \u00d7 109/L and Feno < 25 ppb and T2-high as blood eosinophil counts > 0.3 \u00d7 109/L and Feno > 25 ppb. Weighted gene coexpression network analysis (WGCNA) was applied to identify gene modules associated with T2-low asthma. The BAMSE and U-BIOPRED cohorts were used for replication analyses.\n\nAlthough differentially expressed genes were found in patients with T2-high asthma across all 3 cohorts, no differentially expressed genes were observed in individuals with T2-low disease compared to controls in ATLANTIS, nor consistently across other cohorts. Our assessment of molecular heterogeneity could not attribute this result to greater intersample variability within the T2-low group. WGCNA in ATLANTIS identified \"black\" and \"purple\" gene modules linked to T2-low asthma, with genes enriched in T-cell immunity and ribosomal RNA biology pathways, respectively. The \"black\" module was replicated in U-BIOPRED and showed the same direction in BAMSE.\n\nT2-high asthma shows a distinct nasal gene expression signature compared to healthy controls, while patients with T2-low asthma exhibit no consistent changes. Future studies should explore T-cell immunity in T2-low asthma and integrate lower airway multiomics data.", "doi": "10.1016/j.jaci.2025.10.036", "pmid": "41485495", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0091-6749(25)02261-4"}], "notes": [], "created": "2026-05-27T11:37:51.702Z", "modified": "2026-05-27T11:37:51.706Z"}, {"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": "eff23dc9016246219df7655c04dbc6c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eff23dc9016246219df7655c04dbc6c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eff23dc9016246219df7655c04dbc6c8"}}, "title": "Comparative Transcriptome Profiling of Nicotiana benthamiana Plants Infected with Potato Mop-Top Virus and Its Mutant Lacking a Gene for the 8K Protein Underlines the Role of Chloroplasts During Infection.", "authors": [{"family": "Roy", "given": "Shweta", "initials": "S"}, {"family": "Nemes", "given": "Katalin", "initials": "K"}, {"family": "Saripella", "given": "Ganapathi Varma", "initials": "GV"}, {"family": "Vetukuri", "given": "Ramesh Raju", "initials": "RR", "orcid": "0000-0001-7129-5326", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbb5fb93506a4b3a8faacc38397a741c.json"}}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"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": "2026-03-31", "journal": {"title": "Mol. Plant Microbe Interact.", "issn": "0894-0282", "pages": "MPMI10250146R", "issn-l": null}, "abstract": "Potato mop-top virus (PMTV) is a significant pathogen causing potato \"spraing\" disease worldwide. The PMTV 8K protein functions as a weak viral suppressor of RNA silencing (VSR), has viroporin activity, and plays a role in pathogenicity by promoting viral long-distance movement and modulating host responses. Uniquely, PMTV can establish systemic infection in the absence of the 8K protein, though the infection is slightly delayed. To elucidate the molecular mechanisms underlying PMTV-host interactions, we conducted comprehensive RNA-seq analysis comparing wild-type PMTV with a mutant lacking the 8K gene (PMTV-\u03948K) in Nicotiana benthamiana. Our transcriptomic analysis shows that wild-type PMTV and PMTV-\u03948K elicit largely distinct transcriptional responses in the host, with more unique than shared differentially expressed genes. The analysis also revealed extensive reprogramming of metabolic pathways, stress responses, and defense mechanisms. Notably, wild-type PMTV induced more defense-related transcription factors, including 27 WRKY genes compared with 8 in PMTV-\u03948K infections. RNA-silencing pathway genes displayed distinct expression patterns, with AGO2, RDR1, and AGO-MEL1 showing notably enhanced upregulation (up to 9.7-fold) in PMTV-\u03948K infections. Functional analysis identified chloroplast-associated genes GNS2, CHUP1, and KIN5l as host restriction factors. Virus-induced gene silencing experiments confirmed that GNS2 and CHUP1 restrict viral accumulation under both infection scenarios (wild-type PMTV and PMTV-\u03948K), and localization studies revealed that the TGB2 protein and GNS2 colocalize at chloroplast structures. These findings provide insights into PMTV pathogenesis, suggest that 8K is a multifunctional protein operating through diverse mechanisms, and advance understanding of viral suppression strategies. [Formula: see text] Copyright \u00a9 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.", "doi": "10.1094/MPMI-10-25-0146-R", "pmid": "41642887", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:10:49.177Z", "modified": "2026-06-01T11:10:49.273Z"}, {"entity": "publication", "iuid": "4841e395d0f541e6b7f8203d0fa258c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4841e395d0f541e6b7f8203d0fa258c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4841e395d0f541e6b7f8203d0fa258c0"}}, "title": "Medical facemask waste alters detritus decomposition and fungal communities in a freshwater pond.", "authors": [{"family": "Kong", "given": "Ze Hui", "initials": "ZH"}, {"family": "Stangl", "given": "Martina", "initials": "M"}, {"family": "Oester", "given": "Rebecca", "initials": "R"}, {"family": "Rehnstam", "given": "Svante", "initials": "S"}, {"family": "Futter", "given": "Martyn", "initials": "M"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Bundschuh", "given": "Mirco", "initials": "M"}, {"family": "Mckie", "given": "Brendan G", "initials": "BG"}], "type": "journal article", "published": "2026-03-30", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Plastic pollution is an ongoing issue in freshwater ecosystems, including that generated from the spike in disposable facemask use during the COVID-19 pandemic. The degradation products of such plastic waste, including plastic leachate compounds and generation of microplastics, have the potential to affect freshwater ecosystem structure and function. We investigated the effects of facemask-derived polypropylene particles of different sizes and their leachates on fungal communities and detritus decomposition in a pond. We further investigated effects of the presence of wood shavings, used to represent a naturally-occurring, highly refractory, organic reference material. Over five weeks, leaf litter mass loss and cotton cellulose tensile strength loss were quantified weekly, and fungal biomass, community composition, and functional gene abundance at two time points. Wood shavings reduced leaf decomposition (-4.4%) relative to controls, while plastics increased decomposition of labile cotton cellulose (+ 6.6%), with the strongest effect from unleached microplastics (+ 22.7%). After 21 days, litter-associated fungal biomass was reduced by the presence of wood shavings (-20.1%) and plastics (-8.6%). Fungal communities differed between wood- and control treatments, and varied widely under plastic exposure. Our findings highlight size- and leachate-dependent effects of facemask-derived plastic particles on freshwater fungal communities and ecosystem functions, which largely contrasted with those of wood.\n\nThe online version contains supplementary material available at 10.1038/s41598-026-45795-5.", "doi": "10.1038/s41598-026-45795-5", "pmid": "41912744", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13039742"}, {"db": "pii", "key": "10.1038/s41598-026-45795-5"}], "notes": [], "created": "2026-06-01T08:43:00.886Z", "modified": "2026-06-01T08:43:00.918Z"}, {"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": "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": "2026-03-25", "journal": {"title": "Genome Res.", "issn": "1088-9051", "volume": "36", "issue": "4", "pages": "661-670", "issn-l": null}, "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 Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "gr.281175.125"}], "notes": [], "created": "2026-04-10T11:53:57.469Z", "modified": "2026-04-14T14:01:40.457Z"}, {"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": "2253e344ebd94022a1be7f7534701531", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2253e344ebd94022a1be7f7534701531.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2253e344ebd94022a1be7f7534701531"}}, "title": "Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene.", "authors": [{"family": "Mao", "given": "Xiaomeng", "initials": "X"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Ingvarsson", "given": "P\u00e4r K", "initials": "PK"}, {"family": "Karrenberg", "given": "Sophie", "initials": "S"}], "type": "journal article", "published": "2026-03-19", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "27", "issue": "1", "issn-l": "1474-7596"}, "abstract": "Sex chromosomes often evolve faster than autosomes and commonly degenerate after recombination arrest. However, the underlying evolutionary processes are under persistent debate. In particular, it is unclear whether or not recombination arrest generally evolves in a stepwise manner and how switches in sex determination genes contribute to sex chromosome evolution. Here, we investigate sex chromosome evolution in the dioecious plant genus Salix.\n\nWe identify Z- and W-regions (~ 8 Mb) on chromosome 15 of the dwarf willow Salix herbacea using a new haplotype-resolved assembly. The W-region harbours a large (5 Mb) embedded inversion. Analyses of synteny with other Salix species, sequence divergence between sex chromosomes and sequence degeneration suggest that this inversion recently incorporated pseudoautosomal sequence into the W-region, extending its length nearly three-fold. The W-region exclusively contains seven pairs of inverted partial repeats of the male essential floral identity gene PISTILLATA, suggesting a possible PISTILLATA suppression mechanism by interfering RNA in females. Such PISTILLATA pseudogenes are also found in other Salix species with ZW sex determination but not in those with XY sex determination.\n\nOur study provides rare and compelling support for the long-standing theory of inversions underlying stepwise recombination reduction and raises the hypothesis that the turnover of sex chromosomes in the Salicaceae family might be associated with a switch of the sex determination gene.", "doi": "10.1186/s13059-026-04038-6", "pmid": "41857659", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13064059"}, {"db": "pii", "key": "10.1186/s13059-026-04038-6"}], "notes": [], "created": "2026-04-10T06:39:04.743Z", "modified": "2026-06-01T08:43:03.337Z"}, {"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 Short read": "Service", "NGI Other": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41437-026-00830-z"}], "notes": [], "created": "2026-03-23T15:23:33.935Z", "modified": "2026-03-23T15:23:34.639Z"}, {"entity": "publication", "iuid": "654a81a53ea648719ebdd68ff020c8dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/654a81a53ea648719ebdd68ff020c8dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/654a81a53ea648719ebdd68ff020c8dc"}}, "title": "Midostaurin response in AML is shaped by a progenitor-like cell state selectively targeted by SMAC mimetics.", "authors": [{"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Barizza", "given": "Chiara", "initials": "C"}, {"family": "Ploeger", "given": "Hidde", "initials": "H"}, {"family": "Rico Pizarro", "given": "Lucia", "initials": "L"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Hamberg Levedahl", "given": "Kerstin", "initials": "K"}, {"family": "Jafari", "given": "Rozbeh", "initials": "R"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Seashore-Ludlow", "given": "Brinton", "initials": "B"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Erkers", "given": "Tom", "initials": "T"}], "type": "journal article", "published": "2026-03-11", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "FLT3-mutated acute myeloid leukemia (AML) remains difficult to treat due to frequent resistance to FLT3 inhibitors like midostaurin. In this study, we observed a progenitor-like CD38+CD45RA+ leukemic cell population that may be associated with midostaurin resistance. Midostaurin-resistant cells display disrupted membrane architecture and a shift in signaling from STAT5 to PI3K/AKT, favoring survival over apoptosis. Functional drug testing was consistent with clinical response to midostaurin, and together with multi-omic profiling, including single-cell and proteomic analyses, indicated the presence and relevance of this resistant phenotype. Drug combination screening revealed that co-targeting with SMAC mimetics restores apoptotic competence and selectively depletes the resistant population when combined with midostaurin. In contrast, venetoclax combinations preferentially affected CD34hi cells, underscoring distinct subpopulation vulnerabilities. These findings may point to a biologically relevant mechanism underlying midostaurin resistance.", "doi": "10.1038/s41698-026-01363-8", "pmid": "41813823", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996285"}, {"db": "pii", "key": "10.1038/s41698-026-01363-8"}], "notes": [], "created": "2026-05-27T11:37:54.401Z", "modified": "2026-05-27T11:37:54.406Z"}, {"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": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13064042"}, {"db": "pii", "key": "10.1186/s12915-026-02568-w"}], "notes": [], "created": "2026-03-23T13:20:06.509Z", "modified": "2026-06-01T08:42:50.558Z"}, {"entity": "publication", "iuid": "56a35d53dd074855a03836ab41cdc335", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56a35d53dd074855a03836ab41cdc335.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56a35d53dd074855a03836ab41cdc335"}}, "title": "Polycomb repression works without Siesta, the Drosophila ortholog of mammalian PCGF3.", "authors": [{"family": "Kahn", "given": "Tatyana G", "initials": "TG", "orcid": "0000-0001-6109-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/2981d13fc748402cad966852e9d00395.json"}}, {"family": "Garrido", "given": "Andres", "initials": "A", "orcid": "0009-0000-7738-4397", "researcher": {"href": "https://publications.scilifelab.se/researcher/68346f49e1ec4a9f813fc916f7e7fa5d.json"}}, {"family": "Yushkova", "given": "Anastasiya", "initials": "A", "orcid": "0000-0002-9037-6866", "researcher": {"href": "https://publications.scilifelab.se/researcher/93639e0c8c504000a5a2bdf459a149a1.json"}}, {"family": "Kim", "given": "Maria", "initials": "M"}, {"family": "Glotov", "given": "Alexander", "initials": "A"}, {"family": "Sreekumar", "given": "Sweda", "initials": "S"}, {"family": "Larsson", "given": "Jan", "initials": "J", "orcid": "0000-0003-4373-6790", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6f8e41628d4534879edaf229575dec.json"}}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB", "orcid": "0000-0003-4790-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2751a236629d4b8bb9fff42cad6ff614.json"}}], "type": "journal article", "published": "2026-03-06", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "10", "pages": "eaec0733", "issn-l": "2375-2548"}, "abstract": "Polycomb group proteins mediate epigenetic repression via multisubunit complexes, including canonical Polycomb Repressive Complex 1 (PRC1), which monoubiquitylates histone H2A and binds histone H3 trimethylated at lysine-27 (H3K27me3). The RING1 subunit of PRC1, critical for H2A ubiquitylation, forms other complexes. These variant RING1 complexes also ubiquitylate H2A but cannot bind H3K27me3, and their role in epigenetic repression is debated. Using Drosophila genetics, we found that canonical PRC1 and variant RING1 complexes ubiquitylate H2A at distinct genomic regions. We established that the Drosophila PCGF protein specific for variant RING1 complexes, which we named Siesta, is not required for epigenetic repression of developmental genes but controls larval locomotion independently of H2A ubiquitylation. Leveraging a massively parallel transgenic approach, we demonstrated that H2A ubiquitylation has minimal impact on transcriptional repression. Our findings imply that Siesta-RING1 complexes operate outside the Polycomb regulatory system and that the popular PRC1 classification will benefit from revision.", "doi": "10.1126/sciadv.aec0733", "pmid": "41790891", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12965321"}], "notes": [], "created": "2026-06-01T11:10:51.338Z", "modified": "2026-06-01T11:10:51.612Z"}, {"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": "2c15bfb44c23441faf38bf7406cf4d3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c15bfb44c23441faf38bf7406cf4d3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c15bfb44c23441faf38bf7406cf4d3b"}}, "title": "Symbiotic Diversity of Sap-Feeding Auchenorrhyncha (Hemiptera) in the Upland Landscapes of Central Cardamom Mountains, Cambodia.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S"}, {"family": "Sin", "given": "Sopha", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2026-02-28", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "89", "issue": "1", "issn-l": "0095-3628"}, "abstract": "Auchenorrhyncha (Hemiptera) harbor diverse bacterial symbionts that play critical roles in host nutrition, adaptation and vector competence. However, how symbiotic communities vary across host species and ecological gradients in tropical montane ecosystems remains poorly understood. Here, we characterized the bacterial microbiota of eight auchenorrhynchan species collected from the upland landscapes of the Central Cardamom mountains, Cambodia, using 16S rRNA (V3-V4) amplicon sequencing. In total, 83 individuals representing eight species were analyzed. Across 188 amplicon sequence variants (ASVs), the obligate symbiont Candidatus (Ca.) Karelsulcia muelleri dominated all hosts, although its relative abundance varied substantially. While some species (Anagonalia sp., Changwhania sp. and Mukaria sp.) contained nearly exclusively Karelsulcia, others harbored diverse co-obligate (Ca. Zinderia) and secondary symbionts, including Rickettsia, Wolbachia, Arsenophonus, Spiroplasma, Ca. Symbiodolus, Ca. Lariskella, Pectobacterium and Xylella. Symbiont composition was highly host-specific, with Clovia sp. exhibiting the greatest diversity and Hecalus sp. dominated by Rickettsia. \u03b2-diversity analysis confirmed that host species explained most variation (87%), whereas topographic variables (exposure level and mountain locality) contributed little, although Ca. Symbiodolus in Stirellus sp2. was more frequent at high-exposure sites. Cross-correlation analysis revealed that only a restricted subset of bacterial taxa correlated significantly with plants families, suggesting selective ecological filtering. Notably, Spiroplasma was positively associated with sundew plants (Droseraceae), whereas Pectobacterium showed consistent negative correlations with multiple plant families. Overall, these findings demonstrate that microbiota in Auchenorrhyncha are shaped primarily by host species, with minor influences from environment and plant associations, highlighting the ecological and evolutionary drivers of symbiotic diversity in sap-feeding insects inhabiting tropical mountain landscapes.\n\nThe online version contains supplementary material available at 10.1007/s00248-026-02724-3.", "doi": "10.1007/s00248-026-02724-3", "pmid": "41762238", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12999766"}, {"db": "pii", "key": "10.1007/s00248-026-02724-3"}], "notes": [], "created": "2026-06-01T11:13:46.083Z", "modified": "2026-06-01T11:13:46.087Z"}, {"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": "22b56b49adc44dca95b4fd123ed95039", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22b56b49adc44dca95b4fd123ed95039.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22b56b49adc44dca95b4fd123ed95039"}}, "title": "Isotopic insights into long-term socio-economic transformations in prehistoric Kuyavia, Poland", "authors": [{"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141", "orcid": "0000-0003-4676-5802", "researcher": {"href": "https://publications.scilifelab.se/researcher/d372a7903129404c9fb0fdbbee738f74.json"}}, {"family": "Lewis", "given": "Jamie", "initials": "J"}, {"family": "Wiltshire", "given": "Isabel L", "initials": "IL", "orcid": "0009-0002-1681-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a455775963142fcac9dc01182dae358.json"}}, {"family": "Cramp", "given": "Lucy", "initials": "L", "orcid": "0000-0003-2012-2753", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8181ac4ef9148479fd73870aa34aaea.json"}}, {"family": "Giblin", "given": "Julia", "initials": "J"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Borowska", "given": "Beata", "initials": "B"}, {"family": "Makowiecki", "given": "Daniel", "initials": "D"}, {"family": "Rennwanz", "given": "Joanna", "initials": "J"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Goslar", "given": "Tomasz", "initials": "T"}, {"family": "Knowles", "given": "Tim", "initials": "T"}, {"family": "Kristiansen", "given": "Kristian", "initials": "K"}, {"family": "Sj\u00f6gren", "given": "Karl G\u00f6ran", "initials": "KG"}, {"family": "Jakubczak", "given": "Micha\u0142", "initials": "M"}, {"family": "Bednarczyk", "given": "J\u00f3zef", "initials": "J"}, {"family": "B\u0142aszczyk", "given": "Krzysztof", "initials": "K"}, {"family": "Chachlikowski", "given": "Piotr", "initials": "P", "orcid": "0000-0002-2138-2250", "researcher": {"href": "https://publications.scilifelab.se/researcher/264ecd32afc946f4a8140d72152bf275.json"}}, {"family": "Czebreszuk", "given": "Janusz", "initials": "J"}, {"family": "Grossman", "given": "Anna", "initials": "A"}, {"family": "Ignaczak", "given": "Marcin", "initials": "M"}, {"family": "Karczewska-Kaczmarek", "given": "Emilia", "initials": "E"}, {"family": "Ko\u015bko", "given": "Aleksander", "initials": "A"}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P"}, {"family": "Nowaczyk", "given": "Szymon", "initials": "S"}, {"family": "Pearson", "given": "Jessica", "initials": "J"}, {"family": "Roma\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Stanaszek", "given": "\u0141ukasz Maurycy", "initials": "\u0141M"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Starzy\u0144ski", "given": "Krzysztof", "initials": "K"}, {"family": "Roffet-Salque", "given": "M\u00e9lanie", "initials": "M"}], "type": "journal-article", "published": "2026-02-25", "journal": {"issn": "2054-5703", "volume": "13", "issue": "2", "title": "R. Soc. open sci.", "issn-l": "2054-5703"}, "abstract": null, "doi": "10.1098/rsos.250968", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:13:54.764Z", "modified": "2026-06-01T11:13:54.946Z"}, {"entity": "publication", "iuid": "5d87b6dd1cac4792b7e1a9fb481823fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d87b6dd1cac4792b7e1a9fb481823fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d87b6dd1cac4792b7e1a9fb481823fc"}}, "title": "Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.", "authors": [{"family": "G\u00f3mez-Mart\u00ednez", "given": "Daniela", "initials": "D", "orcid": "0000-0001-8834-8930", "researcher": {"href": "https://publications.scilifelab.se/researcher/3013d785572c4733822446d664e538a0.json"}}, {"family": "Ngou", "given": "Judith Sorel", "initials": "JS"}, {"family": "Ugolini", "given": "Valentina", "initials": "V"}, {"family": "Lai", "given": "Foon Yin", "initials": "FY"}, {"family": "Nilsson", "given": "R Henrik", "initials": "RH"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}], "type": "journal article", "published": "2026-02-19", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "102", "issue": "3", "issn-l": "0168-6496"}, "abstract": "Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river G\u00f6ta \u00c4lv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in the river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the G\u00f6ta \u00c4lv and their diversity differs from that of the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.", "doi": "10.1093/femsec/fiag007", "pmid": "41632094", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12917318"}, {"db": "pii", "key": "8456379"}], "notes": [], "created": "2026-06-01T08:42:58.103Z", "modified": "2026-06-01T08:42:58.173Z"}, {"entity": "publication", "iuid": "5f52c18408484928a5bdac12a356745d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f52c18408484928a5bdac12a356745d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f52c18408484928a5bdac12a356745d"}}, "title": "Genetic relatedness mattered in the co-burial ritual of Neolithic hunter-gatherers.", "authors": [{"family": "Mattila", "given": "Tiina Maria", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Fraser", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-4714-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8d9acba81e4da4a1efc097e53aa4f3.json"}}, {"family": "Koelman", "given": "Julian", "initials": "J"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Ivarsson-Aalders", "given": "Marieke", "initials": "M", "orcid": "0009-0001-5174-1840", "researcher": {"href": "https://publications.scilifelab.se/researcher/4df153464673466faa2249a0ef253d82.json"}}, {"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": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Wallin", "given": "Paul", "initials": "P", "orcid": "0000-0002-0916-6264", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac2463e759342bdba70ea7e40caebe2.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "journal article", "published": "2026-02-18", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "293", "issue": "2065", "issn-l": "0962-8452"}, "abstract": "Kin relations among past societies can offer valuable information about the social dynamics of the population. Genetic data from prehistoric human remains can reveal genetic relatedness, and when combined with archaeological information, shed light on social factors shaping ancient communities. However, accessing such information on ancient hunter-gatherer societies has been challenging owing to the scarcity of temporally overlapping multi-burial sites. Here, we focused on the Pitted Ware Culture (PWC) cemetery from Ajvide (Gotland, Sweden), one of Stone Age Europe's largest and best-preserved hunter-gatherer burial grounds of the European Stone Age. We generated new genomic data from 10 individuals, primarily from co-burial contexts, and combined these with published genomes from 24 individuals across four PWC sites on Gotland. The genetic analyses revealed dual ancestry of the Gotlandic PWC, showing approximately 80% ancestry associated with earlier Mesolithic hunter-gatherer groups and 20% with farmer groups. We also identified close genetic relatives between the different studied PWC sites on Gotland, indicating mixing of the groups. All individuals buried together were closely related to one another, including first-, second- and third-degree relatives, and showed significantly elevated genetic relatedness. This demonstrates that genetic relatedness played a defining role in the co-burial ritual and extended beyond first-degree relatives.", "doi": "10.1098/rspb.2025.0813", "pmid": "41705298", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "480372"}], "notes": [], "created": "2026-06-01T08:42:52.357Z", "modified": "2026-06-01T08:42:52.890Z"}, {"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": "833c3f2b059a4f12856d43fb4a7e02e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/833c3f2b059a4f12856d43fb4a7e02e3"}}, "title": "Rare germline variants contribute to glioma predisposition: Whole-genome analysis of a regional cohort of glioma patients.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A", "orcid": "0009-0003-4573-5174", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6fcd448d744a99945a361353add88f.json"}}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Hammermeister Suger", "given": "Austin", "initials": "A", "orcid": "0000-0002-6599-2202", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5c4526d1504762a430373285155fab.json"}}, {"family": "Pensch", "given": "Raphaela", "initials": "R", "orcid": "0000-0002-0313-8369", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bfb52298bf146c9a327c2fbe2e5e7cb.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Thomas", "initials": "T", "orcid": "0000-0002-4201-8204", "researcher": {"href": "https://publications.scilifelab.se/researcher/086ede39254945288fb9c708f98eb0cd.json"}}, {"family": "Rentoft", "given": "Matilda", "initials": "M"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Lindstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Dahlin", "given": "Anna Margareta", "initials": "AM"}, {"family": "Melin", "given": "Beatrice", "initials": "B", "orcid": "0000-0002-9982-3757", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ee34db763294de2b7dec15a9ffe8aee.json"}}], "type": "journal article", "published": "2026-02-12", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "8", "issue": "1", "pages": "vdag038", "issn-l": null}, "abstract": "Gliomas are the most common malignant primary tumor of the central nervous system and show a high mortality, particularly at higher grades. Cancer predisposition syndromes and common low-penetrance single nucleotide polymorphisms have been shown to contribute to glioma risk, but the contribution of rare germline variants remains incompletely understood. Here, we investigated rare germline variants in glioma patients.\n\nWe performed whole-genome sequencing on 113 glioma patients from Northern Sweden, analyzing rare germline variants across 651 genes. Variants were compared to population controls (ACpop, gnomAD) and validated in TCGA glioma data, a UK Biobank glioma nested case-control study, and a separate cohort of 105 Swedish glioblastomas.\n\n17.6% of glioma cases carried a Pathogenic or Likely Pathogenic (P/LP) variant within 1 of the 651 genes, and the number of alleles carrying a P/LP was significantly more than in the reference data (P = ). Many of the observed candidate genes also harbored P/LP variants in our Swedish validation cohort. Overall, gene-based comparison of rare coding variants indicated an enrichment in several genes, including 3.2 \u00d7 10 - 3TP53, CREBBP, and DNMT3A.\n\nRare P/LP germline variants were more frequent among glioma patients than in the reference population within our predefined gene set. These results suggest a contribution of rare germline variants to glioma risk, particularly in genes involved in DNA repair. While several genes are indicated as enriched with rare variants, only TP53 validates across all 3 patient sets.", "doi": "10.1093/noajnl/vdag038", "pmid": "41878702", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13007284"}, {"db": "pii", "key": "vdag038"}], "notes": [], "created": "2026-03-26T20:20:23.541Z", "modified": "2026-03-26T20:20:24.274Z"}, {"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": "43121743f286455382be9baac0b2e1c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43121743f286455382be9baac0b2e1c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43121743f286455382be9baac0b2e1c9"}}, "title": "Multi-omics data integration from patients with carotid stenosis illuminates key molecular signatures of atherosclerotic instability.", "authors": [{"family": "Das", "given": "Vivek", "initials": "V"}, {"family": "Narayanan", "given": "Sampath", "initials": "S"}, {"family": "Zhang", "given": "Xiang", "initials": "X"}, {"family": "Bergman", "given": "Otto", "initials": "O"}, {"family": "Djordjevic", "given": "Djordje", "initials": "D"}, {"family": "Kronqvist", "given": "Malin", "initials": "M"}, {"family": "Chemaly", "given": "Melody", "initials": "M"}, {"family": "Karadimou", "given": "Glykeria", "initials": "G"}, {"family": "Sundman", "given": "Sofija", "initials": "S"}, {"family": "Prasad", "given": "Inika", "initials": "I"}, {"family": "Buckler", "given": "Andrew J", "initials": "AJ"}, {"family": "Knape", "given": "Karin Conde", "initials": "KC"}, {"family": "Michaelsen", "given": "Natasha Barascuk", "initials": "NB"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Matic", "given": "Ljubica", "initials": "L"}], "type": "journal article", "published": "2026-02-06", "journal": {"title": "Genome Med", "issn": "1756-994X", "volume": "18", "issue": "1", "issn-l": "1756-994X"}, "abstract": "Understanding the pathophysiology of unstable atherosclerosis is imperative to prevent myocardial infarction and stroke. Here, we used multi-omics integration to identify key molecular targets with diagnostic and therapeutic potential.\n\nBiobank of Karolinska Endarterectomies encompassing patients with symptomatic (S) and asymptomatic (AS) carotid atherosclerosis was the main resource. Plaques, peripheral blood monocytes and plasma sampled locally from around plaque or periphery of n > 700 individuals, were profiled by transcriptomics, proteomics and metabolomics. A supervised machine learning method DIABLO was used for patient data integration. Multi-omics layers were integrated separately across local and peripheral disease sites, and their intersection, with stratification for symptomatology. Identified analytes were investigated using scRNAseq, clinical and outcome data.\n\nIn peripheral circulation, FABP4, IL6, Bilirubin and Sphingomyelin were the most prominent analytes. F11, ANGPTL3, ICOSLG, ITGB1 and Sphingomyelin were enriched in the local disease site, while FABP4, C1R, IL6, Bilirubin and Sphingomyelin appeared at the intersection. Coagulation, necroptosis, inflammation and cholesterol metabolism were confirmed as key pathways determining symptomatology. Clinical analyses showed an impact of lipid-lowering therapy on ICOSLG expression, anti-hypertensives on plasma FABP4 and BLVRB levels, anti-diabetics on plasma Sphingomyelins, while no medications affected ANGPTL3. Association with future adverse events was shown for plasma Bilirubin, Sphingomyelin, ANGPTL3 and ICOSLG plaque levels. Open-source target analyses suggested genetic involvement of F11, C1S, EGFR, IL6, ANGPTL3 in the disease.\n\nUsing an innovative, multi-modal data integration machine learning framework, this study provides confirmatory and novel information on mechanisms behind atherosclerotic instability. The findings raise possibilities for translational prioritizations to aid personalized medicine.\n\nThe online version contains supplementary material available at 10.1186/s13073-026-01601-5.", "doi": "10.1186/s13073-026-01601-5", "pmid": "41652626", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12927228"}, {"db": "pii", "key": "10.1186/s13073-026-01601-5"}], "notes": [], "created": "2026-05-27T11:37:57.073Z", "modified": "2026-05-27T11:37:57.076Z"}, {"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": "1f47f9fb4e1e4013a73952ad427c61e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f47f9fb4e1e4013a73952ad427c61e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f47f9fb4e1e4013a73952ad427c61e2"}}, "title": "TGF\u03b2 signaling promotes cell cycle progression and resistance to the CDK4/6 inhibitor palbociclib through SOX4 transcriptional modulation in breast cancer cells.", "authors": [{"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Badji", "given": "Aisha Mariama Pereira", "initials": "AMP"}, {"family": "Gallant", "given": "Sarah", "initials": "S", "orcid": "0009-0003-9742-4706", "researcher": {"href": "https://publications.scilifelab.se/researcher/666f2f479a3e4421b0aa834d49c0d724.json"}}, {"family": "Tsirigoti", "given": "Chrysoula", "initials": "C", "orcid": "0000-0001-6554-738X", "researcher": {"href": "https://publications.scilifelab.se/researcher/369717d5e92a4045b701964c37fd0aa8.json"}}, {"family": "Bai", "given": "Yu", "initials": "Y", "orcid": "0009-0002-0812-8917", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f57827cead428f8a7d7e4386eca3a3.json"}}, {"family": "Filipek-G\u00f3rniok", "given": "Beata", "initials": "B"}, {"family": "Miyazawa", "given": "Keiji", "initials": "K", "orcid": "0000-0002-7835-7718", "researcher": {"href": "https://publications.scilifelab.se/researcher/71984836d37c463eaf5ded53bed887dc.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2026-02-04", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "17", "issue": "1", "pages": "209", "issn-l": "2041-4889"}, "abstract": "Cancer signaling encompasses a wide array of entangled molecular cascades that promote oncogenic progression and counteract the effect of tumor suppressors. Transforming growth factor \u03b2 (TGF\u03b2) induces complex and stage-dependent effects throughout tumor progression. During pre-malignant hyperplastic growth, TGF\u03b2 restricts cell proliferation and inflammation, while on the other hand, TGF\u03b2 promotes migration and distal metastasis of cancer cells. To dissect the temporal chromatin-based transcriptional response to TGF\u03b2, we employed 3D culture models of isogenic human breast epithelial cells, exemplified by non-oncogenic MCF-10A (MI) and their HRAS-transformed counterpart (MII). Genome-wide chromatin accessibility profiling revealed an extensive chromatin opening induced by TGF\u03b2 at transcription start sites and enhancer elements in both models, with a marked enrichment of SOX4 binding motifs in oncogenic cells. Transcriptomic analyses unexpectedly revealed the upregulation of DNA replication and DNA damage response pathways, following TGF\u03b2 stimulation of oncogenic MII 3D cultures. Canonical TGF\u03b2-driven programs, including epithelial-mesenchymal transition and metabolic reprogramming, were activated in both models. Notably, single-cell RNA-seq of primary breast tumors confirmed co-expression of SOX4 and cell cycle regulators. Mechanistically, we show that TGF\u03b2 induces the interaction between the MH2 domain of SMAD3 and the intrinsically disordered regions of SOX4, co-activating downstream gene targets. Validating the genome-wide analyses, we found that resistance of breast cancer cells to the CDK4/6 inhibitor palbociclib conferred by TGF\u03b2 stimulation was functionally dependent on SOX4. Collectively, our findings reveal an apparent oncogenic function of TGF\u03b2 in promoting cell cycle progression and drug resistance through SOX4, highlighting the pro-tumorigenic role of TGF\u03b2 signaling in breast cancer progression.", "doi": "10.1038/s41419-026-08435-4", "pmid": "41639049", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12895049"}, {"db": "pii", "key": "10.1038/s41419-026-08435-4"}], "notes": [], "created": "2026-06-01T08:42:55.172Z", "modified": "2026-06-01T08:42:55.598Z"}, {"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": "57ccb7a2e57747c5885ff80d4f036529", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57ccb7a2e57747c5885ff80d4f036529.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57ccb7a2e57747c5885ff80d4f036529"}}, "title": "Single-Cell Comparison of Small Intestinal Neuroendocrine Tumors and Enterochromaffin Cells from Two Patients.", "authors": [{"family": "Axling", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3748-3176", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d84ca11d6f2449583a0fa81eaf1e64c.json"}}, {"family": "Barazeghi", "given": "Elham", "initials": "E"}, {"family": "Hellman", "given": "Per", "initials": "P", "orcid": "0000-0002-5322-5073", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c7a23c0741d444b82657b10fc7a4916.json"}}, {"family": "Norl\u00e9n", "given": "Olov", "initials": "O"}, {"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P", "orcid": "0000-0002-9625-1394", "researcher": {"href": "https://publications.scilifelab.se/researcher/6698ec6bc9a44d9d84edd62232083ec1.json"}}], "type": "journal article", "published": "2026-01-29", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "18", "issue": "3", "issn-l": "2072-6694"}, "abstract": "Several studies have attempted to identify the initiating drivers of small intestinal neuroendocrine tumor (SI-NET) development and the molecular mechanisms underlying their progression and metastatic spread. Previous gene expression studies have used bulk microarrays or RNA sequencing to compare tumor tissue with normal intestinal mucosa. However, the intestine comprises multiple distinct cell types, and bulk analyses are limited by this cellular heterogeneity, which can confound tumor-specific signals.\n\nWe performed single-cell RNA sequencing on primary SI-NETs and paired normal mucosa from two patients to directly compare tumor cells with their cells of origin, the enterochromaffin (EC) cells. To minimize type I errors, we applied a two-step validation strategy by overlapping differentially expressed genes with an external single-cell dataset and cross-referencing candidate genes for enteroendocrine expression in the Human Protein Atlas.\n\nFor further distinction and characterization, ECs were subdivided into serotonergic and non-serotonergic clusters. This analysis revealed that the SI-NET cells are transcriptionally more similar to serotonergic ECs, consistent with serum metabolite profiles derived from clinical parameters. Our analyses uncovered a loss-of-expression program characterized by regulators of epithelial differentiation and in parallel, a gain-of-expression program displayed neuronal signaling gene induction, implicating functional reprogramming toward neuronal-like properties. Together, these specific losses and gains suggest that our patient-derived SI-NETs undergo adaptation through both loss of enteroendocrine functions and acquisition of neurobiological-promoting signaling pathways.\n\nThese findings nominate candidate drivers for further functional validation and highlight potential therapeutic strategies in our patient cohort, including restoring suppressed Notch signaling and targeting aberrant neuronal signaling networks. However, even with a two-step validation procedure, the modest cohort size limits statistical power and generalizability, particularly for the proposed association to a serotonergic phenotype. Larger, multi-patient single-cell studies are required to confirm these mechanisms and establish their clinical relevance.", "doi": "10.3390/cancers18030435", "pmid": "41681906", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12897003"}, {"db": "pii", "key": "cancers18030435"}], "notes": [], "created": "2026-06-01T08:42:46.361Z", "modified": "2026-06-01T08:42:47.207Z"}, {"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": "8cb122c7905e4043bd3f13414014d2fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8cb122c7905e4043bd3f13414014d2fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8cb122c7905e4043bd3f13414014d2fe"}}, "title": "The long noncoding RNA VIM-AS1 and nucleoporin Nup358/RanBP2 regulate SMAD nuclear accumulation during TGF-\u03b2 signaling.", "authors": [{"family": "Rodrigues-Junior", "given": "Dorival Mendes", "initials": "DM", "orcid": "0000-0002-8861-9240", "researcher": {"href": "https://publications.scilifelab.se/researcher/3334d6f77c1f42c2b10fd3e9bef23efb.json"}}, {"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM"}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Ferreira", "given": "Mafalda Sousa", "initials": "MS"}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Fu", "given": "Hao", "initials": "H"}, {"family": "Hoelz", "given": "Andr\u00e9", "initials": "A"}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH"}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "54", "issue": "2", "issn-l": "0305-1048"}, "abstract": "The transforming growth factor \u03b2 (TGF-\u03b2) pathway is a developmental signaling network that regulates tissue homeostasis and malfunctions in human diseases, including cancer. TGF-\u03b2 signals via two receptors, which activate SMAD and alternative signaling pathways. We show that TGF-\u03b2 induces the expression of the mammalian long noncoding RNA (lncRNA) VIM-AS1 (Vimentin antisense RNA1) variant-2 (v.2) via a transcriptional SMAD-GATA6-SPI1 complex. VIM-AS1 v.1 and v.2 localize in different cell compartments, including the nuclear border. Unbiased whole transcriptomic analysis and functional gain and loss of function assays establish that VIM-AS1 v.2 enhances TGF-\u03b2 signaling. Mechanistically, VIM-AS1 v.2 interacts with the nucleoporin Nup358/RanBP2, contributing to the binding of Nup358/RanBP2 to SMAD2/3 and enhancing SMAD nuclear accumulation. In the context of cancer biology, VIM-AS1 did not affect the antiproliferative actions of TGF-\u03b2, yet had an impact on the epithelial-mesenchymal transition gene program, and increased the invasion and motility of tumor cells, whereas its silencing sensitized cancer cells to chemotherapeutic agents. The molecular mechanism highlights how a lncRNA can modulate the nuclear pore's capacity to import SMAD complexes, by facilitating their capture by Nup358/RanBP2 and thereby enhancing nuclear accumulation of SMADs with distinct isoform composition, thus promoting selectively TGF-\u03b2 signaling responses.", "doi": "10.1093/nar/gkaf1526", "pmid": "41556346", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12817083"}, {"db": "pii", "key": "8431143"}], "notes": [], "created": "2026-06-01T11:10:58.548Z", "modified": "2026-06-01T11:10:58.802Z"}, {"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": "956e57bde6744efc807a93e14f61238f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/956e57bde6744efc807a93e14f61238f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/956e57bde6744efc807a93e14f61238f"}}, "title": "Cefiderocol resistance genes identified in environmental samples using functional metagenomics.", "authors": [{"family": "Gschwind", "given": "Remi", "initials": "R", "orcid": "0000-0001-7741-9764", "researcher": {"href": "https://publications.scilifelab.se/researcher/d15bb307008d40968a53a320eb2f4571.json"}}, {"family": "Bonnet", "given": "Mehdi", "initials": "M"}, {"family": "Abramova", "given": "Anna", "initials": "A"}, {"family": "Jarqu\u00edn-D\u00edaz", "given": "Victor Hugo", "initials": "VH"}, {"family": "Wenne", "given": "Marcus", "initials": "M"}, {"family": "L\u00f6ber", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-7468-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/7180811b734042c0b3b8fb3f2ee03e5e.json"}}, {"family": "Godron", "given": "Nicolas", "initials": "N"}, {"family": "Kampouris", "given": "Ioannis D", "initials": "ID"}, {"family": "Tskhay", "given": "Faina", "initials": "F"}, {"family": "Nahid", "given": "Fouzia", "initials": "F"}, {"family": "Debroucker", "given": "Chlo\u00e9", "initials": "C"}, {"family": "Bui-Hai", "given": "Maximilien", "initials": "M"}, {"family": "El Aiba", "given": "In\u00e8s", "initials": "I"}, {"family": "Kl\u00fcmper", "given": "Uli", "initials": "U", "orcid": "0000-0002-4169-6548", "researcher": {"href": "https://publications.scilifelab.se/researcher/effd67c0296c4d539c41292224ba310a.json"}}, {"family": "Berendonk", "given": "Thomas U", "initials": "TU"}, {"family": "Forslund-Startceva", "given": "Sofia K", "initials": "SK"}, {"family": "Zahra", "given": "Rabaab", "initials": "R"}, {"family": "Bengtsson-Palme", "given": "Johan", "initials": "J", "orcid": "0000-0002-6528-3158", "researcher": {"href": "https://publications.scilifelab.se/researcher/267ff77d11e04a30bacdd0ae7492bea8.json"}}, {"family": "Rupp\u00e9", "given": "Etienne", "initials": "E"}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "20", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the \"One Health\" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a \"Trojan Horse\" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/l), including \ua7b5-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.", "doi": "10.1093/ismejo/wrag010", "pmid": "41603547", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12915585"}, {"db": "pii", "key": "8443128"}], "notes": [], "created": "2026-06-01T11:11:00.738Z", "modified": "2026-06-01T11:11:00.948Z"}, {"entity": "publication", "iuid": "458be5facf88424ab597423133f064c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/458be5facf88424ab597423133f064c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/458be5facf88424ab597423133f064c6"}}, "title": "Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.", "authors": [{"family": "van Dam", "given": "Femke", "initials": "F", "orcid": "0000-0002-5526-5044", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6869844c377483abb30634c303da5fb.json"}}, {"family": "Westmeijer", "given": "George", "initials": "G"}, {"family": "Rezaei Somee", "given": "Maryam", "initials": "M"}, {"family": "Ketzer", "given": "Marcelo", "initials": "M"}, {"family": "Kiet\u00e4v\u00e4inen", "given": "Riikka", "initials": "R"}, {"family": "Ono", "given": "Shuhei", "initials": "S"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "McIntosh", "given": "Jennifer C", "initials": "JC"}, {"family": "Dopson", "given": "Mark", "initials": "M"}, {"family": "Drake", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7230-6509", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25c4627832844518873bb13021a2ef0.json"}}], "type": "journal article", "published": "2026-01-14", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "17", "issue": "1", "pages": "e0301725", "issn-l": null}, "abstract": "Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a \u03b413Cmethanol-methane isotope enrichment of up to 98.6\u2030. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.", "doi": "10.1128/mbio.03017-25", "pmid": "41288100", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12802149"}], "notes": [], "created": "2026-06-01T11:13:52.580Z", "modified": "2026-06-01T11:13:52.612Z"}, {"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": "cc266f15720044ff97f0c84859c74dbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc266f15720044ff97f0c84859c74dbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc266f15720044ff97f0c84859c74dbf"}}, "title": "Airborne eDNA captures three decades of ecosystem biodiversity.", "authors": [{"family": "Sullivan", "given": "Alexis R", "initials": "AR"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Svensson", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4476-9255", "researcher": {"href": "https://publications.scilifelab.se/researcher/75bc51f60237478abec1fb2969abc873.json"}}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-8524-778X", "researcher": {"href": "https://publications.scilifelab.se/researcher/75f852c1e5144ff3acda53bcec520001.json"}}, {"family": "Villegas", "given": "Jose Antonio", "initials": "JA"}, {"family": "Mikko", "given": "Amanda", "initials": "A", "orcid": "0009-0002-7701-8180", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bca394a219142d68195e45f756dd686.json"}}, {"family": "Bellieny", "given": "Daniel", "initials": "D"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB", "orcid": "0000-0002-3178-523X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a19c155f873b4ec194a0ba07d9bbff92.json"}}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Grahn", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8936-3101", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5806ae054ec4cf1b67ee151bfd95b2f.json"}}, {"family": "Sundell", "given": "David", "initials": "D"}, {"family": "Norman", "given": "Anita", "initials": "A", "orcid": "0000-0002-9499-758X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1966d9c4e0f4c2c89702c8ef319264c.json"}}, {"family": "Esseen", "given": "Per-Anders", "initials": "PA"}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Singh", "given": "Navinder J", "initials": "NJ", "orcid": "0000-0002-5131-0004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bae3b76bb4a4f95a77e41cd929637ff.json"}}, {"family": "Brodin", "given": "Tomas", "initials": "T", "orcid": "0000-0003-1086-7567", "researcher": {"href": "https://publications.scilifelab.se/researcher/8140649bc5e140369d031c78fc416ae2.json"}}, {"family": "Forsman", "given": "Mats", "initials": "M", "orcid": "0000-0002-4466-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52b5a759a3e452b80728241c50c76dd.json"}}, {"family": "Stenberg", "given": "Per", "initials": "P", "orcid": "0000-0003-4738-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9b9949cf994f6c93d60261eb530d1b.json"}}], "type": "journal article", "published": "2025-12-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "11281", "issn-l": "2041-1723"}, "abstract": "Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.", "doi": "10.1038/s41467-025-67676-7", "pmid": "41413054", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12717267"}, {"db": "pii", "key": "10.1038/s41467-025-67676-7"}], "notes": [], "created": "2026-03-25T07:37:10.622Z", "modified": "2026-03-25T07:37:11.494Z"}, {"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": "fdb2a58a717e4bbca202566f67f5792b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdb2a58a717e4bbca202566f67f5792b"}}, "title": "A co-speciation dilemma and a lifestyle transition with genomic consequences in Wolbachia of Neotropical Drosophila", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Miller", "given": "Wolfgang J", "initials": "WJ"}, {"family": "Klasson", "given": "Lisa", "initials": "L", "orcid": "0000-0002-5874-7153", "researcher": {"href": "https://publications.scilifelab.se/researcher/409de77af489419db6d2b599b590d02f.json"}}], "type": "journal-article", "published": "2025-12-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "27", "issue": "1", "pages": "41", "issn-l": "1471-2164"}, "abstract": "Long-term persistent symbiotic associations may result in co-speciation and can be inferred if species trees of hosts and symbionts are congruent in topology and divergence times. Co-speciation has been seen to occur relatively frequently in obligate associations, but is less common in parasitic or facultative ones, mainly due to the difference in horizontal transmission rates. The long-term vertical inheritance and close host association of obligate endosymbionts also generally result in smaller genomes than in facultative endosymbionts. Here, we investigate co-speciation and genome reduction using highly similar strains of the endosymbiont Wolbachia infecting Drosophila species from the willistoni and saltans groups, where only one strain, wPau, infecting D. paulistorum, is obligate.\n\nWe sequenced the Wolbachia genomes from five species of the willistoni and saltans groups and constructed phylogenies. Topological congruence was found between these Wolbachia strains and the nuclear DNA of their hosts, except for wPau and D. paulistorum, but full topological congruence was observed between Wolbachia and the host mitochondrial DNA. However, assuming temporal congruence, we estimated extremely low evolutionary rates in Wolbachia of 10- 10-10- 11 changes/site/year. Additionally, the obligate wPau strain was found to have a larger genome than closely related facultative strains, mainly due to an ongoing expansion of an IS4 element. Furthermore, wPau has lost a large proportion of its prophage WO genes, but the cif genes, known to be involved in the CI phenotype, are intact. Finally, nine of the eleven genes from the prophage WO-associated Undecim cluster are uniquely duplicated.\n\nThe congruent topologies between Wolbachia and their willistoni and saltans group hosts indicate co-speciation. However, the high similarity between Wolbachia strains, which results in low mutation rate estimates, challenges this interpretation. Contrary to the expectations of the genome reduction theory, we observed an increase in genome size in the obligate wPau strain, potentially driven by a decreased population size. Finally, the duplication of the Undecim cluster, despite a major loss of other prophage-associated genes, suggests that the genes in the Undecim cluster are under strong selection and potentially play a role in the obligate association between wPau and their D. paulistorum hosts.", "doi": "10.1186/s12864-025-12340-z", "pmid": "41366724", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12801941"}, {"db": "pii", "key": "10.1186/s12864-025-12340-z"}], "notes": [], "created": "2026-01-19T08:58:08.199Z", "modified": "2026-01-20T07:53:24.298Z"}, {"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": "b8ca2a2dba2049ec8de7192c162898c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4"}}, "title": "Homo sapiens-specific evolution unveiled by ancient southern African genomes.", "authors": [{"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Hollfelder", "given": "Nina", "initials": "N", "orcid": "0000-0002-1567-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81a63833c146999d73fa38f588ea06.json"}}, {"family": "Vicente", "given": "Mario", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Brink", "given": "James", "initials": "J"}, {"family": "Zipfel", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-4251-884X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d1041d932a49c9bc2baca44273d4a4.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": null, "issue": null, "pages": null}, "abstract": "Homo sapiens evolved hundreds of thousands of years ago in Africa, later spreading across the globe1, but the early evolutionary process is debated2-6. Here we present whole-genome sequencing data for 28 ancient southern African individuals, including six individuals with 25\u00d7 to 7.2\u00d7 genome coverage, dated to between 10,200 and 150 calibrated years before present (cal. BP). All ancient southern Africans dated to more than 1,400 cal. BP show a genetic make-up that is outside the range of genetic variation in modern-day humans (including southern African Khoe-San people, although some retain up to 80% ancient southern African ancestry), manifesting in a large fraction of Homo sapiens-specific variants that are unique to ancient southern Africans. Homo sapiens-specific variants at amino acid-altering sites fixed for all humans-which are likely to have evolved rapidly on the Homo sapiens branch-were enriched for genes associated with kidney function. Some Homo sapiens-specific variants fixed in ancient southern Africans-which are likely to have adapted rapidly on the southern African branch-were enriched for genes associated with protection against ultraviolet light. The ancient southern Africans show little spatiotemporal stratification for 9,000 years, consistent with a large, stable Holocene population transcending archaeological phases. While southern Africa served as a long-standing geographical refugium, there is outward gene flow over 8,000 years ago; however, inward gene flow manifests only after around 1,400 years ago. The ancient genomes reported here are therefore key to the evolution of Homo sapiens, and are important for advancing our understanding of human genomic variation.", "doi": "10.1038/s41586-025-09811-4", "pmid": "41339558", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09811-4"}], "notes": [], "created": "2025-12-04T08:12:48.745Z", "modified": "2025-12-05T10:16:26.469Z"}, {"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": "bed19b398aa143d28064d622d7f4babf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bed19b398aa143d28064d622d7f4babf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bed19b398aa143d28064d622d7f4babf"}}, "title": "Holotype genome of the lesula provides insights into demography and evolution of a threatened primate lineage.", "authors": [{"family": "Jensen", "given": "Axel", "initials": "A", "orcid": "0000-0003-1766-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f139b7f3dac49e28ef6430637d88592.json"}}, {"family": "Horton", "given": "Emma R", "initials": "ER"}, {"family": "Koko", "given": "Mardoch\u00e9 B", "initials": "MB"}, {"family": "Detwiler", "given": "Kate M", "initials": "KM"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2025-12-01", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "26", "issue": "1", "pages": "408"}, "abstract": "The development of genome sequencing techniques has revolutionized evolutionary biology, facilitating the study of adaptation and speciation at the genome level. Genomic data has also become a cornerstone in conservation management, allowing inferences of population demography and genetic diversity.\n\nWe sequence the genome of the holotype specimen of the elusive lesula (Cercopithecus lomamiensis), a recently described member of the guenons (tribe Cercopithecini), endemic to the Democratic Republic of the Congo. Using published and novel genomic data, we explore the evolutionary and demographic history of C. lomamiensis and its sister species C. hamlyni. We estimate that the two species split ca. 3\u20134 million years ago, and find that they both show high genetic diversity despite being listed as Vulnerable on the IUCN Red List. We identify signatures of positive selection in genes involved in pelage coloration and immune functions, as well as skeletal morphology and locomotor behavior, potentially related to the terrestrial lifestyle of C. lomamiensis and C. hamlyni, which stand out among the otherwise arboreal Cercopithecus genus. We specifically explore whether introgression from more distantly related terrestrial guenons was involved in the evolution of terrestriality in the hamlyni group, but found low molecular convergence suggesting that putative terrestrial adaptations occurred largely independently.\n\nThis study provides insights into the demography and evolutionary history in a poorly known, threatened primate lineage. Furthermore, our results suggest that genomic erosion is not an imminent threat to these species, and that conservation management should prioritize actions to prevent further population decline.\n\nThe online version contains supplementary material available at 10.1186/s13059-025-03877-z.", "doi": "10.1186/s13059-025-03877-z", "pmid": "41327385", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12667059"}, {"db": "pii", "key": "10.1186/s13059-025-03877-z"}], "notes": [], "created": "2025-12-04T13:28:29.798Z", "modified": "2025-12-21T19:09:46.579Z"}, {"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": "823c71158dcd4b9fb085d01e55d13e48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/823c71158dcd4b9fb085d01e55d13e48"}}, "title": "scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.", "authors": [{"family": "Yadav", "given": "Ram Prakash", "initials": "RP"}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Hollander", "given": "Peter", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Xie", "given": "Minglu", "initials": "M"}, {"family": "Salehi", "given": "Maede", "initials": "M"}, {"family": "Torell", "given": "Emma", "initials": "E"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Swartling", "given": "Fredrik Johansson", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Glimelius", "given": "Ingrid", "initials": "I"}, {"family": "Micke", "given": "Patrick", "initials": "P", "orcid": "0000-0003-1210-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc0cba74e74a4c39a8f96319cb9a3034.json"}}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "10022", "issn-l": "2041-1723"}, "abstract": "Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8-12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.", "doi": "10.1038/s41467-025-66170-4", "pmid": "41238550", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-025-66170-4"}, {"db": "pmc", "key": "PMC12618699"}], "notes": [], "created": "2025-11-17T09:00:46.632Z", "modified": "2025-11-17T09:00:47.092Z"}, {"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": "edba25a5b1e54a32865c02915ee9ff5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edba25a5b1e54a32865c02915ee9ff5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edba25a5b1e54a32865c02915ee9ff5e"}}, "title": "Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.", "authors": [{"family": "Moraitou", "given": "Markella", "initials": "M", "orcid": "0000-0003-0860-5920", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f3b54ad837e4860a81b0bd5a886b416.json"}}, {"family": "Richards", "given": "John L", "initials": "JL", "orcid": "0000-0003-4428-1580", "researcher": {"href": "https://publications.scilifelab.se/researcher/23d3051397fd422b94afdb6eb8be17c4.json"}}, {"family": "Bolyos", "given": "Chanah", "initials": "C"}, {"family": "Saliari", "given": "Konstantina", "initials": "K", "orcid": "0000-0002-1344-0756", "researcher": {"href": "https://publications.scilifelab.se/researcher/b32afde8cb454fa3bb0e880e2cff5d0b.json"}}, {"family": "Gilissen", "given": "Emmanuel", "initials": "E"}, {"family": "Timmons", "given": "Zena", "initials": "Z"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC"}, {"family": "Pauwels", "given": "Olivier S G", "initials": "OSG"}, {"family": "Sabin", "given": "Richard", "initials": "R", "orcid": "0000-0003-0699-7596", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7d0503256fd45e687c1eebc9ce0c797.json"}}, {"family": "Kokkini", "given": "Phaedra", "initials": "P", "orcid": "0000-0002-7652-0956", "researcher": {"href": "https://publications.scilifelab.se/researcher/223e41a72db2480aa5fbfd015702b525.json"}}, {"family": "Portela Miguez", "given": "Roberto", "initials": "R", "orcid": "0000-0003-3094-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/103b88f38bcb494e8b42096d632e9f71.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": "2025-11-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "25", "issue": "8", "pages": "e70039"}, "abstract": "Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.", "doi": "10.1111/1755-0998.70039", "pmid": "40889349", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550474"}], "notes": [], "created": "2025-09-08T07:07:00.224Z", "modified": "2025-11-28T10:50:40.774Z"}, {"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": "19188c6729144072978d9a3d01d09133", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19188c6729144072978d9a3d01d09133"}}, "title": "Genetic Analysis of Apple Autumn Canopy Senescence in a Nordic Climate.", "authors": [{"family": "Skytte Af S\u00e4tra", "given": "Jonas", "initials": "J", "orcid": "0000-0002-2827-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b323220517477eb3c4acda1bb64c81.json"}}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Physiol Plantarum", "issn": "1399-3054", "volume": "177", "issue": "6", "pages": "e70599", "issn-l": "0031-9317"}, "abstract": "Autumn phenology traits are likely to be essential for the adaptation of apple to boreal climate. However, the genetic control of these traits is not well understood, and, for example, growth cessation does not appear to be controlled by day length as in many other boreal tree species. Here, I combine a quantitative genetic and population genomic approach to study autumn senescence in apple. I phenotyped a diverse germplasm collection for the timing of autumn senescence, performed quantitative trait loci (QTL) mapping in a multiparental population (MPP), and investigated genomic signals of selection to identify candidate genes. The timing of 50% autumn senescence was negatively correlated with adaptation to higher (boreal) climate zones. Two QTL were found to control the timing of autumn senescence in the MPP, exhibiting both dominance and epistatic interactions. The QTL on linkage group (LG) 17 was also variable in the diversity germplasm, while the QTL on LG11 was not. Cultivars adapted to boreal climate showed weak signals of selection at two loci within the genomic region of chromosome 17 corresponding to the LG17 QTL interval, consistent with a recent expansion to northern Sweden. These loci coincide with two predicted UGT85 genes and a possible copy number variation in PHYC, respectively. Thus, this study provides valuable information for further research and breeding of apple in light of the ongoing climate change.", "doi": "10.1111/ppl.70599", "pmid": "41164927", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12573221"}], "notes": [], "created": "2025-11-07T07:26:45.450Z", "modified": "2025-11-14T11:08:25.063Z"}, {"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": "85c5bdfdbc81457e81767eab223261e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85c5bdfdbc81457e81767eab223261e3"}}, "title": "Diagnostic and prognostic biomarkers associated with histotype in advanced epithelial ovarian cancer.", "authors": [{"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Swenson", "given": "Hugo", "initials": "H"}, {"family": "Werner", "given": "Lucas", "initials": "L"}, {"family": "R\u00f6nnerman", "given": "Elisabeth Werner", "initials": "EW"}, {"family": "Mateoiu", "given": "Constantina", "initials": "C"}, {"family": "Kov\u00e1cs", "given": "Anik\u00f3", "initials": "A"}, {"family": "Dahm-K\u00e4hler", "given": "Pernilla", "initials": "P"}, {"family": "Saed", "given": "Ghassan", "initials": "G"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Parris", "given": "Toshima Z", "initials": "TZ", "orcid": "0000-0003-0834-5540", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d528a2bce6c40829c1a6fed69c9f9ef.json"}}, {"family": "Helou", "given": "Khalil", "initials": "K"}], "type": "journal article", "published": "2025-10-23", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "37171", "issn-l": "2045-2322"}, "abstract": "Despite advances in cancer treatments, epithelial ovarian cancer (EOC) remains the leading cause of death among gynecologic cancers. EOC is stratified into five main histopathological subtypes: high-grade serous carcinoma (HGSC), low-grade serous carcinoma (LGSC), endometrioid carcinoma (EC), clear cell carcinoma (CCC), and mucinous carcinoma (MC). However, personalized treatment strategies and reliable biomarkers for all histotypes remain elusive. Building on our previous work with early-stage EOC, we aim to explore diagnostic and prognostic biomarkers in advanced-stage EOC, updated to the latest World Health Organization classification guidelines from 2020, using comprehensive transcriptomic profiling from total RNA sequencing of 146 EOCs. Differential expression analysis identified top 9 histotype-specific gene panels for HGSC, CCC, MC, and EC, including S100A1 (HGSC), ARID3A (CCC), LGALS4 (MC), and PAX9 (EC). We also identified gene candidates associated with overall survival and disease-specific survival, reflecting both favorable (e.g., OTOF, EEF1E1-BLOC1S5, and STAC3) and unfavorable (e.g., SMOC1, GDPGP1, EPRS1) clinical outcome. Additionally, enrichment analysis revealed tumor progression-related pathways unique to each histotype, offering insights into the molecular mechanisms underlying disease progression and potential therapeutic targets. These findings provide valuable insights into the molecular landscape of advanced-stage EOC, paving the way for more effective diagnostic and prognostic tools across diverse histotypes.", "doi": "10.1038/s41598-025-24938-0", "pmid": "41131133", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12550092"}, {"db": "pii", "key": "10.1038/s41598-025-24938-0"}], "notes": [], "created": "2025-11-07T07:25:02.175Z", "modified": "2025-11-28T10:47:09.805Z"}, {"entity": "publication", "iuid": "c34e73cd03bb4bea92a8c1741dafab9d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c34e73cd03bb4bea92a8c1741dafab9d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c34e73cd03bb4bea92a8c1741dafab9d"}}, "title": "Transcriptomic responses of beet to infection by beet mild yellowing virus.", "authors": [{"family": "Puthanveed", "given": "Vinitha", "initials": "V"}, {"family": "Sajeevan", "given": "Radha Sivarajan", "initials": "RS", "orcid": "0000-0002-8671-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d0cdc56cd144c628d3c90000b782581.json"}}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Alexandersson", "given": "Erik", "initials": "E", "orcid": "0000-0001-6320-2492", "researcher": {"href": "https://publications.scilifelab.se/researcher/eae8dc98de79429495f0a1727a342e9f.json"}}, {"family": "Joshi", "given": "Pratikshya", "initials": "P", "orcid": "0000-0002-6361-5059", "researcher": {"href": "https://publications.scilifelab.se/researcher/46050ddec8f64054b3bab46c5016aebf.json"}}, {"family": "Snell", "given": "Per", "initials": "P"}, {"family": "Lennefors", "given": "Britt-Louise", "initials": "BL"}, {"family": "Kvarnheden", "given": "Anders", "initials": "A", "orcid": "0000-0001-9394-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf67998333e74016847b7a6d3f121e7b.json"}}], "type": "journal article", "published": "2025-10-21", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "25", "issue": "1", "pages": "1406", "issn-l": "1471-2229"}, "abstract": "Virus yellows (VY) disease of sugar beet is caused by a complex of aphid-transmitted viruses, including beet mild yellowing virus (BMYV). Neonicotinoids have been used for preventing VY through aphid management, but with the recent ban on neonicotinoids in Europe, the risks for outbreaks of VY have increased dramatically. To study the host responses to BMYV infection and identify the differentially expressed genes (DEGs), we conducted an RNAseq experiment using a resistant genotype of wild beet and a susceptible breeding line of sugar beet. The experiment contained four plant treatments: exposure to aphids with or without BMYV, only insecticide spray and untreated control. Leaves were collected for analyses at 0, 1, 4, 14, 21 and 28 days post-inoculation (DPI).\n\nFollowing BMYV inoculation, resistant plants did not show any chlorosis even at 28 DPI, whereas susceptible plants displayed typical virus symptoms. Using RT-qPCR, BMYV was detected already at 1 DPI in both genotypes. At 14, 21 and 28 DPI, the virus titre in young and inoculated leaves of the susceptible genotype was higher. RNAseq revealed more DEGs as a response to BMYV infection for the susceptible genotype. In inoculated leaves, the number of DEGs increased faster for the susceptible genotype, while in young leaves, the trend was similar for susceptible and resistant genotypes. This shows that the plant responses in inoculated leaves to virus infection appeared at a larger scale in the susceptible genotype. Seven of the significantly upregulated genes in the resistant genotype encoded proteins involved in protein processing in the ER. This could be one mechanism contributing to the absence of symptoms in this genotype.\n\nThis study offers new insights into the transcriptomic events and genetic pathways regulating the defence response to BMYV in a partially resistant genotype. We present 14 candidate genes for partial resistance to BMYV and one of the possible mechanisms contributing to reduced virus levels and absence of symptoms. The findings will be of importance for future functional studies to understand the mechanisms of resistance and susceptibility as well as for the breeding of BMYV resistance.", "doi": "10.1186/s12870-025-07514-6", "pmid": "41120973", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12538817"}, {"db": "pii", "key": "10.1186/s12870-025-07514-6"}], "notes": [], "created": "2025-11-07T07:24:57.182Z", "modified": "2025-11-14T11:08:40.919Z"}, {"entity": "publication", "iuid": "d9c76d2925724acb9c140d062e9a55ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9c76d2925724acb9c140d062e9a55ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9c76d2925724acb9c140d062e9a55ad"}}, "title": "Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Sin", "given": "Sopha", "initials": "S"}, {"family": "Uk", "given": "Onnorong", "initials": "O"}, {"family": "Hap", "given": "Sophorn", "initials": "S"}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "88", "issue": "1", "pages": "109", "issn-l": "0095-3628"}, "abstract": "Rice-associated leafhoppers (Cicadellidae) play a significant role in rice agroecosystems, contributing not only to direct crop damage but also to the transmission of plant pathogens. This study investigates the symbiont diversity of seventeen leafhopper species from the tropical floodplains of Tonle Sap Lake (TSL), Cambodia. The dominant symbiont across most species was Candidatus (Ca.) Karelsulcia muelleri, an obligate primary endosymbiont essential for nutrient synthesis. The co-obligate symbiont Ca. Nasuia deltocephalinicola was also consistently detected, particularly in Deltocephalinae hosts. In addition, several secondary symbionts, including Sodalis, Arsenophonus, Diplorickettsia, Rickettsia, Wolbachia, and Ca. Lariskella, were identified, showing species-specific associations and potential roles in host fitness and pathogen transmission. Variations in symbiont diversity were observed across cicadellid species, geographic origins, and between sex-associated symbionts, with notable differences in the bacterial composition of Nephotettix virescens. While geographical differences (Battambang vs. Kampong Thom) did not strongly affect microbial composition, sex-associated variations were evident in N. virescens. Females exhibited a higher abundance of Karelsulcia and Nasuia, suggesting possible microbial adaptation related to reproduction. This study highlights the complex and dynamic nature of cicadellid hosts-symbiont interactions and suggests that microbial communities are primarily structured by host species. While geographic distance can influence these communities, this effect is not the same for every species. These findings provide critical insights into the microbial diversity of rice-associated leafhoppers and their potential for ecological roles in rice farming systems. Further studies, including functional analysis and host-symbiont interactions, are crucial to understanding the ecological roles and evolutionary dynamics of these microbial communities.", "doi": "10.1007/s00248-025-02619-9", "pmid": "41105260", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12534257"}, {"db": "pii", "key": "10.1007/s00248-025-02619-9"}], "notes": [], "created": "2025-11-07T07:26:53.717Z", "modified": "2025-11-28T10:41:02.912Z"}, {"entity": "publication", "iuid": "3026cc0df25b4c178a58bdb7ba158810", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3026cc0df25b4c178a58bdb7ba158810"}}, "title": "Reduced vascular leakage correlates with breast carcinoma T regulatory cell infiltration but not with metastatic propensity.", "authors": [{"family": "He", "given": "Liqun", "initials": "L", "orcid": "0000-0002-4743-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6e2e4c7f88845bb895842e56a7622ae.json"}}, {"family": "Testini", "given": "Chiara", "initials": "C"}, {"family": "Hekmati", "given": "Neda", "initials": "N", "orcid": "0009-0009-4814-869X", "researcher": {"href": "https://publications.scilifelab.se/researcher/59e525846f61401ab94732e578190274.json"}}, {"family": "Bonello", "given": "Altea", "initials": "A"}, {"family": "Schiza", "given": "Aglaia", "initials": "A"}, {"family": "Nwadozi", "given": "Emmanuel", "initials": "E"}, {"family": "Phillipson", "given": "Mia", "initials": "M", "orcid": "0000-0002-2387-0266", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ebf9ffcab3e4a19add4c6dd51b727b1.json"}}, {"family": "Strell", "given": "Carina", "initials": "C", "orcid": "0000-0002-3783-7256", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb77b417ef2b479fb267969c3a557617.json"}}, {"family": "Welsh", "given": "Michael", "initials": "M", "orcid": "0000-0002-5467-9755", "researcher": {"href": "https://publications.scilifelab.se/researcher/c01673aeb9be429c80da30d5407b2725.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Mol Oncol", "issn": "1878-0261", "issn-l": "1574-7891"}, "abstract": "The vasculature and the immune system both play roles in breast cancer progression and metastasis. In an experimental mouse model of Shb-gene deficiency in endothelial cells, breast cancer lung metastasis correlated with immune suppression rather than with vascular leakage. The present study aimed to assess underlying gene expression changes in endothelial and immune cells responsible for this phenotype and to explore their relationship to human disease. Mouse endothelial cell Shb-gene deficiency, leading to 'vessel normalization', resulted in altered expression of chemo/cytokine genes and upregulation of immune checkpoint genes in immune cells. Endothelial cells under these conditions exhibited gene expression patterns compatible with reduced angiogenesis and vascular leakage. Additionally, genes whose products relate to immune cell vascular transmigration and function were affected. In a human triple-negative breast cancer cohort, tumors with reduced vascular leakage exhibited a higher relative proportion of regulatory T cells and larger tumor size. However, these changes were not associated with increased metastasis. In conclusion, a low leakage vascular phenotype reduces tumor cell intravasation/metastasis and modifies the immune response, which in the current context becomes pro-tumoral.", "doi": "10.1002/1878-0261.70144", "pmid": "41102920", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:23:33.643Z", "modified": "2025-11-13T17:36:03.258Z"}, {"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": "6d6faf7279134df68f3e4160a4981f61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61"}}, "title": "The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia.", "authors": [{"family": "Ahlgren", "given": "Louise", "initials": "L"}, {"family": "Pilheden", "given": "Mattias", "initials": "M"}, {"family": "Sturesson", "given": "Helena", "initials": "H"}, {"family": "Song", "given": "Guangchun", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Walsh", "given": "Michael P", "initials": "MP"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Maillard", "given": "Maud", "initials": "M"}, {"family": "Zhao", "given": "Huanbin", "initials": "H", "orcid": "0009-0001-4418-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/02a78b74f32d4670b628a8e3fb78ea0a.json"}}, {"family": "Cheng", "given": "Zhongshan", "initials": "Z"}, {"family": "Singh", "given": "Varsha", "initials": "V"}, {"family": "Castor", "given": "Anders", "initials": "A", "orcid": "0009-0007-4634-0704", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d2dab933049f5b69cdf0ff1e1d8a1.json"}}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ", "orcid": "0000-0002-0073-9660", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e42ba48d824aa0b42e871e9f11b00a.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Lausen", "given": "Birgitte", "initials": "B", "orcid": "0000-0002-5306-0774", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc5eadc48e354c4cb70d68d420bfa6fe.json"}}, {"family": "Schneider", "given": "Pauline", "initials": "P", "orcid": "0000-0003-0162-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a9fea74e284217b80716966bca995b.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Pokrovskaja Tamm", "given": "Katja", "initials": "K", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Menendez", "given": "Pablo", "initials": "P"}, {"family": "Pieters", "given": "Rob", "initials": "R", "orcid": "0000-0003-2997-3570", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb567d1e17e0428c843c07682decb31c.json"}}, {"family": "Zhang", "given": "Jinghui", "initials": "J", "orcid": "0000-0003-3350-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe8464634149a39bc8accf6077bac4.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Yang", "given": "Jun J", "initials": "JJ", "orcid": "0000-0002-0770-9659", "researcher": {"href": "https://publications.scilifelab.se/researcher/023457113ddc4e3a8309d0b4936c097e.json"}}, {"family": "Gruber", "given": "Tanja A", "initials": "TA", "orcid": "0000-0003-1072-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/c16c5b66f56f40fd93a9f398b0487a64.json"}}, {"family": "Stam", "given": "Ronald W", "initials": "RW", "orcid": "0000-0003-4986-1656", "researcher": {"href": "https://publications.scilifelab.se/researcher/f528aaa6b3ba479f85619e1496e3f395.json"}}, {"family": "Ma", "given": "Jing", "initials": "J"}, {"family": "Hagstr\u00f6m-Andersson", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-2904-1311", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc93a87c663d471ba64fc3be63212a89.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8964", "issn-l": "2041-1723"}, "abstract": "To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n = 36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (<9 months, 9%). A marked chemotherapy-exposure signature was detected for mutations in early relapse ALL but not in very early ALL or AML relapse, in line with different mechanisms of relapse. Longitudinal analyses could track residual leukemia cells, clonal drug responses, and the upcoming relapse. These results highlight that KMT2A-r ALL and AML evade therapy differently and provide insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.", "doi": "10.1038/s41467-025-64190-8", "pmid": "41062506", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508131"}, {"db": "pii", "key": "10.1038/s41467-025-64190-8"}], "notes": [], "created": "2025-10-28T09:43:15.594Z", "modified": "2025-11-07T07:22:38.375Z"}, {"entity": "publication", "iuid": "e105bd630ef34bb0a01ca502b207908e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e105bd630ef34bb0a01ca502b207908e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e105bd630ef34bb0a01ca502b207908e"}}, "title": "Climate-driven deoxygenation promoted potential mercury methylators in the past Black Sea water column", "authors": [{"family": "Zhong", "given": "Meifang", "initials": "M", "orcid": "0000-0001-8995-5468", "researcher": {"href": "https://publications.scilifelab.se/researcher/db04492b3b6c4596a4b6eda2007f4dc1.json"}}, {"family": "Barrenechea Angeles", "given": "In\u00e9s", "initials": "I", "orcid": "0000-0002-8051-4110", "researcher": {"href": "https://publications.scilifelab.se/researcher/117e061371ff48088a21ac74e9321dfa.json"}}, {"family": "More", "given": "Kuldeep D", "initials": "KD", "orcid": "0000-0002-8278-8086", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b7cfdaad6614e6986ddd3a9c25434c4.json"}}, {"family": "Picard", "given": "Ma\u00eflys", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Bravo", "given": "Andrea G", "initials": "AG", "orcid": "0000-0002-8341-3462", "researcher": {"href": "https://publications.scilifelab.se/researcher/749bb106ca6b452d82603ef8cf3cbdee.json"}}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E", "orcid": "0000-0001-9570-8738", "researcher": {"href": "https://publications.scilifelab.se/researcher/d52d4c83dda84cea9e018199a8cfc304.json"}}, {"family": "Coolen", "given": "Marco J L", "initials": "MJL", "orcid": "0000-0002-0417-920X", "researcher": {"href": "https://publications.scilifelab.se/researcher/044cf58a620c40d8843b06e37942bdf4.json"}}, {"family": "Capo", "given": "Eric", "initials": "E", "orcid": "0000-0001-9143-7061", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4017e9c8167487b882ee2d045d96494.json"}}], "type": "journal-article", "published": "2025-10-08", "journal": {"title": "Nat Water", "issn": "2731-6084", "issn-l": null}, "abstract": null, "doi": "10.1038/s44221-025-00526-4", "pmid": null, "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:26:40.967Z", "modified": "2025-11-14T11:07:32.517Z"}, {"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": "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": "25dfec9e03fc41aeb351f41e6acf76d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25dfec9e03fc41aeb351f41e6acf76d8"}}, "title": "Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr.", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Fedi", "given": "Mariano Olivera", "initials": "MO"}, {"family": "Baker", "given": "Kendall", "initials": "K"}, {"family": "Barker", "given": "Tom", "initials": "T"}, {"family": "Catchpole", "given": "Leah", "initials": "L"}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Cocco", "given": "Arianna", "initials": "A"}, {"family": "Collins", "given": "Joanna", "initials": "J"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA"}, {"family": "Durrant", "given": "Alex", "initials": "A"}, {"family": "Hindar", "given": "Kjetil", "initials": "K", "orcid": "0000-0002-2769-2284", "researcher": {"href": "https://publications.scilifelab.se/researcher/0093cfa9f60e4e7db25d898de5c194b9.json"}}, {"family": "Iannucci", "given": "Alessio", "initials": "A", "orcid": "0000-0001-7729-4412", "researcher": {"href": "https://publications.scilifelab.se/researcher/da461c1ddb4649928a998aa9802a5ea3.json"}}, {"family": "Irish", "given": "Naomi", "initials": "N"}, {"family": "Knitlhoffer", "given": "Vanda", "initials": "V"}, {"family": "Laikre", "given": "Linda", "initials": "L", "orcid": "0000-0001-9286-3361", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c7ebbb5d7a4af582746b6ab2c2d132.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Lucchini", "given": "Sacha", "initials": "S"}, {"family": "McTaggart", "given": "Seanna", "initials": "S"}, {"family": "P\u00e1lsson", "given": "Arnar", "initials": "A", "orcid": "0000-0002-6525-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbe0e0cea2254ede8a1149cc2b917b6a.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Ryman", "given": "Nils", "initials": "N", "orcid": "0000-0003-3342-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/97201873ea354e959e294d8d2d69be13.json"}}, {"family": "Snorrason", "given": "Sigur\u00f0ur S", "initials": "SS"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Swarbreck", "given": "David", "initials": "D"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Watkins", "given": "Christopher", "initials": "C"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD", "orcid": "0000-0002-7545-2162", "researcher": {"href": "https://publications.scilifelab.se/researcher/c255ed6ec2f246028326f9fece911f74.json"}}, {"family": "Xiao", "given": "Han", "initials": "H", "orcid": "0009-0000-4699-5590", "researcher": {"href": "https://publications.scilifelab.se/researcher/12a89016ae0d41788407e0b5a342d933.json"}}, {"family": "Gharbi", "given": "Karim", "initials": "K"}, {"family": "J\u00f3nsson", "given": "Zophon\u00edas O", "initials": "ZO", "orcid": "0000-0001-5798-9647", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dabaeca1ef54eb289cc48aab86ae2aa.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": "2025-10-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e70085", "volume": "34", "issue": "19", "issn-l": "0962-1083"}, "abstract": "Salmonids have a remarkable ability to form sympatric morphs after postglacial colonisation of freshwater lakes. These morphs often differ in morphology, feeding and spawning behaviour. Here, we explored the genetic basis of morph differentiation in Arctic charr (n = 283) by first establishing a high-quality reference genome and then using this in whole genome sequencing of distinct morphs present in two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions were found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. Our findings are consistent with a highly polygenic basis of morph differentiation with population-specific selection on alleles linked to the development of similar morph phenotypes. The results support a model where morph differentiation is first established through phenotypic plasticity, leading to niche expansion and separation. This may be followed by gradual development of reproductive isolation, locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence.", "doi": "10.1111/mec.70085", "pmid": "40856096", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12456120"}], "notes": [], "created": "2025-09-08T06:59:34.138Z", "modified": "2025-11-28T10:51:42.317Z"}, {"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": "e851d932ff224ce9a80844e9e4e5cd2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e851d932ff224ce9a80844e9e4e5cd2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e851d932ff224ce9a80844e9e4e5cd2c"}}, "title": "The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma.", "authors": [{"family": "Ohata", "given": "Yae", "initials": "Y"}, {"family": "Ali", "given": "Mohamad M", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Tsubakihara", "given": "Yutaro", "initials": "Y"}, {"family": "Itoh", "given": "Yuka", "initials": "Y"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Bergstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Mor\u00e9n", "given": "Anita", "initials": "A"}, {"family": "Gol\u00e1n-Cancela", "given": "Irene", "initials": "I"}, {"family": "Nakada", "given": "Ayana", "initials": "A"}, {"family": "Voytyuk", "given": "Oleksandr", "initials": "O"}, {"family": "Tsuchiya", "given": "Maiko", "initials": "M"}, {"family": "Fukui", "given": "Rei", "initials": "R"}, {"family": "Yamamoto", "given": "Kouhei", "initials": "K"}, {"family": "Mart\u00edn-Rubio", "given": "Paula", "initials": "P", "orcid": "0000-0002-2702-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71065b5619e414bb6401638b76b2160.json"}}, {"family": "Sancho", "given": "Patricia", "initials": "P"}, {"family": "Strell", "given": "Carina", "initials": "C"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Wechsler-Reya", "given": "Robert J", "initials": "RJ"}, {"family": "Hashizume", "given": "Yoshinobu", "initials": "Y"}, {"family": "Miyazono", "given": "Kohei", "initials": "K", "orcid": "0000-0001-7341-0172", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a14a58f628d435a94ad9540478117cb.json"}}, {"family": "Caja", "given": "Laia", "initials": "L", "orcid": "0000-0002-8786-8763", "researcher": {"href": "https://publications.scilifelab.se/researcher/62d8ae2bdac54a6584afeac2b766f628.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Cell Death Differ.", "issn": "1476-5403", "volume": "32", "issue": "10", "pages": "1915-1929", "issn-l": "1350-9047"}, "abstract": "Oncogenic events perturb cerebellar development leading to medulloblastoma, a common childhood brain malignancy. Molecular analyses classify medulloblastoma into the WNT, SHH, Group 3 and Group 4 subgroups. Bone morphogenetic protein (BMP) pathways control cerebellar development and have been linked to the progression of medulloblastoma disease, with major remaining gaps in their mechanistic and clinically-relevant roles. We therefore aimed at exploring BMP mechanisms of action in medulloblastoma. Patient-derived tumors from different subgroups were analyzed in mouse xenografts, complemented by independent tumor immunohistochemical analysis. Cell-based assays analyzed signaling mechanisms. Medulloblastoma cell orthotopic xenografts analyzed tumor growth and metastasis in vivo. Active BMP signaling, detected as nuclear and phosphorylated SMAD1/5, characterized several medulloblastoma subgroups, with enrichment in Group 4, SHH and Group 3 tumors. Spatial transcriptomics in tumor areas, complemented by transcriptomic analysis of multiple cell models, identified BMP-dependent transcriptional induction of the LIM-homeobox gene 2 (LHX2). BMP signaling via SMADs induced LHX2 expression and LHX2 transcriptionally induced BMP type I receptor (ACVR1) expression by association with the proximal promoter region of the ACVR1 gene. BMP signaling and LHX2 gain-of-function expression led to enriched stemness and associated chemoresistance in medulloblastoma cultures. In-mouse orthotopic transplantation of paired primary/recurrent Group 4 medulloblastoma cell populations, correspondingly expressing LHX2-low/BMP-low signaling and LHX2-high/BMP-high signaling, ascribed to the latter (high) group more efficient tumor propagation and spinal cord metastatic potential. Depletion of LHX2 in these recurrent tumor cells suppressed both BMP signaling and tumor propagation in vivo. Thus, LHX2 cooperates with, and enhances, oncogenic BMP signaling in medulloblastoma tumors. The molecular pathway that couples LHX2 function to BMP signaling in medulloblastoma deepens our understanding this malignancy.", "doi": "10.1038/s41418-025-01488-6", "pmid": "40148468", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12501261"}, {"db": "pii", "key": "10.1038/s41418-025-01488-6"}], "notes": [], "created": "2025-09-08T06:54:49.956Z", "modified": "2025-11-28T10:45:02.518Z"}, {"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": "ae53f79971b5422e8d7b0c5ef5626fe0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae53f79971b5422e8d7b0c5ef5626fe0"}}, "title": "Primary and Secondary Symbionts of Cambodian Cicadellidae and the Role of Parasitisation.", "authors": [{"family": "Phauk", "given": "Sophany", "initials": "S", "orcid": "0000-0002-8019-3206", "researcher": {"href": "https://publications.scilifelab.se/researcher/80bf701bd9c14bd08c081d49b0d6ecad.json"}}, {"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Meas", "given": "Seanghun", "initials": "S", "orcid": "0009-0003-8813-8839", "researcher": {"href": "https://publications.scilifelab.se/researcher/829ed324071b46cc8720d6ffcf68b701.json"}}, {"family": "Terenius", "given": "Olle", "initials": "O", "orcid": "0000-0002-9909-1859", "researcher": {"href": "https://publications.scilifelab.se/researcher/3042a807e20d444cafee3f760c38d5d1.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Environ Microbiol Rep", "issn": "1758-2229", "volume": "17", "issue": "5", "pages": "e70196", "issn-l": "1758-2229"}, "abstract": "Leafhoppers (Hemiptera: Cicadellidae) are important vectors of plant pathogens in agricultural systems. Biological control via parasitisation is a key management strategy, but little is known about how microbial symbionts mediate host-parasitoid interactions. Here, we characterise the bacterial communities of six Cambodian leafhopper species (Cofana spectra, Exitianus sp., Goniagnathus punctifer, Maiestas dorsalis, Nephotettix virescens, and Stirellus sp.) and their parasitoids from the families Dryinidae (Hymenoptera) and Halictophagidae (Strepsiptera). We found that the bacterial symbiont Sulcia dominates cicadellid microbiotas, often coexisting with secondary symbionts. For example, Nasuia is present alongside Sulcia in Nephotettix, while Wolbachia is prevalent in Exitianus and Goniagnathus. Parasitoids exhibited distinct microbiotas with greater diversity; Rhodobacteraceae and Comamonadaceae were in dryinids, while Wolbachia was common in Halictophagidae. We analysed the microbiota of individual pairs of host-parasitoid and although parasitism did not significantly alter cicadellid overall microbiotas, some secondary symbionts (e.g., Arsenophonus, Wolbachia, Rickettsia, and Sodalis) were detected in both hosts and parasitoids, suggesting possible microbial transmission that warrants further investigation. These findings improve our understanding of host-parasitoid microbial interactions and highlight the relationship between primary and secondary symbiont communities.", "doi": "10.1111/1758-2229.70196", "pmid": "40957832", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12440678"}], "notes": [], "created": "2025-11-07T07:26:49.751Z", "modified": "2025-11-28T10:50:56.250Z"}, {"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": "e35988a7938b44638700ddc6625bc6aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e35988a7938b44638700ddc6625bc6aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e35988a7938b44638700ddc6625bc6aa"}}, "title": "Major Histocompatibility Complex modulation of Batrachochytrium dendrobatidis and Ranavirus infections in amphibians.", "authors": [{"family": "Cortazar-Chinarro", "given": "M", "initials": "M", "orcid": "0000-0003-4604-1441", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eeac642337c4ca5aab0275dcae9a8b9.json"}}, {"family": "Richter-Boix", "given": "A", "initials": "A"}, {"family": "Halvarsson", "given": "P", "initials": "P"}, {"family": "Palomar", "given": "G", "initials": "G"}, {"family": "Bosch", "given": "J", "initials": "J"}], "type": "journal article", "published": "2025-09-24", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "Genetic variation in immune genes is an important component of genetic diversity. The genes in the Major Histocompatibility Complex (MHC) provide an excellent model system for studying the mechanisms that generate and maintain genetic diversity in natural populations. While both demographic factors and pathogen-mediated selection processes contribute to the extreme diversity observed in the MHC systems, determining the relative importance of these evolutionary mechanisms has remained challenging. We investigated the role of pathogen-mediated selection in driving MHC diversity in three amphibian species: Ichthyosaura alpestris, Pleurodeles waltl and Pelophilax perezi. Our study examined the relationships between individual MHC diversity, infection status, infection intensity, and co-infection with two major amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus sp. (Rv) in natural populations. Our research demonstrated significant differences in Bd and Rv infection intensities among individuals with varying numbers of MHC loci. However, co-infection showed no discernible influence on infection intensities. We observed stronger associations of specific MHC alleles and supertypes with infection intensity and status in I. alpestris. These findings suggest that, in the context of multi-host infections, MHC genes may provide valuable insights into the evolutionary forces shaping MHC diversity, although the specific effects of individual MHC alleles on disease dynamics are yet to be clarified.", "doi": "10.1093/jeb/voaf112", "pmid": "40990944", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "8262903"}], "notes": [], "created": "2025-11-07T07:26:58.477Z", "modified": "2025-11-07T07:26:58.555Z"}, {"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": "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": "a321ba70d5a8449193a0b042ea632cc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a321ba70d5a8449193a0b042ea632cc6"}}, "title": "Sex Dependent and Sj\u00f6gren Disease Like Immune Responses Against Phosphoantigens in Balb/C Mice.", "authors": [{"family": "Czwakiel", "given": "Paulina", "initials": "P"}, {"family": "Brindefalk", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Eghbali", "given": "Atiyeh", "initials": "A"}, {"family": "Dircksen", "given": "Heinrich", "initials": "H"}, {"family": "Kamal", "given": "Kahkashan", "initials": "K", "orcid": "0000-0003-0968-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/56449fc911fd48b98b207c394d635507.json"}}, {"family": "Payandeh", "given": "Zahra", "initials": "Z"}, {"family": "Ozata", "given": "Deniz", "initials": "D", "orcid": "0000-0001-5215-8684", "researcher": {"href": "https://publications.scilifelab.se/researcher/933850bed34c4517b01e915cf8831686.json"}}, {"family": "Troye-Blomberg", "given": "Marita", "initials": "M"}, {"family": "Faye", "given": "Ingrid", "initials": "I", "orcid": "0000-0003-4382-7238", "researcher": {"href": "https://publications.scilifelab.se/researcher/28e762d6a5a845e79a7a107f700a82b5.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Scand. J. Immunol.", "issn": "1365-3083", "volume": "102", "issue": "3", "pages": "e70052", "issn-l": "0300-9475"}, "abstract": "The initial aim of this study on Balb/C mice was to investigate the putative effects on feeding and appetite of isopentenyl pyrophosphate (IPP) and E-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), also known as phosphoantigens (pAgs). HMBPP was recently shown to increase blood meal appetite in malaria mosquitoes. Both IPP and HMBPP are metabolites produced by the normal gut microbiota and apicomplexan parasites such as Plasmodium. To explore potential effects on appetite, male and female mice were treated by gavage with these metabolites, and body mass and gene expression were monitored in brain, stomach and small intestine at 3 h and 7 weeks. Body mass gain did not clearly differ between pAg-treated and water control mice. However, beginning between 4 and 7 weeks, the salivary glands of IPP-treated males began to swell. With the autoimmune Sj\u00f6gren disease (SjD) in mind, we subsequently investigated the salivary glands after 1, 4 and 7 weeks of IPP treatment. Fast gene set enrichment analysis (FGSEA) of marginal zone B-cell (MZB) transcripts from salivary glands, together with B-cell infiltration in both sexes at 4 weeks, suggested similarities to SjD pathology. Using ELISA, we measured serum autoantibodies against Ro52, Ro60 and La. Multivariate analysis at 7 weeks showed treatment-associated trends: levels of anti-Ro52 and anti-La tended to increase in IPP-treated males, but not in females. Notably, IL-6 serum levels displayed a sex-dependent pattern, and PCA analyses of transcriptomic data from brain, stomach and small intestine-though with some exceptions-also indicated differential responses to pAgs between males and females.", "doi": "10.1111/sji.70052", "pmid": "40898584", "labels": {"Autoimmunity and Serology Profiling": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12405675"}], "notes": [], "created": "2025-09-10T08:38:36.714Z", "modified": "2025-11-07T07:24:59.576Z"}, {"entity": "publication", "iuid": "e679aca133c2422599ac1891a96c1a05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05"}}, "title": "Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil", "authors": [{"family": "M\u00fcller", "given": "Laura J", "initials": "LJ", "orcid": "0009-0009-5747-2432", "researcher": {"href": "https://publications.scilifelab.se/researcher/11dad561c7e24e68b9ed71a015aa2263.json"}}, {"family": "Alicke", "given": "Mara", "initials": "M", "orcid": "0009-0000-0244-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d4c9a20fc04322a8babeaded66302f.json"}}, {"family": "Romdhane", "given": "Sana", "initials": "S", "orcid": "0000-0003-0295-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/494ad3e37974440988db1f7b377bae76.json"}}, {"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-2723-6019", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c04ad1e78da45ee8b383fb09fc5d44a.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.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": "2025-09-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "208", "pages": "109846", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2025.109846", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:13:11.714Z", "modified": "2025-09-08T07:13:12.028Z"}, {"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": "2cac753de106445cbf229064ef982197", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197"}}, "title": "Genomic determinants of therapy response in ETV6::RUNX1 leukemia.", "authors": [{"family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}}, {"family": "Moisio", "given": "Sanni", "initials": "S", "orcid": "0009-0009-4446-015X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1112350e9042bfa9a8707d2c255bf5.json"}}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea06b85057744018f754c373fef3ca5.json"}}, {"family": "Kramer", "given": "Roger", "initials": "R"}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Jayasingha", "given": "Buddika", "initials": "B"}, {"family": "M\u00e4kinen", "given": "Artturi", "initials": "A", "orcid": "0000-0002-5521-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/74542e2da6d542d8a40b93b692c7b760.json"}}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Suhonen", "given": "Janne", "initials": "J"}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Voutilainen", "given": "Miikka", "initials": "M", "orcid": "0000-0001-9367-3471", "researcher": {"href": "https://publications.scilifelab.se/researcher/390e63751ebb46e3873d801ce0c620d1.json"}}, {"family": "Lahnalampi", "given": "Mari", "initials": "M", "orcid": "0000-0003-4050-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d154912d9f4b9ca680f9d019035d46.json"}}, {"family": "Veps\u00e4l\u00e4inen", "given": "Kaisa", "initials": "K"}, {"family": "Huang", "given": "Sui", "initials": "S"}, {"family": "Duque-Afonso", "given": "Jesus", "initials": "J", "orcid": "0000-0002-8287-5673", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc78f208850b4a999859f110a3850bfa.json"}}, {"family": "Hauer", "given": "Julia", "initials": "J", "orcid": "0000-0002-4058-3058", "researcher": {"href": "https://publications.scilifelab.se/researcher/9387a9c586f74172a9d251fff4d71637.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": "39", "issue": "9", "pages": "2125-2139"}, "abstract": "ETV6::RUNX1 leukemia is the second most common subtype of childhood B cell acute lymphoblastic leukemia (B-ALL). Although it generally has a low relapse risk, a significant proportion of B-ALL relapses occur within this subtype due to its relatively high incidence. Measurable residual disease at the end of induction therapy is a well-established biomarker predicting treatment outcomes, while no genomic biomarkers are routinely applied in clinics. In this study, we used multiomic data from ETV6::RUNX1 leukemias to identify genomic features predictive of therapy response at disease presentation. In the deeply characterized sub-cohort we discovered that fast-responding cases frequently exhibited the APOBEC mutational signature and the gene expression signature of high cell cycle activity. In contrast, rearrangements of IGK genes were more frequent in slow responders. Additionally, response-related mutations were identified in transcriptional regulators and tumor suppressor genes (INTS1, NF1, TP53). Copy number analysis revealed that fast responders harbored more frequent deletions of chr12 p-arm, leading to transcriptomic changes affecting genes associated with induction therapy response (KRAS, FKBP4), while a shorter gain in chr12 was more common in slow responders. The identified genetic and transcriptomic markers of treatment sensitivity pave the way for improved disease classification at presentation, potentially improving clinical outcomes.", "doi": "10.1038/s41375-025-02683-7", "pmid": "40634509", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380598"}, {"db": "pii", "key": "10.1038/s41375-025-02683-7"}], "notes": [], "created": "2025-09-08T11:39:55.025Z", "modified": "2025-11-18T20:46:15.313Z"}, {"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": "b0aa84ad1a984c4d8b3eb1996eddfbe1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0aa84ad1a984c4d8b3eb1996eddfbe1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0aa84ad1a984c4d8b3eb1996eddfbe1"}}, "title": "Disease-specific U1 spliceosomal RNA mutations in mature B-cell neoplasms.", "authors": [{"family": "Nadeu", "given": "Ferran", "initials": "F", "orcid": "0000-0003-2910-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4654f6b3cd74ddfb4d859edff5fbc95.json"}}, {"family": "Shuai", "given": "Shimin", "initials": "S", "orcid": "0000-0002-9527-8018", "researcher": {"href": "https://publications.scilifelab.se/researcher/31c2a26041304b0390208fac7884e36c.json"}}, {"family": "Clot", "given": "Guillem", "initials": "G", "orcid": "0000-0003-2588-7413", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6a4380b01f4aa9a2fab0f19a0d34d9.json"}}, {"family": "Hilton", "given": "Laura K", "initials": "LK", "orcid": "0000-0002-6413-6586", "researcher": {"href": "https://publications.scilifelab.se/researcher/cebd0963fd1b4f7a836b380f3cb8a22d.json"}}, {"family": "Diaz-Navarro", "given": "Ander", "initials": "A"}, {"family": "Mart\u00edn", "given": "Silvia", "initials": "S"}, {"family": "Royo", "given": "Romina", "initials": "R"}, {"family": "Baumann", "given": "Tycho", "initials": "T"}, {"family": "Kulis", "given": "Marta", "initials": "M"}, {"family": "L\u00f3pez-Oreja", "given": "Irene", "initials": "I"}, {"family": "Cossio", "given": "Manuel", "initials": "M"}, {"family": "Lu", "given": "Junyan", "initials": "J", "orcid": "0000-0002-9211-0746", "researcher": {"href": "https://publications.scilifelab.se/researcher/08813991edd84a809d5a3e0e0bfaaa2e.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Young", "given": "Emma", "initials": "E"}, {"family": "Plevova", "given": "Karla", "initials": "K", "orcid": "0000-0002-6148-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a6c579cb91f4096a7f8a9143262ce9b.json"}}, {"family": "Knisbacher", "given": "Binyamin A", "initials": "BA"}, {"family": "Lin", "given": "Ziao", "initials": "Z"}, {"family": "Hahn", "given": "Cynthia K", "initials": "CK"}, {"family": "Bousquets", "given": "Pablo", "initials": "P", "orcid": "0000-0002-2969-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e3865ff15a94e8abfc95c039825adac.json"}}, {"family": "Alcoceba", "given": "Miguel", "initials": "M", "orcid": "0000-0002-3819-4846", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb06b84631cf4a259476737674499d1c.json"}}, {"family": "Gonz\u00e1lez", "given": "Marcos", "initials": "M"}, {"family": "Colado", "given": "Enrique", "initials": "E", "orcid": "0000-0001-8675-8207", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f9a05ff8f434fbe81d1227335f431ae.json"}}, {"family": "Payer", "given": "\u00c1ngel R", "initials": "\u00c1R"}, {"family": "Aymerich", "given": "Marta", "initials": "M"}, {"family": "Terol", "given": "Mar\u00eda J", "initials": "MJ"}, {"family": "Rivas-Delgado", "given": "Alfredo", "initials": "A"}, {"family": "Enjuanes", "given": "Anna", "initials": "A"}, {"family": "Ruiz-Gasp\u00e0", "given": "S\u00edlvia", "initials": "S"}, {"family": "Chatzikonstantinou", "given": "Thomas", "initials": "T", "orcid": "0000-0003-4105-1253", "researcher": {"href": "https://publications.scilifelab.se/researcher/428007841de74249a101c9cc5182cd5e.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Stranska", "given": "Kamila", "initials": "K", "orcid": "0000-0001-7678-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/130a65c3d64a4c57bbd619d7dc033b45.json"}}, {"family": "Doubek", "given": "Michael", "initials": "M", "orcid": "0000-0002-1269-6282", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b574229235d455890fd703d2c722a17.json"}}, {"family": "van Gastel-Mol", "given": "Ellen J", "initials": "EJ"}, {"family": "Davis", "given": "Zadie", "initials": "Z"}, {"family": "Walewska", "given": "Renata", "initials": "R"}, {"family": "Scarf\u00f2", "given": "Lydia", "initials": "L", "orcid": "0000-0002-0844-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/47c4c336efb24d86b41c872d03836c78.json"}}, {"family": "Trentin", "given": "Livio", "initials": "L", "orcid": "0000-0003-1222-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/005d6d4e9e294ab7a1d7448c9aae45da.json"}}, {"family": "Visentin", "given": "Andrea", "initials": "A", "orcid": "0000-0003-0271-7200", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f11f2e170b04d83a4d0f0ee3fbffdec.json"}}, {"family": "Parikh", "given": "Sameer A", "initials": "SA", "orcid": "0000-0002-3221-7314", "researcher": {"href": "https://publications.scilifelab.se/researcher/88e9511c65bb4c069a0fbeb9d1f46872.json"}}, {"family": "Rabe", "given": "Kari G", "initials": "KG", "orcid": "0000-0002-7313-1875", "researcher": {"href": "https://publications.scilifelab.se/researcher/107eb83790e54331b7069c5eda2e2303.json"}}, {"family": "Moia", "given": "Riccardo", "initials": "R", "orcid": "0000-0001-7393-1138", "researcher": {"href": "https://publications.scilifelab.se/researcher/68e9d84703624f578568c1a2775f3442.json"}}, {"family": "Armand", "given": "Marine", "initials": "M", "orcid": "0000-0001-8906-3128", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d2e8c325db8415cb723a9718d49ae78.json"}}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Gaidano", "given": "Gianluca", "initials": "G", "orcid": "0000-0002-4681-0151", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9af4cedf69e47a5a4ecf0da0ed88c8e.json"}}, {"family": "Kay", "given": "Neil E", "initials": "NE", "orcid": "0000-0002-5951-5055", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef074d0fdb0b4070b5216be063317bf8.json"}}, {"family": "Shanafelt", "given": "Tait D", "initials": "TD"}, {"family": "Ghia", "given": "Paolo", "initials": "P", "orcid": "0000-0003-3750-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f24783739d44c7b73a1be28c344a35.json"}}, {"family": "Oscier", "given": "David", "initials": "D"}, {"family": "Langerak", "given": "Anton W", "initials": "AW", "orcid": "0000-0002-2078-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/769a5b06013b43d6af8d3e13804cd50c.json"}}, {"family": "Be\u00e0", "given": "S\u00edlvia", "initials": "S", "orcid": "0000-0001-7192-2385", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c087ad28194469892e86a69bdd4bab.json"}}, {"family": "L\u00f3pez-Guillermo", "given": "Armando", "initials": "A"}, {"family": "Neuberg", "given": "Donna", "initials": "D", "orcid": "0000-0003-2566-3145", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2f9cbb622f040bebdfcb68657035be1.json"}}, {"family": "Wu", "given": "Catherine J", "initials": "CJ", "orcid": "0000-0002-3348-5054", "researcher": {"href": "https://publications.scilifelab.se/researcher/049091c641354ab2855757db72404195.json"}}, {"family": "Getz", "given": "Gad", "initials": "G", "orcid": "0000-0002-0936-0753", "researcher": {"href": "https://publications.scilifelab.se/researcher/974b292190aa40c4a3b0c1d7ab735376.json"}}, {"family": "Pospisilova", "given": "Sarka", "initials": "S", "orcid": "0000-0001-7136-2680", "researcher": {"href": "https://publications.scilifelab.se/researcher/241cf7f1344c4016b40dfcf439c0b43d.json"}}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}, {"family": "Huber", "given": "Wolfgang", "initials": "W"}, {"family": "Zenz", "given": "Thorsten", "initials": "T", "orcid": "0000-0001-7890-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6b107b1ec94de7bbc260f92f2dcc9f.json"}}, {"family": "Colomer", "given": "Dolors", "initials": "D", "orcid": "0000-0001-7486-8484", "researcher": {"href": "https://publications.scilifelab.se/researcher/0747c24c7c744799b7f0e73147dbbd05.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 I", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "Delgado", "given": "Julio", "initials": "J", "orcid": "0000-0002-5157-4376", "researcher": {"href": "https://publications.scilifelab.se/researcher/def9787862d247299e08c4cdbfb6a993.json"}}, {"family": "Morin", "given": "Ryan D", "initials": "RD", "orcid": "0000-0003-2932-7800", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1d13b9d68534df3a8a271742b55b240.json"}}, {"family": "Stein", "given": "Lincoln D", "initials": "LD"}, {"family": "Puente", "given": "Xose S", "initials": "XS", "orcid": "0000-0001-9525-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c757bd329184ea2a2aa9183802fefb1.json"}}, {"family": "Campo", "given": "El\u00edas", "initials": "E", "orcid": "0000-0001-9850-9793", "researcher": {"href": "https://publications.scilifelab.se/researcher/5642afaa4ed648dfabe66194e42bc01b.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "39", "issue": "9", "pages": "2076-2086", "issn-l": "0887-6924"}, "abstract": "Recurrent mutations in the third base of U1 spliceosomal RNA responsible for marked splicing and expression abnormalities have been described in chronic lymphocytic leukemia (CLL) and some solid tumors. However, the clinical significance of these mutations in large and independent CLL cohorts as well as their presence in other B-cell neoplasms is unknown. Here we characterized U1 mutations in 1670 CLL and 363 mature B-cell lymphomas. We confirmed that the g.3A>C U1 mutation is found in 3.5% of CLL, which conferred rapid disease progression independently of the main biological and clinical prognostic markers of the disease. Additionally, a recurrent g.9C>T mutation was found in 1.5% of CLL causing downstream splicing alterations and associated with adverse prognosis. We also identified a g.4C>T mutation in 10% of diffuse large B-cell lymphomas of the germinal center subtype and a g.7A>G mutation in 30% of EBV-negative Burkitt lymphomas, both of which altered the splicing pattern of multiple genes. This study reveals novel, recurrent, and tumor-specific U1 mutations in mature B-cell neoplasms with biological and prognostic implications, thus establishing U1 as a novel pan-B-cell malignancy driver gene.", "doi": "10.1038/s41375-025-02667-7", "pmid": "40588565", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380619"}, {"db": "pii", "key": "10.1038/s41375-025-02667-7"}], "notes": [], "created": "2025-09-08T07:17:22.103Z", "modified": "2025-09-08T07:17:23.018Z"}, {"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": "6091da69a89748ddb71ea83d5824cd31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6091da69a89748ddb71ea83d5824cd31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6091da69a89748ddb71ea83d5824cd31"}}, "title": "Whole genome transcriptional analysis of intestinal biopsies and blood cells indicate genes involved in antioxidant defense systems, amino acid metabolism and antigen presentation in the pathogenesis of celiac disease.", "authors": [{"family": "Torinsson Naluai", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-0504-6492", "researcher": {"href": "https://publications.scilifelab.se/researcher/bcf3474dc7054c598cbe3a195deb8a1b.json"}}, {"family": "Sabbag", "given": "Shafir", "initials": "S"}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Gudj\u00f3nsd\u00f3ttir", "given": "Audur H", "initials": "AH"}, {"family": "Arnell", "given": "Henrik", "initials": "H"}, {"family": "Agardh", "given": "Daniel", "initials": "D"}], "type": "journal article", "published": "2025-08-29", "journal": {"title": "BMC Med", "issn": "1741-7015", "volume": "23", "issue": "1", "pages": "507", "issn-l": "1741-7015"}, "abstract": "Celiac disease is associated with HLA-risk haplotypes, but non-HLA genes and environmental factors are also linked to disease susceptibility. In this study, we explore the molecular pathways involved in celiac disease by analyzing the differential expression of genes in both the gut and peripheral blood across various celiac disease phenotypes.\n\nWhole genome RNA sequencing was performed on 283 samples from intestinal mucosa and peripheral blood from 72 cases with either active, potential, or treated celiac disease and 73 disease controls. Enrichr pathway analysis of top differentially expressed genes was performed.\n\nOverall, 7565 genes in intestinal biopsies and 542 genes in blood samples were differentially expressed between cases and controls. Compared with controls, immunoglobulin heavy variable 5-51 (IGHV5-51) (p = 1.05 \u00d7 10-14) and tissue transglutaminase (TGM2) (p = 5.29 \u00d7 10-10), encoding for TG2, the main autoantigen in celiac disease, were two of the top up-regulated genes in intestinal biopsies from celiac cases. TGM2 was also slightly upregulated in blood cells from cases with active disease compared with controls (p = 0.05). The topmost differentially expressed genes in peripheral blood were HLA-DQB1, HLA-DQB2, and GSTM1. Among pathways identified containing transcriptionally differentiated genes were antioxidant defense systems (e.g., nuclear factor (erythroid-derived 2)-like 2 (Nrf2), glutathione, ergothioneine, and peroxisome metabolism), as well as MHC class 1 antigen presentation, amino acid transport, mTORC1, bilirubin and lipid metabolism, liver homeostasis, the complement system, and interferon signaling.\n\nDifferentially expressed genes in cases and controls indicate crosstalk between molecular pathways involved in antioxidant defense, immune regulation, and nutrient signaling in the pathogenesis of celiac disease.", "doi": "10.1186/s12916-025-04261-1", "pmid": "40883722", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12398127"}, {"db": "pii", "key": "10.1186/s12916-025-04261-1"}], "notes": [], "created": "2025-09-08T07:11:35.688Z", "modified": "2025-09-18T07:36:17.364Z"}, {"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": "a820631626024f32811c8031777bf540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540"}}, "title": "Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation.", "authors": [{"family": "Atienza P\u00e1rraga", "given": "Alba", "initials": "A"}, {"family": "Nylund", "given": "Patrick", "initials": "P", "orcid": "0000-0002-1274-4010", "researcher": {"href": "https://publications.scilifelab.se/researcher/683976ea3c094b198998dabb0d433f4b.json"}}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Garrido-Zabala", "given": "Berta", "initials": "B"}, {"family": "Tziola", "given": "Stefania Iliana", "initials": "SI"}, {"family": "Vasquez", "given": "Louella", "initials": "L", "orcid": "0000-0002-5758-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479eadb09d44ece8523730e1e0fd0b1.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69051a0275c442c8c0d5621b4000929.json"}}, {"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ma", "given": "Anqi", "initials": "A", "orcid": "0000-0002-9293-4753", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c70ee5b7bd4136a74d7605ec7b1614.json"}}, {"family": "Jin", "given": "Jian", "initials": "J", "orcid": "0000-0002-3774-1609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed488bfe2c024a6b874b3b964ce80b97.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "\u00d6berg", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3609-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/c68243c8cc754cdb8b380db120f3b771.json"}}, {"family": "De Bruyne", "given": "Elke", "initials": "E", "orcid": "0000-0003-4012-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2715df4e920432c9723d8fdf4ff897b.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Jernberg Wiklund", "given": "Helena", "initials": "H"}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df89c7522b7b4af3b3cef8555380fe8c.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "31568"}, "abstract": "Comprehensive epigenomic studies in multiple myeloma (MM) that unravel the connections between major epigenetic regulators, their intertwined collaboration and the potential of combinatorial targeting remain limited. Utilizing ChIP-seq, ATAC-seq, RNA-seq, and DNA methylation (DNAme) data, we generated whole-genome chromatin annotations from normal plasma cells and MM patients, revealing epigenomic re-configuration affecting downstream genes involved in tumour growth and survival. Primary MM samples showed global DNA hypomethylation but site-specific hypermethylation was observed at transcription start sites, promoters, and enhancers. Moreover, increased deposition of H3K27me3 was observed in clinically relevant functional chromatin clusters. Combined EZH2 and DNMTs inhibition resulted in extensive epigenomic alterations activating apoptosis and cell cycle genes, leading to increased G2/M arrest and apoptosis in MM cell lines. Our findings provide novel insights into the role of epigenetic gene silencing in MM tumorigenesis and the interplay between the Polycomb repressive complex 2 and DNAme.\r\n\r\nThe online version contains supplementary material available at 10.1038/s41598-025-17093-z.", "doi": "10.1038/s41598-025-17093-z", "pmid": "40866476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12391466"}, {"db": "pii", "key": "10.1038/s41598-025-17093-z"}], "notes": [], "created": "2025-09-08T07:11:30.283Z", "modified": "2025-10-06T12:40:33.288Z"}, {"entity": "publication", "iuid": "4ed7da9adac244919a18efaef8b67a03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03"}}, "title": "MALNC: a new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response.", "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": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications.scilifelab.se/researcher/b625a888935a42a89d7df3522e249413.json"}}, {"family": "Gamboa-Cede\u00f1o", "given": "Angelica Mar\u00eda", "initials": "AM"}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "My", "initials": "M", "orcid": "0000-0002-2325-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cc743cdb2604ffdbc78303d70985c48.json"}}, {"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Karlsson", "given": "Kasper", "initials": "K"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "M\u00e5nsson", "given": "Alma", "initials": "A", "orcid": "0009-0006-1982-7712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ccda3e6f49f43f5bcf5576d7acc16e5.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Christer", "initials": "C", "orcid": "0000-0003-0695-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f78180b33fa48cd86474d5c3cdaa852.json"}}, {"family": "Fiskesund", "given": "Roland", "initials": "R"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Kallioniemi", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "Cancer Gene Ther", "issn": "1476-5500", "issn-l": null}, "abstract": "As the non-coding genome remains poorly characterized in acute myeloid leukemia (AML), we aimed to identify and functionally characterize novel long non-coding RNAs (lncRNAs) relevant to AML biology and treatment. We first identified lncRNAs overexpressed in AML blasts and, among them, discovered a novel transcript, which we named myeloid and AML-associated intergenic long non-coding RNA (MALNC). MALNC is overexpressed in AML, particularly in cases with the PML-RARA fusion or IDH2R140/NPM1 co-mutations, and is associated with a distinct gene expression profile. Functional studies showed that MALNC knockout impairs AML cell proliferation and colony formation, enhances ATRA-induced differentiation, and sensitizes cells to arsenic trioxide. Transcriptomic analysis revealed that MALNC loss alters the expression of retinoic acid pathway genes, and chromatin binding studies showed that MALNC binds to genes related to the retinoic acid and Rho GTPase pathways. In conclusion, we have identified MALNC as a novel lncRNA that promotes leukemic cell proliferation, counteracts ATRA-induced differentiation, and modulates drug sensitivity in AML.", "doi": "10.1038/s41417-025-00954-0", "pmid": "40849353", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41417-025-00954-0"}], "notes": [], "created": "2025-09-08T07:03:20.085Z", "modified": "2025-11-14T11:06:29.062Z"}, {"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": "5736722e01b74b29baf8fe43d4ce6819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5736722e01b74b29baf8fe43d4ce6819"}}, "title": "RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters.", "authors": [{"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Alameddine", "given": "Asmaa", "initials": "A"}, {"family": "Sp\u00f6rndly-Nees", "given": "Ellinor", "initials": "E"}, {"family": "Montigny", "given": "Mathilde", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Jansson", "given": "Anna", "initials": "A"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2025-08-18", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "751", "issn-l": "1471-2164"}, "abstract": "Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we conducted a polyA-selected RNA-seq experiment on tissue from the growth zone at the coronary band of the hoof. This experiment compared tissues from Standardbred trotters capable of repeatedly racing barefoot without injury (n = 11) to those that could not (n = 7). By combining stringent phenotyping with racing records and trainer interviews, we aimed to elucidate the biological factors related to hoof strength in barefoot racing, focusing on differential abundant genes.\n\nThe RNA-seq analysis identified five significantly downregulated genes in horses capable of competing barefoot across consecutive races. These genes are associated with various biological processes relevant for hoof strength: ACCS, IRX2 and TRAPPAC6A contribute to enhancing the structural integrity of the hoof; MT2A regulates its metal homeostasis and SLC35F3 likely influences local vasoconstriction in the hoof. These gene findings suggest a coordinated genetic basis for structural reinforcement and physiological support of the hoof, which may be critical for sustaining performance under barefoot conditions.\n\nOur findings suggest that the ability of Standardbred trotters to race barefoot in consecutive events is reflected in distinct gene expression patterns, underscoring a genetic basis for hoof strength. This supports further genome-wide scans aimed at identifying genetic markers for hoof durability in these horses. The focused design of our study- comparing horses that could consistently race barefoot with those that could not- enabled us to isolate a select group of genes involved in diverse aspects of hoof biology essential for quality and resilience of horse hooves. This insight could ultimately be applied to augment both the performance and wellbeing of equine athletes across disciplines.", "doi": "10.1186/s12864-025-11814-4", "pmid": "40826322", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12363045"}, {"db": "pii", "key": "10.1186/s12864-025-11814-4"}], "notes": [], "created": "2025-09-08T07:04:42.067Z", "modified": "2025-09-09T13:14:43.091Z"}, {"entity": "publication", "iuid": "4cb1f3bbbd73476d85743dd1a3b24932", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4cb1f3bbbd73476d85743dd1a3b24932"}}, "title": "Early germline sequestration in a basidiomycete fungus.", "authors": [{"family": "Thor\u00e9n", "given": "Markus Hiltunen", "initials": "MH", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Olsson", "given": "Boel", "initials": "B", "orcid": "0009-0006-4157-2664", "researcher": {"href": "https://publications.scilifelab.se/researcher/219a75999b65464ca3d405ac20898743.json"}}, {"family": "Vonk", "given": "Peter Jan", "initials": "PJ", "orcid": "0000-0001-5325-7430", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5684212a1f5478cab0943d5064e74a7.json"}}, {"family": "Siljestam", "given": "Mattias", "initials": "M", "orcid": "0000-0002-3720-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/653d5e0ec2bc4925a19db2697ad61a2d.json"}}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J", "orcid": "0000-0003-1518-2014", "researcher": {"href": "https://publications.scilifelab.se/researcher/db7ebacfd8764a988ee41f2e5ab23e50.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2025-08-14", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "389", "issue": "6761", "pages": "720-723"}, "abstract": "In sexual organisms, inheritance of new mutations is highly dependent on the timing of germline definition. Here, we used the fairy ring-forming fungus Marasmius oreades to challenge the general assumption of a late germline separation in the Fungi. We collected mushrooms from different parts of rings over a 7-year period and identified new mutations in different tissues by whole-genome sequencing. We found evidence that fertile and sterile tissues had accumulated different mutations, suggesting that the germ line, destined for spore production, is already defined in the mycelium in this species. Moreover, the germ line carried fewer mutations than sterile tissues, indicating a lower mutation rate. Our findings suggest that early germline sequestration is more widespread than previously considered across multicellular life.", "doi": "10.1126/science.adu8580", "pmid": "40811541", "labels": {"Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-08-29T12:41:10.841Z", "modified": "2025-11-21T13:14:48.967Z"}, {"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": "741f4c91234245268da4ddfa1e0b9efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/741f4c91234245268da4ddfa1e0b9efa"}}, "title": "Lrig3-deficient mice exhibit strain-specific alterations in liver fat accumulation, intestinal morphology, and middle ear inflammation.", "authors": [{"family": "Herdenberg", "given": "Carl", "initials": "C"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0001-6891-6996", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b1b2d57a55e415aa17acbd0318a019e.json"}}, {"family": "Rondahl", "given": "Veronica", "initials": "V"}], "type": "journal article", "published": "2025-08-10", "journal": {"title": "Gene", "issn": "1879-0038", "issn-l": "0378-1119", "volume": "960", "issue": null, "pages": "149539"}, "abstract": "The transmembrane protein leucine-rich repeats and immunoglobulin-like domains 3 (LRIG3) regulates fat metabolism and bone morphogenetic protein (BMP) signaling. Lrig3-deficient mice exhibit impaired development of the snout and the inner ear lateral canal, neural defects, and cardiac hypertrophy in adulthood. However, no thorough and unbiased analysis of the physiological functions of Lrig3 has previously been performed. To address this knowledge gap, we performed histopathological examination of 42 tissues and organs from 1-year-old female C57BL/6JBomTac and 129S1-U mice with different Lrig3 genotypes. Among the scored pathologies, three were significantly associated with Lrig3 genotype: spontaneous macrovesicular hepatocellular degeneration (hepatocellular steatosis) was less prevalent in Lrig3-deficient C57BL/6JBomTac mice, whereas dilated or flaccid ileum and otitis media were more common in Lrig3-deficient 129S1-U mice. To further investigate hepatic steatosis phenotypes, 8-week-old C57BL/6JBomTac mice of both sexes and different Lrig3 genotypes were subjected to consuming a high-fat diet (HFD) for 8 weeks. The HFD regimen led to relatively few cases of hepatocellular steatosis, with no significant differences among the genotypes; however, female Lrig3-deficient mice presented reduced microvesicular hepatocellular degeneration compared with their wild-type littermates. This study revealed that Lrig3 regulates liver fat accumulation, intestinal morphology, and middle ear inflammation in a mouse strain-dependent manner.", "doi": "10.1016/j.gene.2025.149539", "pmid": "40320098", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S0378-1119(25)00327-0"}], "notes": [], "created": "2025-09-08T07:06:55.862Z", "modified": "2025-11-19T13:14:56.377Z"}, {"entity": "publication", "iuid": "ab9b4fd3312a411fa7600da6cc9fc651", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9b4fd3312a411fa7600da6cc9fc651"}}, "title": "Precise mapping of single-stranded DNA breaks by sequence-templated erroneous DNA polymerase end-labelling.", "authors": [{"family": "Wenson", "given": "Leonie", "initials": "L", "orcid": "0000-0002-1864-1258", "researcher": {"href": "https://publications.scilifelab.se/researcher/989e0534adbd426386cec5526c5e9668.json"}}, {"family": "Heldin", "given": "Johan", "initials": "J", "orcid": "0000-0002-0915-5303", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8a546798d014cd3a44537ae5db9f889.json"}}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Erbilgin", "given": "Y\u00fccel", "initials": "Y"}, {"family": "Salman", "given": "Bar\u0131\u015f", "initials": "B", "orcid": "0000-0002-7657-8576", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb919f7fcc794c8898fe800056d42f38.json"}}, {"family": "Sundqvist", "given": "Anders", "initials": "A"}, {"family": "Schaal", "given": "Wesley", "initials": "W", "orcid": "0000-0001-6770-0878", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab184845a24f4effb22ec2b338ab8960.json"}}, {"family": "Sandbaumh\u00fcter", "given": "Friederike A", "initials": "FA"}, {"family": "Jansson", "given": "Erik T", "initials": "ET"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}, {"family": "Davidsson", "given": "Anton", "initials": "A"}, {"family": "Stenerl\u00f6w", "given": "Bo", "initials": "B", "orcid": "0000-0001-8878-8071", "researcher": {"href": "https://publications.scilifelab.se/researcher/22437ff9315d43089232926973feb0d2.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael", "initials": "M", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Spjuth", "given": "Ola", "initials": "O", "orcid": "0000-0002-8083-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/605dbd52684d4e54ae4150a9933abe6e.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O", "orcid": "0000-0003-2883-1925", "researcher": {"href": "https://publications.scilifelab.se/researcher/68df823efa304c0b9962684ac1515808.json"}}], "type": "journal article", "published": "2025-08-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "16", "issue": "1", "pages": "7130"}, "abstract": "The ability to analyze whether DNA contains lesions is essential in identifying mutagenic substances. Currently, the detection of single-stranded DNA breaks (SSBs) lacks precision. To address this limitation, we develop a method for sequence-templated erroneous end-labelling sequencing (STEEL-seq), which enables the mapping of SSBs. The method requires a highly error-prone DNA polymerase, so we engineer a chimeric DNA polymerase, Sloppymerase, capable of replicating DNA in the absence of one nucleotide. Following the omission of a specific nucleotide (e.g., dATP) from the reaction mixture, Sloppymerase introduces mismatches directly downstream of SSBs at positions where deoxyadenosine should occur. This mismatch pattern, coupled with the retention of sequence information flanking these sites, ensures that the identified hits are bona fide SSBs. STEEL-seq is compatible with a variety of sequencing technologies, as demonstrated using Sanger, Illumina, PacBio, and Nanopore systems. Using STEEL-seq, we determine the SSB/base pair frequency in the human genome to range between 0.7 and 3.8 \u00d7 10-6 with an enrichment in active promoter regions.", "doi": "10.1038/s41467-025-62512-4", "pmid": "40759655", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12322144"}, {"db": "pii", "key": "10.1038/s41467-025-62512-4"}], "notes": [], "created": "2025-08-19T13:16:23.958Z", "modified": "2025-11-28T10:45:45.544Z"}, {"entity": "publication", "iuid": "06ca672ce48846a38877306910ec4cd1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/06ca672ce48846a38877306910ec4cd1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/06ca672ce48846a38877306910ec4cd1"}}, "title": "Small\u2010scale thermal habitat variability may not determine seagrass resilience to climate change", "authors": [{"family": "Hattich", "given": "Giannina S I", "initials": "GSI", "orcid": "0000-0003-4660-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/86fec49ce8324a27aa3da020810cd115.json"}}, {"family": "Jahnke", "given": "Marlene", "initials": "M", "orcid": "0000-0001-7262-315X", "researcher": {"href": "https://publications.scilifelab.se/researcher/88ddc399062a4cc792c36feb725f3ecd.json"}}, {"family": "Enge", "given": "Swantje", "initials": "S", "orcid": "0000-0003-4292-0051", "researcher": {"href": "https://publications.scilifelab.se/researcher/d92a4e95bf294c34855b27f30ba39dce.json"}}, {"family": "Niemi", "given": "Niklas", "initials": "N", "orcid": "0009-0008-8279-4049", "researcher": {"href": "https://publications.scilifelab.se/researcher/65c382595e5140b18c6ffa7b504f3434.json"}}, {"family": "Bernal\u2010G\u00f3mez", "given": "Maru", "initials": "M", "orcid": "0009-0006-0275-6620", "researcher": {"href": "https://publications.scilifelab.se/researcher/09f54c2d6291411c87843cf10056e32d.json"}}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Havenhand", "given": "Jonathan N", "initials": "JN", "orcid": "0000-0003-0253-3428", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d1c6ad9fb0a40418db6e99f127ea8ab.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "70", "issue": "8", "pages": "2039-2052", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.70049", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:11:32.834Z", "modified": "2025-11-14T11:05:36.890Z"}, {"entity": "publication", "iuid": "f94b305344964e2abd50b277f36990ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f94b305344964e2abd50b277f36990ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f94b305344964e2abd50b277f36990ad"}}, "title": "Mast Cell Phenotypic Heterogeneity Impacts the Interplay with Pathogenic Salmonella Typhimurium Bacteria.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Andersson", "given": "Julia H M", "initials": "JHM"}, {"family": "Pejler", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-6779-391X", "researcher": {"href": "https://publications.scilifelab.se/researcher/97b2d5f8dec04bc3b7631370d77a2236.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}], "type": "journal article", "published": "2025-08-00", "journal": {"title": "Eur. J. Immunol.", "issn": "1521-4141", "volume": "55", "issue": "8", "pages": "e70040", "issn-l": "0014-2980"}, "abstract": "Mast cells (MCs) lodge within barrier tissues and respond to infectious microbes. Recent work demonstrated that MCs differentiate their cytokine response to extracellular versus invasive Gram-negative enterobacteria by a two-step activation mechanism that integrates Toll-like-receptor (TLR) sensing with signals elicited by type-III-secretion-system (TTSS) effectors during bacterial invasion. However, multiple MC subtypes exist, and it remains unclear how their phenotypic heterogeneity impacts microbial interactions. We find that murine MCs maintained in IL-3, or differentiated toward a connective-tissue phenotype (CT-MCs), respond potently to the enteropathogen Salmonella enterica Typhimurium (S.Tm) through two-step activation, with the TLR component explained by functional TLR4 and TLR2. By contrast, murine mucosal mast cells (M-MCs) express insignificant levels of these TLRs, therefore being unresponsive to extracellular S.Tm, but still mounting a response to invasive bacteria. Following invasion, MC granule maintenance by serglycin restricts S.Tm vacuolar and cytosolic colonization. Notably, this has no impact on the cytokine release from infected MCs, thus uncoupling S.Tm\u00b4s intracellular life-cycle from the MC cytokine response. Finally, human LUVA MCs employ a variant of two-step activation where TLR2/6 signaling combines with the TTSS-elicited signals. Together, this study explains how MC subtypes can respond differently to S.Tm-infection depending on their TLR expression and granule features.", "doi": "10.1002/eji.70040", "pmid": "40838737", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12369454"}], "notes": [], "created": "2025-09-08T07:06:53.513Z", "modified": "2025-09-09T13:13:50.740Z"}, {"entity": "publication", "iuid": "3b9b5a866e2a4139b03c9bbe033fc083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b9b5a866e2a4139b03c9bbe033fc083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b9b5a866e2a4139b03c9bbe033fc083"}}, "title": "Landscape connectivity and genetic structure of animal populations in urban ponds", "authors": [{"family": "Yildirim", "given": "Yeserin", "initials": "Y"}, {"family": "Hyseni", "given": "Chaz", "initials": "C", "orcid": "0000-0003-2567-8013", "researcher": {"href": "https://publications.scilifelab.se/researcher/7327304d59cb41a7a97cdcba953f9cdc.json"}}, {"family": "Heino", "given": "Jani", "initials": "J"}, {"family": "Bini", "given": "Luis Mauricio", "initials": "LM", "orcid": "0000-0003-3398-9399", "researcher": {"href": "https://publications.scilifelab.se/researcher/490cfde8f1824571a07f21bf11ea61f0.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Johansson", "given": "Frank", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c14b327f44fd8a802acd9c3f1fb2.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "26", "issue": "4", "pages": "703-714", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-025-01697-z", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:17:17.339Z", "modified": "2025-09-09T13:13:41.822Z"}, {"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": "1d0370becf604d269d8bc287ea19cd6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d0370becf604d269d8bc287ea19cd6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d0370becf604d269d8bc287ea19cd6b"}}, "title": "Genetic diversity and structure among Acropora austera populations in Mozambique suggest low resilience potential of one of the world\u2019s most charismatic coral reefs", "authors": [{"family": "Duvane", "given": "Jossias Alberto", "initials": "JA", "orcid": "0009-0008-6595-3415", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23044e5482b4936bb376823b8dee593.json"}}, {"family": "Dupont", "given": "Sam", "initials": "S"}, {"family": "Sola", "given": "Erwan", "initials": "E"}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Coral Reefs", "issn": "0722-4028", "volume": "44", "issue": "4", "pages": "1185-1195", "issn-l": null}, "abstract": null, "doi": "10.1007/s00338-025-02679-w", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:17:08.995Z", "modified": "2025-09-08T07:17:09.074Z"}, {"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": "c0b630a30a1a46ce900790a05a054996", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0b630a30a1a46ce900790a05a054996"}}, "title": "Assessing Sperm Quality Parameters in Mass\u2010Spawning Norwegian Arctic Charr", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K", "orcid": "0000-0002-9852-1896", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ba96d1e78654b6992ef1c25035e93da.json"}}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Thomason", "given": "Benjamin", "initials": "B"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Aquaculture Fish &amp; Fisheries", "issn": "2693-8847", "volume": "5", "issue": "4", "issn-l": null}, "abstract": null, "doi": "10.1002/aff2.70111", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:02:14.701Z", "modified": "2025-09-09T13:12:28.648Z"}, {"entity": "publication", "iuid": "56d7b9a10ca7456c955235973fcb394e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56d7b9a10ca7456c955235973fcb394e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56d7b9a10ca7456c955235973fcb394e"}}, "title": "An east\u2013west distribution of genetic diversity in Nordic populations of caraway (Carum carvi L.) and its consequences for conservation prioritisation", "authors": [{"family": "de Haro Reyes", "given": "Bernardo", "initials": "B", "orcid": "0000-0003-0871-094X", "researcher": {"href": "https://publications.scilifelab.se/researcher/bebf9f96b8ae43d38df1dc8a4f3ac389.json"}}, {"family": "Palm\u00e9", "given": "Anna", "initials": "A", "orcid": "0000-0002-8012-8359", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa8ff1168d27459e9b02b7c59afa94f0.json"}}, {"family": "Fitzgerald", "given": "Heli", "initials": "H", "orcid": "0000-0002-6754-6409", "researcher": {"href": "https://publications.scilifelab.se/researcher/79bdf20a416b49509431dd29201d28f2.json"}}, {"family": "G\u00f6ransson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-0081-2207", "researcher": {"href": "https://publications.scilifelab.se/researcher/13cca49312994a8fa45dc1fb7db8a42f.json"}}, {"family": "Lyytik\u00e4inen", "given": "Virva", "initials": "V", "orcid": "0009-0006-0207-9789", "researcher": {"href": "https://publications.scilifelab.se/researcher/315e8b253f184ca081297937e28c5225.json"}}, {"family": "Madsen", "given": "Bjarke", "initials": "B", "orcid": "0000-0002-4490-8710", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8a2e6641fec437f8624b6125d907bdd.json"}}, {"family": "Normand", "given": "Signe", "initials": "S", "orcid": "0000-0002-8782-4154", "researcher": {"href": "https://publications.scilifelab.se/researcher/c676988310824f518a646427dfed6600.json"}}, {"family": "Thorbj\u00f6rnsson", "given": "Hj\u00f6rtur", "initials": "H", "orcid": "0000-0003-1768-3699", "researcher": {"href": "https://publications.scilifelab.se/researcher/98e074fa60a24b3aa9ffcb54c238db8f.json"}}, {"family": "Treier", "given": "Urs Albert", "initials": "UA", "orcid": "0000-0003-4027-739X", "researcher": {"href": "https://publications.scilifelab.se/researcher/985ba0c9228a43f1a1132383266b7579.json"}}, {"family": "Hagenblad", "given": "Jenny", "initials": "J", "orcid": "0000-0002-9850-5546", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d1a751682448a3b6485cb67c6474f0.json"}}], "type": "journal-article", "published": "2025-08-00", "journal": {"title": "Conserv Genet", "issn": "1566-0621", "volume": "26", "issue": "4", "pages": "771-785", "issn-l": null}, "abstract": null, "doi": "10.1007/s10592-025-01702-5", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:30:05.435Z", "modified": "2025-11-14T11:05:47.156Z"}, {"entity": "publication", "iuid": "94bc601b34d44e4c92d9c87e8a71600f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94bc601b34d44e4c92d9c87e8a71600f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94bc601b34d44e4c92d9c87e8a71600f"}}, "title": "Sex-Biased Gene Expression Under Sexually Antagonistic and Sex-Limited Selection.", "authors": [{"family": "Wiberg", "given": "R Axel W", "initials": "RAW", "orcid": "0000-0002-8074-8670", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e9fd2f8f36a4be4a40b87ce2b65133c.json"}}, {"family": "Zwoinska", "given": "Martyna K", "initials": "MK", "orcid": "0000-0003-3356-7284", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8ceb1ef19c4089bf685928da01b9e8.json"}}, {"family": "Kaufmann", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7164-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/4214ade17fff4c30a690c13c43623ee7.json"}}, {"family": "Howie", "given": "James M", "initials": "JM", "orcid": "0000-0001-7142-5100", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1e0979df2194651916b36b39b11064f.json"}}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}], "type": "journal article", "published": "2025-07-30", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "42", "issue": "8", "issn-l": "0737-4038"}, "abstract": "Sex differences in gene expression are ubiquitous, evolve quickly, and are expected to underlie phenotypic sexual dimorphism (SD). Despite long-standing interest, the impact of sex-specific selection on the transcriptome remains poorly understood. Here, we test fundamental questions on the role of constraints on gene expression evolution arising from the mode of selection and genetic architecture. We also test the relationship between sex-biased expression and evolved SD. We assess these using body size selection lines in the seed beetle, Callosobruchus maculatus, that have evolved variation in SD in response to either sex-limited (SL) or sexually antagonistic (SA). We find that sex differences in the phenotypic responses and expression changes are generally well aligned. SL selection, despite a phenotypic response similar to SA selection in males, but not in females, resulted in a more extensive expression differentiation and increase of sex-biased expression than SA selection. These patterns show that SA selection imposes a transcriptomic constraint and is not required for sex-bias to evolve. Sex-biased transcripts show lower cross-sex correlations in expression changes than unbiased transcripts, suggesting greater sex differences in their underlying genetic architecture. Although male-biased transcripts are disproportionately affected when selection targeted males, we find no support for a transcriptome-wide association between sex-bias and SD. In the light of these unique experimental insights into how sex-specific selection on size changes adult transcription, our findings have important implications for inferring selection history and mode from patterns of sex-biased gene expression in natural populations.", "doi": "10.1093/molbev/msaf178", "pmid": "40729508", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12371189"}, {"db": "pii", "key": "8217438"}], "notes": [], "created": "2025-11-07T07:27:03.269Z", "modified": "2025-11-28T10:50:04.075Z"}, {"entity": "publication", "iuid": "3f3eeca95ed34ac385bdad9bbf4f1a2f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f3eeca95ed34ac385bdad9bbf4f1a2f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f3eeca95ed34ac385bdad9bbf4f1a2f"}}, "title": "Predicting immune responsiveness in ER-positive breast cancer for personalized therapy: a population-based study.", "authors": [{"family": "Stenmark Tullberg", "given": "Axel", "initials": "A"}, {"family": "Woxlin", "given": "Sara", "initials": "S"}, {"family": "Sj\u00f6lin", "given": "Filippa", "initials": "F"}, {"family": "Ittner", "given": "Ella", "initials": "E"}, {"family": "Kov\u00e0cs", "given": "Anik\u00f2", "initials": "A"}, {"family": "Helou", "given": "Khalil", "initials": "K"}, {"family": "Holmberg", "given": "Erik", "initials": "E"}, {"family": "Karlsson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2025-07-23", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "9", "issue": "1", "pages": "250", "issn-l": null}, "abstract": "The immune system's role in estrogen receptor (ER)-positive breast cancer is poorly understood. A population-based cohort of 428 breast cancer patients with clinical and molecular data was analyzed to assess how immune biomarkers can inform treatment decisions. Tumor-intrinsic immune responsiveness and local immune infiltration were quantified, and epithelial cell states were derived using EcoTyper. The interaction between ProliferativeIndex and Immunescore predicted risk of local recurrence in ER-positive tumors (HR 0.56, 95% CI 0.36-0.88, p = 0.012). EcoTyper identified two epithelial cell states, S04 and S05, with distinct immunomodulatory properties. S04 tumors showed higher proliferation, enrichment for M1 macrophages, CD8 effector T-cells, and plasma cells, alongside hypomethylation of immune-related pathways and hypermethylation of the PI3K signaling pathway. In contrast, S05-enriched tumors were associated with fibroblast activation, immune exclusion, and enrichment for glycosylation-related pathways. These findings suggest that epithelial cell states shape immune responsiveness in ER-positive breast cancer and may inform biomarker-driven treatment strategies.", "doi": "10.1038/s41698-025-01035-z", "pmid": "40702082", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12287262"}, {"db": "pii", "key": "10.1038/s41698-025-01035-z"}], "notes": [], "created": "2025-09-08T07:07:03.551Z", "modified": "2025-09-08T07:07:03.584Z"}, {"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": "ec61d27d2c1246fd953c84e68a7f1129", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec61d27d2c1246fd953c84e68a7f1129.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec61d27d2c1246fd953c84e68a7f1129"}}, "title": "Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations.", "authors": [{"family": "Varg", "given": "Javier Edo", "initials": "JE", "orcid": "0000-0002-7895-4563", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cb1019516e49f7b8f39b18924babc2.json"}}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC", "orcid": "0000-0001-7068-2017", "researcher": {"href": "https://publications.scilifelab.se/researcher/eeb2930d582f4483afc1f5bd52e37818.json"}}, {"family": "Benha\u00efm", "given": "David", "initials": "D"}, {"family": "Losada-Germain", "given": "Rafael", "initials": "R"}, {"family": "Boughman", "given": "Janette W", "initials": "JW"}], "type": "journal article", "published": "2025-07-19", "journal": {"title": "NPJ Biofilms Microbiomes", "issn": "2055-5008", "volume": "11", "issue": "1", "pages": "138", "issn-l": "2055-5008"}, "abstract": "The impact of microbial composition on stress-related behavior in aquatic organisms is poorly understood. This study explored the link between antipredator behavior, parasitism, and the gut microbiome in wild stickleback from two lakes: clear, spring-fed Galtab\u00f3l and turbid, glacial-fed \u00deristikla. Behavioral analysis revealed differences between populations, with each exhibiting unique baseline behaviors. Microbiome analysis showed that a small proportion of its variation was explained by population, likely reflecting differences in lake environments. Only the marine genus Pseudoalteromonas abundance differed between populations. Our findings suggest that behavior and microbiome correlations may primarily reflect environmental adaptations and parasite status rather than direct gut-brain interactions. However, some tentative evidence suggests a potential innate connection between some antipredator behavior and microbiome composition. The study highlights the complexity of the gut-brain axis in wild populations and suggests future research directions, including experimental manipulations to uncover causal relationships between microbiome composition and behavior.", "doi": "10.1038/s41522-025-00758-y", "pmid": "40683872", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12276351"}, {"db": "pii", "key": "10.1038/s41522-025-00758-y"}], "notes": [], "created": "2025-09-08T11:37:13.990Z", "modified": "2025-09-09T13:13:05.326Z"}, {"entity": "publication", "iuid": "3a670a7d749a49c1bc72990a94337d2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a670a7d749a49c1bc72990a94337d2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a670a7d749a49c1bc72990a94337d2a"}}, "title": "Sequencing airborne DNA to monitor crop pathogens and pests.", "authors": [{"family": "Mikko", "given": "Amanda", "initials": "A"}, {"family": "Villegas", "given": "Jose Antonio", "initials": "JA"}, {"family": "Svensson", "given": "Daniel", "initials": "D"}, {"family": "Karlsson", "given": "Edvin", "initials": "E"}, {"family": "Esseen", "given": "Per-Anders", "initials": "PA"}, {"family": "Albrectsen", "given": "Benedicte Riber", "initials": "BR"}, {"family": "Lundin", "given": "Ola", "initials": "O"}, {"family": "Forsman", "given": "Mats", "initials": "M"}, {"family": "Berlin", "given": "Anna", "initials": "A"}, {"family": "Stenberg", "given": "Per", "initials": "P", "orcid": "0000-0003-4738-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e9b9949cf994f6c93d60261eb530d1b.json"}}], "type": "journal article", "published": "2025-07-18", "journal": {"title": "iScience", "issn": "2589-0042", "pages": "112912", "volume": "28", "issue": "7", "issn-l": "2589-0042"}, "abstract": "Crop pests and diseases increasingly challenge the global food system. To prepare for and detect outbreaks, surveillance plays an important role. Traditional monitoring methods are often organism-specific, making large-scale monitoring of crop pathogens and pests impractical. We here investigate the potential for using shotgun sequencing of airborne eDNA for large-scale surveillance of crop pathogens and pests. We show that it is possible to detect DNA from all types of organisms in air, and that DNA can be classified down to species level. However, the accuracy of the identification is highly dependent on the quality of reference genomes of both the pathogens or pests, and their close relatives present in the region. Finally, we find that observed degree of crop damages correlate with amount of DNA from crop pathogens and pests in air, showing the promise of this approach for surveillance of all types of crop pathogens and pests.", "doi": "10.1016/j.isci.2025.112912", "pmid": "40678541", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12269458"}, {"db": "pii", "key": "S2589-0042(25)01173-3"}], "notes": [], "created": "2025-06-30T07:24:39.046Z", "modified": "2025-11-14T11:06:13.683Z"}, {"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": "d936680b828c47f8a2753c7de07ce0de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de"}}, "title": "DNA Methylation Reflects Cis-Genetic Differentiation Across the European Crow Hybrid Zone.", "authors": [{"family": "Merondun", "given": "Justin", "initials": "J", "orcid": "0000-0001-5077-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/38e6336366e1418685f36244f39ecde6.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e70026"}, "abstract": "Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation during speciation in crows, we leveraged genome and methylome sequencing data from an incipient avian species: all-black carrion crows, grey-coated hooded crows, and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone, we show that 5mC methylation variation was largely explained by genome properties and the ontogenetic programme of the organism. Taxonomically related methylation divergence clustered in intergenic space, with the only genomic region of strongly elevated genetic differentiation encoding the diagnostic colour contrast between taxa. We conclude that methylation variation with relevance to speciation largely follows cis-genetic polymorphism in this system and does not constitute an autonomous axis of evolution.", "doi": "10.1111/mec.70026", "pmid": "40637207", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:59:29.504Z", "modified": "2025-11-03T08:42:37.319Z"}, {"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": "0711daac3c544b8fb60416da8e9cb152", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0711daac3c544b8fb60416da8e9cb152.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0711daac3c544b8fb60416da8e9cb152"}}, "title": "Bladder cancer subtypes exhibit limited plasticity across different microenvironments and in metastases.", "authors": [{"family": "Bernardo", "given": "Carina", "initials": "C"}, {"family": "Chattopadhyay", "given": "Subhayan", "initials": "S"}, {"family": "Andersson", "given": "Natalie", "initials": "N"}, {"family": "Eriksson", "given": "Pontus", "initials": "P"}, {"family": "Medle", "given": "Benjamin", "initials": "B"}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Dain Marzouka", "given": "Nour Al", "initials": "NA"}, {"family": "Mattsson", "given": "Adam", "initials": "A"}, {"family": "Zadoroznyj", "given": "Aymeric", "initials": "A"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Liedberg", "given": "Fredrik", "initials": "F"}, {"family": "H\u00f6glund", "given": "Mattias", "initials": "M"}, {"family": "Sj\u00f6dahl", "given": "Gottfrid", "initials": "G"}], "type": "journal article", "published": "2025-07-02", "journal": {"title": "Exp Hematol Oncol", "issn": "2162-3619", "volume": "14", "issue": "1", "pages": "91", "issn-l": null}, "abstract": "Transcriptomic and genomic analyses of bladder cancer (BC) reveal a highly diverse disease stratified into molecular subtypes with distinct molecular features and biological behaviors. Intratumor heterogeneity (ITH) and plasticity can significantly impact diagnosis and patient management, yet their extent in BC remains highly debated. Here, we investigated whether the three main bladder cancer subtypes maintain or alter their identity in response to changes in the microenvironment and during metastatic colonization.\n\nSeven patient-derived xenograft (PDX) models representing the major BC subtypes were propagated into three distinct tissue microenvironments: subcutaneous, mammary fat pad and under the kidney capsule. Metastatic lesions were generated via systemic injection of tumor cells. Tumor samples were analysed using RNA- and exome sequencing, SNP-arrays and histopathology to assess subtype fidelity, genomic evolution, and clonal dynamics.\n\nA comprehensive, longitudinal multiomics analysis showed that tumors consistently maintain their molecular subtype, as well as their transcriptomic and genomic profiles, across different environments. No evidence of emerging ITH or subtype transitions was observed, regardless of the microenvironment. The transcriptomic adaptations observed in metastases and different implantation sites are limited and are associated primarily with hypoxia, epithelial-mesenchymal transition (EMT), and invasion.\n\nOur results suggest that invasive bladder cancers have a strong intrinsic tumor identity that is not easily reprogrammed by the microenvironment.", "doi": "10.1186/s40164-025-00682-z", "pmid": "40605119", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12225047"}, {"db": "pii", "key": "10.1186/s40164-025-00682-z"}], "notes": [], "created": "2025-08-22T08:26:48.445Z", "modified": "2025-11-12T06:56:23.529Z"}, {"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": "e0d1dc8451a44076825e43da0bc8506c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0d1dc8451a44076825e43da0bc8506c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0d1dc8451a44076825e43da0bc8506c"}}, "title": "Ex vivo drug responses and molecular profiles of 597 pediatric acute lymphoblastic leukemia patients.", "authors": [{"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Krali", "given": "Olga", "initials": "O"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Frost", "given": "Britt-Marie", "initials": "BM"}, {"family": "Ryh\u00e4nen", "given": "Samppa", "initials": "S"}, {"family": "Fl\u00e6gstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G", "initials": "\u00d3G"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Nygren", "given": "Peter", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "Hemasphere", "issn": "2572-9241", "volume": "9", "issue": "7", "pages": "e70176", "issn-l": null}, "abstract": "Ex vivo drug response profiling is emerging as a valuable tool for identifying drug resistance mechanisms and advancing precision medicine in hematological cancers. However, the functional impact of dysregulation of the epigenome and transcriptome in this context remains poorly understood. In this study, we combined ex vivo drug sensitivity profiling with transcriptomic and epigenomic analyses in diagnostic samples from 597 pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Ex vivo resistance to antimetabolites (e.g., cytarabine, thioguanine), glucocorticoids (e.g., dexamethasone, prednisolone), and doxorubicin was independently associated with reduced relapse-free survival (P < 0.05). Molecular profiling identified pretreatment DNA methylation and gene expression patterns distinguishing resistant from sensitive cases, revealing key drug resistance signatures. These included aberrant expression of genes related to heme metabolism (e.g., ATPV06A) and KRAS signaling (e.g., GS02). Notably, we also observed atypical expression of genes usually restricted to T cells and other immune cells (e.g., ITK) in resistant BCP-ALL cells. Our findings demonstrate that ex vivo drug response patterns are predictive of clinical outcomes and reflect intrinsic molecular states associated with drug tolerance. This integrative multi-omics approach highlights potential therapeutic targets and underscores the value of functional precision medicine in identifying treatment vulnerabilities in pediatric ALL.", "doi": "10.1002/hem3.70176", "pmid": "40727946", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12301861"}, {"db": "pii", "key": "HEM370176"}], "notes": [], "created": "2025-09-08T07:17:19.785Z", "modified": "2025-11-28T10:40:21.057Z"}, {"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": "5993e1e4e51044008a8a228e19ce6f0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5993e1e4e51044008a8a228e19ce6f0b"}}, "title": "Deep plasma proteomics identifies and validates an eight-protein biomarker panel that separate benign from malignant tumors in ovarian cancer.", "authors": [{"family": "Moskov", "given": "Mikaela", "initials": "M"}, {"family": "Hedlund Lindberg", "given": "Julia", "initials": "J"}, {"family": "Lycke", "given": "Maria", "initials": "M"}, {"family": "Ivansson", "given": "Emma", "initials": "E", "orcid": "0000-0002-4630-1576", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d2acd6a50fe49178f424c55df0a6b51.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Sundfeldt", "given": "Karin", "initials": "K"}, {"family": "St\u00e5lberg", "given": "Karin", "initials": "K", "orcid": "0000-0001-5527-8796", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a9c8e243994dccb4730266b0431d6d.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}], "type": "journal article", "published": "2025-06-12", "journal": {"title": "Commun Med (Lond)", "issn": "2730-664X", "volume": "5", "issue": "1", "pages": "230", "issn-l": null}, "abstract": "Ovarian cancer has the highest mortality of all gynecological cancers and surgery is commonly used as final diagnostic. Available literature indicates that women with benign tumors could often be conservatively managed, but accurate molecular tests are needed for triaging when gold-standard imaging techniques are inconclusive or lacking.\n\nHere, we analyzed 5416 plasma proteins in two independent cohorts (N1 = 171, N2 = 233) with women surgically diagnosed with benign or malignant tumors. Using one cohort as discovery, we compared protein levels of benign tumors with early stage (I-II), late stage (III-IV) or any stage (I-IV) ovarian cancer and trained risk-score reporting multivariate models including a fixed cut-off for malignancy. Associations and model performance was then evaluated in the replication cohort.\n\nWe identify 327 biomarker associations, corresponding to 191 unique proteins, and replicate 326 (99.7%). By comparing the 191 proteins with their corresponding tumor gene expression we find that only 11% (21/191) have significant correlation. Through analyzes of protein-protein correlation networks, we find that 62 of the 191 proteins have high correlation with at least one other protein, suggesting that many of the associations are secondary effects. In the replication cohort, our model has areas under the curve (AUC = 0.96) corresponding to 97% sensitivity at 68% specificity. For early-stage tumors, we estimate the sensitivity to 91% at a specificity of 68% as compared to 85% and 54% for CA-125 alone.\n\nOur results indicates that up to one third of benign cases can be identified by molecular measures thereby reducing the need for diagnostic surgery.", "doi": "10.1038/s43856-025-00945-0", "pmid": "40506476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12162877"}, {"db": "pii", "key": "10.1038/s43856-025-00945-0"}], "notes": [], "created": "2025-09-08T07:17:14.990Z", "modified": "2025-11-14T11:07:27.366Z"}, {"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": "43c900f054f54ac892c881ee00972405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43c900f054f54ac892c881ee00972405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43c900f054f54ac892c881ee00972405"}}, "title": "Genomic insights into antimicrobial resistance and virulence of E. coli in central Ethiopia: a one health approach.", "authors": [{"family": "Chekole", "given": "Wagaw Sendeku", "initials": "WS"}, {"family": "Potgieter", "given": "Lizel", "initials": "L"}, {"family": "Adamu", "given": "Haileeyesus", "initials": "H"}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S"}, {"family": "Tessema", "given": "Tesfaye Sisay", "initials": "TS"}, {"family": "Magnusson", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2025-06-10", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "16", "pages": "1597580", "issn-l": "1664-302X"}, "abstract": "Antimicrobial resistance is a global threat causing millions of deaths annually. The study aimed to identify antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence genes (VGs) and track their dissemination among E. coli isolates. Seventy-seven isolates from calves, environments, and human sources were studied. The study involved WGS sequencing, bacterial strains characterized; pan genome, multi-locus sequence typing, and serotyping using O-, and H-typing. The ARGs, VGs, and MGEs were identified using ABRicate against selected respective databases. A maximum likelihood SNP (single nucleotide polymorphism) tree was constructed and visualized with an interactive tree of life (IToL). Descriptive statistics were used to analyze the data. Seventy-seven of the isolates were identified as E. coli, later grouped into 5 clades and four known phylogroups. ST10 and O16:H48 were most prevalent in 12 and 42 isolates, respectively. There were about 106 unique ARGs detected between 1.3% and 91.9%, with 57 detected in 40% of isolates. In terms of ARGs, the most common were bla-ampH (90.9%), bla-AmpC1 (89.6%), tet(A) (84.4%), mdf(A) (81.8%), aph(3\")-Ib (79%), sul2 (79%), aph(6)-Id (75%), and bla-PBP (70%). It was found that 95 percent (96/106) of ARGs came from at least two sources. The majority of detected ARGs exhibited high concordance between phenotypic resistance and ARGs profiles (JSI \u2265 0.5). In eight isolates, mutations in the gyrA (3) and par-C/E (5) genes led to ciprofloxacin and nalidixic acid resistance. The most common co-occurrences of ARG and MGE were Tn3 with bla-TEM-105 (34), Int1 with sul1 (13), and dhfr7 (11). Meanwhile, the most frequently detected VGs (n \u2265 71 isolates) included elfA-G, fimB-I, hcpA-C, espL, ibeC, entA, fepA-C, ompA, ecpA-E, fepD, fes, and ibeB. Nearly, 88.3% (128/1450) VGs were shared in isolates from at least two sources. ETEC (53.2%), EAEC (22.1%), and STEC (14.3%) were the three most frequently predicted pathotypes. Despite significant ST diversity, ARGs and VGs showed an extensive distribution among the study groups. These findings suggest limited clonal transmission of isolates. In comparison, the wide distribution of ARGs and VGs may be attributed to horizontal gene transfer driven by similar antibiotic selection pressures in the study area.", "doi": "10.3389/fmicb.2025.1597580", "pmid": "40556891", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12185407"}], "notes": [], "created": "2025-09-08T07:13:07.348Z", "modified": "2025-09-08T07:13:07.354Z"}, {"entity": "publication", "iuid": "cbd3115766d1403b90d47770ed1ebec6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbd3115766d1403b90d47770ed1ebec6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbd3115766d1403b90d47770ed1ebec6"}}, "title": "Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.", "authors": [{"family": "Bergholm", "given": "Julia", "initials": "J"}, {"family": "Tessema", "given": "Tesfaye Sisay", "initials": "TS"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2025-06-07", "journal": {"title": "Virol J", "issn": "1743-422X", "volume": "22", "issue": "1", "pages": "188", "issn-l": "1743-422X"}, "abstract": "Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.\n\nFecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.\n\nThe metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.\n\nTo our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.", "doi": "10.1186/s12985-025-02821-8", "pmid": "40483486", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12145588"}, {"db": "pii", "key": "10.1186/s12985-025-02821-8"}, {"db": "BioProject", "key": "PRJNA1224038"}, {"db": "SRA", "key": "PRJNA1224038"}, {"db": "GENBANK", "key": "PV076094-PV076105."}, {"db": "GENBANK", "key": "PV053516"}, {"db": "GENBANK", "key": "PV061389-PV061398"}], "notes": [], "created": "2025-06-09T05:48:13.273Z", "modified": "2025-11-14T11:08:51.197Z"}, {"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": "aeb9fc21fabb4b8f8b5a91ef25b0c7a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aeb9fc21fabb4b8f8b5a91ef25b0c7a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aeb9fc21fabb4b8f8b5a91ef25b0c7a8"}}, "title": "Antimicrobial resistance and serotype distribution of Salmonella spp. isolated from fresh foods in Cambodia.", "authors": [{"family": "Huoy", "given": "Laingshun", "initials": "L", "orcid": "0000-0002-0194-4754", "researcher": {"href": "https://publications.scilifelab.se/researcher/6683581dbb2448008f33711ca1ada131.json"}}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L", "orcid": "0000-0003-0282-1227", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9465e8d872740a083579657d96bb431.json"}}, {"family": "Phan", "given": "Kongkea", "initials": "K", "orcid": "0000-0003-2965-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/0826a7f731ac490b84b1e6823b9cedb5.json"}}, {"family": "Tieng", "given": "Siteng", "initials": "S", "orcid": "0000-0002-9037-6671", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd94295461f642cca1a44b46e4b923a2.json"}}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S", "orcid": "0000-0001-7907-8377", "researcher": {"href": "https://publications.scilifelab.se/researcher/41bff7b199434422b316875f399f5ebe.json"}}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Boqvist", "given": "Sofia", "initials": "S", "orcid": "0000-0002-8072-7132", "researcher": {"href": "https://publications.scilifelab.se/researcher/04e91c7a79164ce88c1a2aeaed836ca7.json"}}], "type": "journal article", "published": "2025-06-02", "journal": {"title": "J Appl Microbiol", "issn": "1365-2672", "volume": "136", "issue": "6", "issn-l": "1364-5072"}, "abstract": "To determine the Salmonella serotype distribution, antimicrobial resistance profiles, and antimicrobial resistance genes (ARGs) in food samples obtained from local markets in a low-income urban setting and nearby farms in Cambodia.\n\nOne hundred and thirty-nine Salmonella isolates from various food sources were tested for antibiotic susceptibility using a panel of 12 antibiotics, and 81 selected Salmonella isolates were further sequenced for serotype distribution and ARG identification. The results showed that 71% (99/139) of the isolates exhibited resistance to at least one antibiotic, with 39% (39/99) classified as multidrug-resistant (MDR). The highest resistance was observed against azithromycin (37%), followed by oxytetracycline (35%). A total of 32 serotypes were identified, with the six most common being S. Corvallis (7%), S. Haifa (6%), S. Weltevreden (6%), S. Agona (5%), S. Kentucky (5%), and S. Livingstone (5%). A broad range of ARGs was observed across multiple antibiotic classes, including macrolides, aminoglycosides, tetracyclines, phenicols, fluoroquinolones, sulfonamide-trimethoprim, beta-lactams, and MDR genes.\n\nThe results highlight the potential role of fresh food products in the widespread dissemination of Salmonella strains resistant to multiple antibiotics.", "doi": "10.1093/jambio/lxaf137", "pmid": "40459912", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "8155881"}], "notes": [], "created": "2025-06-04T12:59:02.555Z", "modified": "2025-09-08T06:59:27.016Z"}, {"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": "19d4f0ca29364061b137e9116162d5d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19d4f0ca29364061b137e9116162d5d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19d4f0ca29364061b137e9116162d5d2"}}, "title": "Genetically Determined Inflammation-Related Proteins in Asthma and Type-2 Signatures.", "authors": [{"family": "Hernandez-Pacheco", "given": "Natalia", "initials": "N", "orcid": "0000-0002-6313-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/833e75515e024830b827806684d61126.json"}}, {"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": "Kere", "given": "Maura", "initials": "M", "orcid": "0000-0002-5725-2773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d213ed52d084d79a7a87e09a3688d01.json"}}, {"family": "Kumar", "given": "Ashish", "initials": "A", "orcid": "0000-0002-7075-5930", "researcher": {"href": "https://publications.scilifelab.se/researcher/de86e6bb6d154c2db787a769da96323b.json"}}, {"family": "Klevebro", "given": "Susanna", "initials": "S", "orcid": "0000-0002-1261-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cace10c20c847f6a04259937e74891e.json"}}, {"family": "Mogensen", "given": "Ida", "initials": "I", "orcid": "0000-0002-0198-2718", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e3b914932c4470ba02ff73278972c8.json"}}, {"family": "Ekstr\u00f6m", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2060-8190", "researcher": {"href": "https://publications.scilifelab.se/researcher/d813a2fda4fc410cb5db71c62af9d0ea.json"}}, {"family": "Janson", "given": "Christer", "initials": "C", "orcid": "0000-0001-5093-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/bae457d633714159a73704f9ebe7bfa6.json"}}, {"family": "Palmberg", "given": "Lena", "initials": "L", "orcid": "0000-0001-5650-4484", "researcher": {"href": "https://publications.scilifelab.se/researcher/c77734a210e146dbaadc33363eaaaa6f.json"}}, {"family": "van Hage", "given": "Marianne", "initials": "M", "orcid": "0000-0003-3091-1596", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e9a55cd378c46d5a1fc6b4694423849.json"}}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A", "orcid": "0000-0003-2608-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70c845d32264b448e0b4631b826be6d.json"}}, {"family": "Merritt", "given": "Anne-Sophie", "initials": "AS", "orcid": "0000-0002-4497-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a96b69dc76435a83ea3dc089a5b657.json"}}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-9701-1130", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d97eee1803d4ce3a85c1fcb423c75d9.json"}}, {"family": "Bergstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0002-7981-6314", "researcher": {"href": "https://publications.scilifelab.se/researcher/70d058e4d5bc49d7a3c958950c9d4e6d.json"}}, {"family": "Kull", "given": "Inger", "initials": "I", "orcid": "0000-0001-6096-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f248045358c4711b1d10d7b9fe9649c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Mel\u00e9n", "given": "Erik", "initials": "E", "orcid": "0000-0002-8248-0663", "researcher": {"href": "https://publications.scilifelab.se/researcher/3af5a23ba0a847778eea300f745cb143.json"}}], "type": "journal article", "published": "2025-06-00", "journal": {"title": "Allergy", "issn": "1398-9995", "volume": "80", "issue": "6", "pages": "1702-1714", "issn-l": "0105-4538"}, "abstract": "Protein quantitative trait loci (pQTLs) remain underexplored in asthma but might provide valuable insights into the underlying molecular mechanisms. This study aimed to investigate associations between genetic variation and inflammation-related plasma proteins and to assess differences in the levels of genetically determined proteins in subjects with signatures of type-2 inflammation and/or asthma.\n\nA pQTL mapping of 92 inflammation-related plasma proteins was conducted in young adults from the Swedish BAMSE cohort (n = 1538). Replication of sentinel pQTLs was attempted, and the overlap and colocalization of pQTLs with expression quantitative trait loci (eQTLs) were investigated using publicly available data. Proteins with significant pQTLs were tested for association with type-2 signatures defined as high levels of fractional exhaled nitric oxide, blood eosinophils, and/or sensitization to airborne allergens in subjects with or without asthma in BAMSE.\n\nForty-five sentinel pQTLs (33 cis, 12 trans) for 39 inflammation-related proteins were identified (p \u2264 7.14 \u00d7 10-11), and a high proportion of these were validated in independent populations. A high likelihood for colocalization of cis-pQTLs and cis-eQTLs was observed for 19 proteins in different tissues. Six of the 39 circulating proteins with significant pQTLs were associated with type-2 signatures and/or asthma, and matrix metalloproteinase-10 (MMP-10) showed the most significant associations.\n\nThese findings underscore the existence of a genetic component influencing the plasma levels of proteins involved in inflammatory processes, including MMP-10, which is suggested to have a role in high type-2 inflammation in asthma subjects.", "doi": "10.1111/all.16608", "pmid": "40464643", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12186602"}], "notes": [], "created": "2025-09-08T07:17:11.553Z", "modified": "2025-11-25T19:21:03.863Z"}, {"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": "92e3372715cf4361b696885f895c9243", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92e3372715cf4361b696885f895c9243.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92e3372715cf4361b696885f895c9243"}}, "title": "Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prolonged immune response.", "authors": [{"family": "Fineschi", "given": "Serena", "initials": "S"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Lopez Egido", "given": "Juan Ramon", "initials": "JR"}, {"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Kaden", "given": "Ren\u00e9", "initials": "R"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2025-05-30", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "16", "pages": "1589589", "issn-l": "1664-3224"}, "abstract": "Post-acute sequelae of SARS-CoV-2 infection (PASC), also known as post-COVID-19 condition (here abbreviated as post-COVID) is an escalating global health issue. The aim of our study was to investigate the mechanisms and clinical manifestations of post-COVID following a mild SARS-CoV-2 infection.\n\nWe analyzed the gene expression profile in PBMCs from 60 middle-aged post-COVID patients and 50 age-matched controls at a median time of 28 months following a mild SARS-CoV-2 infection. The clinical assessments included intensity of post-COVID symptoms, physical and mental fatigue, depression and anxiety. Sixty-seven participants performed a mild exertion ergometer test with assessment of lactate concentrations. Transcriptome analysis was performed on mRNA selected by poly-A enrichment and SARS-CoV-2 RNA fragments were analyzed using the ARTIC protocol.\n\nWe identified 463 differentially expressed transcripts in PBMCs, of which 324 were upregulated and 129 downregulated in post-COVID patients. Upregulated genes in post-COVID individuals were enriched for processes involving JAK-STAT signaling, negative regulation of ubiquitination, IL9 signaling, and negative regulation of viral process, suggesting chronic inflammation. Downregulated genes were enriched for processes involving mitochondrial ATP synthesis, and oxidative phosphorylation, suggesting mitochondrial dysfunction. No SARS-CoV-2 gene fragments were detected in PBMCs of patients with post-COVID and no IFN genes were found differentially expressed in post-COVID patients. Post-COVID was associated with elevated lactate levels in blood, both at rest and after a short recovery phase following exertion, suggesting increased anaerobic activity in skeletal muscles. We did not find differences in the transcriptional profiles or clinical manifestations when comparing patients who contracted the infection from early SARS-CoV-2 variants with those who contracted the infection during the period when the Omicron variant was prevalent.\n\nOur findings highlight molecular changes compatible with a persistent immune response in PBMCs of post-COVID subjects at a median follow-up of 28 months after a mild infection, supporting the hypothesis that post-COVID is a chronic inflammatory condition. The upregulation of JAK/STAT signaling suggests a potential therapeutic target in post-COVID.", "doi": "10.3389/fimmu.2025.1589589", "pmid": "40519915", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12162955"}], "notes": [], "created": "2025-06-18T07:32:51.275Z", "modified": "2025-11-26T14:14:30.711Z"}, {"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": "5b6d8c72800145a294f1fab88be77e43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43"}}, "title": "Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication-Related Brain Composition.", "authors": [{"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Moradinour", "given": "Zahra", "initials": "Z"}, {"family": "Katajama", "given": "Rebecca", "initials": "R"}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17788", "issn-l": "0962-1083"}, "abstract": "Domestication involves huge phenotypic shifts via strong directional selection. The resulting changes, often termed the Domestication Syndrome, typically encompass numerous traits; however, the most universal of these are changes in reduced fear of humans (tameness) and brain composition. To assess how early domestication selection may have focused on tameness and its interaction with brain composition, a Red Junglefowl (Gallus gallus) population (the wild progenitor of the domestic chicken) was used to create two lines bidirectionally selected for fear of humans over eight generations of selection. These selection lines were then used to make an intercross population. Using a combination of genome-wide mapping in the intercross and between-line analysis of the selection lines, we show that the genetic loci for tameness co-localise with genetic loci for brain composition and anxiety behaviour. Furthermore, the detected loci for brain composition also co-localise with brain composition loci identified in a separate wild \u00d7 domestic intercross. These results indicate that tameness and brain composition are either pleiotropic or genetically linked, and that tameness selection appears to recapitulate the same loci that have been selected by domestication itself. Therefore, selection for increased tameness could be the initial selection pressure driving the core of the domestication syndrome.", "doi": "10.1111/mec.17788", "pmid": "40386851", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:29.894Z", "modified": "2025-11-28T10:51:37.135Z"}, {"entity": "publication", "iuid": "d87a1093323d4610a405b3a7a6fcc248", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d87a1093323d4610a405b3a7a6fcc248.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d87a1093323d4610a405b3a7a6fcc248"}}, "title": "Brain tumors induce immunoregulatory dendritic cells in draining lymph nodes that can be targeted by OX40 agonist treatment.", "authors": [{"family": "Badillo-Godinez", "given": "Oscar", "initials": "O", "orcid": "0000-0002-3840-9448", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a36cfe85dec4e5099c4fb754f8c4b7e.json"}}, {"family": "Niemi", "given": "Jenni", "initials": "J"}, {"family": "Helfridsson", "given": "Liam", "initials": "L"}, {"family": "Karimi", "given": "Shokoufeh", "initials": "S"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Mangukiya", "given": "Hitesh Bhagavanbhai", "initials": "HB", "orcid": "0000-0002-8460-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/d32958c394c749d19d7444dac9fe6c3b.json"}}, {"family": "Nelander", "given": "Sven", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "J Immunother Cancer", "issn": "2051-1426", "volume": "13", "issue": "5", "issn-l": null}, "abstract": "Primary and metastatic brain tumors have a poor prognosis, partly owing to the unique characteristics of the central nervous system (CNS) and tumor immune microenvironment (TIME). One distinct feature of the CNS TIME is the limited infiltration and activation of dendritic cells (DCs). The impact of CNS versus non-CNS TIME can be assessed by injecting tumor cells from the same model, either subcutaneously (peripherally) or into the brain. Subcutaneous tumors drain into the tumor-draining lymph nodes in the skin (TdLN-p), whereas brain tumors drain into the deep cervical TdLN (TdLN-c). We previously showed that CNS tumors that are not responsive to immune checkpoint inhibition become responsive when grown peripherally, and that non-responsiveness correlates with a tolerogenic immune response in the local TIME and TdLN-c.\n\nIn this study, we investigated the immunoregulatory potential of cervical DCs (DC-c) compared with that of peripheral DCs (DC-p) using high-resolution flow cytometry, single-cell RNA sequencing, and ex vivo and in vivo functional characterization of TdLNs from mouse models of glioma and lymphoma.\n\nOur analysis revealed that DC-c promoted regulatory T-cell expansion and poorly cytotoxic CD8+ T cells compared with DC-p. Furthermore, we identified OX40 (Tnfrsf4) as a modulator of immunoregulatory DC-c function and found that its antitumor effect depended on lymphocyte trafficking and the DC transcription factor Batf3. CCR7+OX40+ DCs were efficient in antigen processing and presentation, and OX40 agonists further enhanced DC activation. In TIME, the CCR7+OX40+ DCs expressed OX40L, and blocking it promoted Treg formation ex vivo.\n\nOur findings highlight the unique immunoregulatory functions of DC-c in TdLNs and suggest the importance of OX40 signaling through direct effects on CCR7+OX40+ DCs and indirect effects on T cells.", "doi": "10.1136/jitc-2025-011548", "pmid": "40389372", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12090865"}, {"db": "pii", "key": "jitc-2025-011548"}], "notes": [], "created": "2025-09-08T07:10:13.442Z", "modified": "2025-09-08T07:10:13.516Z"}, {"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": "5adffdb972b34ba1ad08ce191ce10297", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5adffdb972b34ba1ad08ce191ce10297.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5adffdb972b34ba1ad08ce191ce10297"}}, "title": "Revised phylogeny of mouflon based on expanded sampling of mitogenomes.", "authors": [{"family": "Mereu", "given": "Paolo", "initials": "P", "orcid": "0000-0001-6615-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/422d206c68a94124a43bed3c4db41999.json"}}, {"family": "Pirastru", "given": "Monica", "initials": "M"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P", "orcid": "0000-0001-7678-9691", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a48ddd9e9b491ea55ec2ac0bd4328f.json"}}, {"family": "Ata\u011f", "given": "G\u00f6zde", "initials": "G"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Wilkens", "given": "Barbara", "initials": "B"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Zedda", "given": "Marco", "initials": "M", "orcid": "0000-0003-2347-9264", "researcher": {"href": "https://publications.scilifelab.se/researcher/0108c75581c44c61a3f1bcaa0728e77a.json"}}, {"family": "Columbano", "given": "Nicol\u00f2", "initials": "N", "orcid": "0000-0003-2201-8773", "researcher": {"href": "https://publications.scilifelab.se/researcher/b39bcac149fd4b8ca83c833bf86da2f7.json"}}, {"family": "Barbato", "given": "Mario", "initials": "M", "orcid": "0000-0002-7203-1549", "researcher": {"href": "https://publications.scilifelab.se/researcher/2cf7e142b2894c9f8e3249dda9bc6728.json"}}, {"family": "Naitana", "given": "Salvatore", "initials": "S"}, {"family": "Hadjisterkotis", "given": "Eleftherios", "initials": "E"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Leoni", "given": "Giovanni Giuseppe", "initials": "GG"}], "type": "journal article", "published": "2025-05-14", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "5", "pages": "e0323354", "issn-l": "1932-6203"}, "abstract": "Mouflons are flagship species of the Mediterranean islands where they persist. Once thought to be the remnants of a European wild sheep population, archaeology suggests they were introduced by humans to the islands of Cyprus in the Early Neolithic (~10,000 years ago) and later to Corsica and Sardinia. Their status as truly wild animals remains a subject of debate. To investigate the phylogenetic relationship between these island populations and other domestic and wild sheep from the Mediterranean region, we sequenced 50 mitogenomes of mouflons from Sardinia and Corsica, and modern and ancient Sardinian domestic sheep. A total of 68 additional publicly available mitogenomes were included in the comparative analysis and used to reconstruct the phylogeny of sheep and its closest wild relative, the mouflon (Ovis gmelini). Our study analyzed the evolutionary relationships within the C-E-X and haplogroup B clusters, showing that: a) Cyprus mouflons are more related to Anatolian and Iranian mouflons belonging to the wild haplogroup X, which seems to be basal to the domestic C and E haplogroups; b) Corsican and Sardinian mouflon arise from basal lineages associated with the early European expansion of domestic sheep. These results highlight the phylogenetic distinctiveness of the mouflon populations from the Mediterranean islands, suggesting a revision of their systematic classification and an update of the nomenclature for Sardinian and Corsican mouflons from the current status of subspecies of domestic sheep (Ovis aries musimon) to subspecies of their wild relatives (Ovis gmelini musimon) which would facilitate conservation efforts.", "doi": "10.1371/journal.pone.0323354", "pmid": "40367058", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12077669"}, {"db": "pii", "key": "PONE-D-25-02476"}], "notes": [], "created": "2025-09-08T07:03:22.964Z", "modified": "2025-11-14T11:09:06.543Z"}, {"entity": "publication", "iuid": "188369759b0648d5ae25d06f97ae8ef1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/188369759b0648d5ae25d06f97ae8ef1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/188369759b0648d5ae25d06f97ae8ef1"}}, "title": "CpG island methylator phenotype classification improves risk assessment in pediatric T-cell acute lymphoblastic leukemia.", "authors": [{"family": "Sch\u00e4fer Hackenhaar", "given": "Fernanda", "initials": "F", "orcid": "0000-0002-9395-2216", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ac3981903a34a4d855647822d5339d1.json"}}, {"family": "Refhagen", "given": "Nina", "initials": "N"}, {"family": "Hagleitner", "given": "Melanie", "initials": "M"}, {"family": "van Leeuwen", "given": "Frank", "initials": "F", "orcid": "0000-0003-1107-6513", "researcher": {"href": "https://publications.scilifelab.se/researcher/97425d5c32d14c86b3b8414b24f6a387.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Madsen", "given": "Hans Ole", "initials": "HO"}, {"family": "Landfors", "given": "Mattias", "initials": "M", "orcid": "0000-0003-3974-4245", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2393ca69324818ac8bcb976da908be.json"}}, {"family": "Osterman", "given": "Pia", "initials": "P"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur", "initials": "\u00d3"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Heyman", "given": "Mats", "initials": "M", "orcid": "0000-0001-7637-1949", "researcher": {"href": "https://publications.scilifelab.se/researcher/d810139e533a4c2493e62b3e03bb9623.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": "Hultdin", "given": "Magnus", "initials": "M"}, {"family": "Degerman", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2783-0712", "researcher": {"href": "https://publications.scilifelab.se/researcher/8611162e883645f59195c4221199967f.json"}}], "type": "journal article", "published": "2025-05-08", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "145", "issue": "19", "pages": "2161-2178", "issn-l": "0006-4971"}, "abstract": "Current intensive treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has substantial side effects, highlighting a need for novel biomarkers to improve risk stratification. Canonical biomarkers, such as genetics and immunophenotype, are largely not used in pediatric T-ALL stratification. This study aimed to validate the prognostic relevance of DNA methylation CpG island methylator phenotype (CIMP) risk stratification in 2 pediatric T-ALL patient cohorts: the Nordic Society of Paediatric Haematology (NOPHO) ALL2008 T-ALL study cohort (n = 192) and the Dutch Childhood Oncology Group (DCOG) ALL-10/ALL-11 validation cohorts (n = 156). Both cohorts revealed that combining CIMP classification at diagnosis with measurable residual disease (MRD) at treatment day 29 (D29) or 33 (D33) significantly improved outcome prediction. The poor prognosis subgroup, characterized by CIMP low/D29 or D33 MRD \u2265 0.1%, had a cumulative incidence of relapse (pCIR5yr) of 29% and 23% and overall survival (pOS5yr) of 59.7% and 65.4%, in NOPHO and DCOG, respectively. Conversely, a good prognosis subgroup was also identified representing CIMP high/D29 or D33 MRD < 0.1% with pCIR5yr of 0% and 3.4% and pOS5yr of 98.2% and 94.8%, in NOPHO and DCOG, respectively. For NOPHO, MRD was also evaluated on D15, and the relapse prediction accuracy of CIMP/D29 MRD (0.79) and CIMP/D15 MRD (0.75) classification was comparable, indicating potential for earlier stratification. The evaluation of the biology behind the CIMP subgroups revealed associations with transcriptome profiles, genomic aberrations, and mitotic history, suggesting distinct routes for leukemia development. In conclusion, integrating MRD assessment with the novel CIMP biomarker has the potential to improve risk stratification in pediatric T-ALL and guide future therapeutic decisions.", "doi": "10.1182/blood.2024026027", "pmid": "39841000", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "535228"}], "notes": [], "created": "2025-05-12T06:17:29.072Z", "modified": "2025-05-12T06:17:30.354Z"}, {"entity": "publication", "iuid": "592bb323bd1c4346b9df99f55f08eb97", "links": {"self": {"href": "https://publications.scilifelab.se/publication/592bb323bd1c4346b9df99f55f08eb97.json"}, "display": {"href": "https://publications.scilifelab.se/publication/592bb323bd1c4346b9df99f55f08eb97"}}, "title": "Elucidation of short linear motif-based interactions of the MIT and rhodanese domains of the ubiquitin-specific protease 8.", "authors": [{"family": "Konstantinou", "given": "Aimiliani", "initials": "A"}, {"family": "Varga", "given": "Julia K", "initials": "JK"}, {"family": "C\u00f3rdova-P\u00e9rez", "given": "Alicia", "initials": "A"}, {"family": "Simonetti", "given": "Leandro", "initials": "L"}, {"family": "Gomez-Lucas", "given": "Lidia", "initials": "L"}, {"family": "Schueler-Furman", "given": "Ora", "initials": "O"}, {"family": "Davey", "given": "Norman E", "initials": "NE"}, {"family": "Kulathu", "given": "Yogesh", "initials": "Y"}, {"family": "Ivarsson", "given": "Ylva", "initials": "Y"}], "type": "journal article", "published": "2025-05-06", "journal": {"title": "Biol. Direct", "issn": "1745-6150", "volume": "20", "issue": "1", "pages": "59", "issn-l": "1745-6150"}, "abstract": "Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme with essential functions in protein trafficking and stability. It is a multidomain protein, with an N-terminal MIT (microtubule interacting and trafficking) domain, followed by a non-catalytic rhodanese (Rhod) domain, a long intrinsically disordered region, and a C-terminal catalytic domain. The N-terminal MIT domain of USP8 is known to mediate protein-protein interactions through binding to short linear motifs. The non-catalytic Rhod domain is also involved in protein-protein interactions, however detailed insights into these interactions remain limited. In this study we explore the short linear motif-based interactions of the MIT and Rhod domains of USP8 using a combination of proteomic peptide-phage display, peptide arrays and deep mutational scanning. We show that the MIT domain can bind ligands with a general [DE][LIF]x{2,3}R[FYIL]xxL[LV] consensus motif. We uncover that the rhodanese domain of USP8 is a peptide-binding domain, and define two distinct binding motifs (Rx[LI]xGxxxPxxL and G[LV][DE][IM]WExKxxxLxE) for this domain by deep mutational scanning of two different peptide ligands. Using the motif information, we predict binding sites within known USP8 interactors and substrates and validate interactions through peptide array analysis. Our findings demonstrate that both the USP8 MIT and rhodanese domains are peptide-binding domains that can be bound by degenerate and distinct binding motifs. The detailed information on the peptide binding preference of the two N-terminal domains of USP8 provide novel insights into the molecular recognition events that underlie the function of this essential deubiquitinating enzyme.", "doi": "10.1186/s13062-025-00638-7", "pmid": "40329301", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12057046"}, {"db": "pii", "key": "10.1186/s13062-025-00638-7"}], "notes": [], "created": "2025-09-08T11:30:02.875Z", "modified": "2025-09-08T11:30:02.896Z"}, {"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": "0269c77319e74b068198bff24d911079", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0269c77319e74b068198bff24d911079.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0269c77319e74b068198bff24d911079"}}, "title": "Integrative analyses of circulating microRNA expression profile in hexavalent chromium exposed workers - A cross-sectional study within the SafeChrom project.", "authors": [{"family": "Jiang", "given": "Zheshun", "initials": "Z"}, {"family": "Pan", "given": "Mengyu", "initials": "M"}, {"family": "Liu", "given": "Yishan", "initials": "Y"}, {"family": "Lundh", "given": "Thomas", "initials": "T"}, {"family": "Pineda", "given": "Daniela", "initials": "D"}, {"family": "Schenk", "given": "Linda", "initials": "L"}, {"family": "Saber", "given": "Anne T", "initials": "AT"}, {"family": "Vogel", "given": "Ulla", "initials": "U"}, {"family": "Ljunggren", "given": "Stefan", "initials": "S"}, {"family": "Ricklund", "given": "Niklas", "initials": "N"}, {"family": "Engfeldt", "given": "Malin", "initials": "M"}, {"family": "Krais", "given": "Annette M", "initials": "AM"}, {"family": "Broberg", "given": "Karin", "initials": "K"}, {"family": "SafeChrom Project Team", "given": "", "initials": ""}], "type": "journal article", "published": "2025-05-05", "journal": {"title": "J Hazard Mater", "issn": "1873-3336", "volume": "488", "pages": "137367", "issn-l": null}, "abstract": "Exposure to hexavalent chromium (Cr(VI)) can occur during occupational activities and leading lung cancer. MicroRNA (miRNA) plays an important part in carcinogenesis. Whether Cr(VI) exposure causes cancer-related miRNA changes is yet uncharacterized.\n\nThis study included 89 Cr(VI) exposed workers and 47 controls. MiRNAs were extracted from plasma followed by library preparations, miRNA sequencing, and differentially expressed miRNAs (DEMs) analysis. To understand the underlying biological functions, we used bioinformatics approaches, and qPCR was performed to validate the expression of potential target genes.\n\nA total of 2100 miRNAs were detected. In the exposed workers, 59 DEMs were identified: 21 up-regulated and 38 down-regulated. Target genes for both up- and down-regulated DEMs were significantly enriched in: miRNAs in cancer, small cell lung cancer and non-small cell lung cancer. Protein-protein interactions showed a high number of interactions, in which CCNE2, CDK4 and E2F1 were predicted as hub genes, and the messenger RNA expression of those genes was significantly higher in the exposed workers compared with controls.\n\nOur study suggests that low-to-moderate Cr(VI) exposure results in differential expression of lung-cancer-related miRNAs and associated target genes. Further studies are needed to validate our findings and clarify whether these changes predict cancer risk.", "doi": "10.1016/j.jhazmat.2025.137367", "pmid": "40098212", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pii", "key": "S0304-3894(25)00279-1"}], "notes": [], "created": "2025-09-29T11:23:20.679Z", "modified": "2025-09-29T11:23:20.682Z"}, {"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": "54e65a8ce2c94cf5ac271086444360f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54e65a8ce2c94cf5ac271086444360f9"}}, "title": "Sperm DNA methylation landscape and its links to male fertility in a non-model teleost using EM-seq.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F", "orcid": "0000-0003-3696-5069", "researcher": {"href": "https://publications.scilifelab.se/researcher/238d355f0f5f4dd798fdc7f58d4c5a41.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Debes", "given": "Paul V", "initials": "PV", "orcid": "0000-0003-4491-9564", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1887c01f5b343e19e398b3fcd96ba14.json"}}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "134", "issue": "5", "pages": "293-305", "issn-l": "0018-067X"}, "abstract": "Differential DNA methylation due to epigenetic phenomena is crucial in regulating gene expression. Understanding the consequences of such differential expression on sperm quality parameters may provide insights into the underlying mechanisms of male reproductive success. Nonetheless, male fertility in fish remains understudied despite its critical importance to overall reproductive success in nature and captivity. This study investigated the DNA methylation landscape in spermatozoa of domesticated Arctic charr (Salvelinus alpinus) and its associations with sperm quality parameters. Computer assisted-semen analysis (CASA) was performed in 47 sperm samples of farmed Arctic charr, followed by enzymatic methylation sequencing (EM-seq). Our results showed that the DNA of Arctic charr sperm is highly methylated (mean value of ~86%), though variations were observed in genomic features involved in gene regulation. Methylation at variable CpG sites exhibited regional correlation decaying by physical distance, while methylation similarities among individuals were strongly coupled with genetic variation and mirrored pedigree structure. Comethylation network analyses for promoters, CpG islands and first introns revealed genomic modules significantly correlated with sperm quality traits (p < 0.05; Bonferroni adjusted), with distinct patterns suggesting a resource trade-off between sperm concentration and kinematics. Furthermore, annotation and gene-set enrichment analysis highlighted biological mechanisms related to spermatogenesis, cytoskeletal regulation, and mitochondrial function, all vital to sperm physiology. These findings suggest that DNA methylation is a critical and fundamental factor influencing male fertility in Arctic charr, providing insights into the underlying mechanisms of male reproductive success.", "doi": "10.1038/s41437-025-00756-y", "pmid": "40097595", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12056074"}, {"db": "pii", "key": "10.1038/s41437-025-00756-y"}], "notes": [], "created": "2025-09-08T06:59:19.759Z", "modified": "2025-11-14T11:06:34.293Z"}, {"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": "2db32f8194a7438484ff5bbd2844c22e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2db32f8194a7438484ff5bbd2844c22e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2db32f8194a7438484ff5bbd2844c22e"}}, "title": "Mutational signatures and kataegis in pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R", "orcid": "0000-0002-2283-786X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12601745d2c74562bf83d22879f212eb.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lundin-Str\u00f6m", "given": "Kristina B", "initials": "KB"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Castor", "given": "Anders", "initials": "A"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Paulsson", "given": "Kajsa", "initials": "K"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "letter", "published": "2025-05-00", "journal": {"title": "Hemasphere", "issn": "2572-9241", "volume": "9", "issue": "5", "pages": "e70136", "issn-l": null}, "abstract": null, "doi": "10.1002/hem3.70136", "pmid": "40395431", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12088958"}, {"db": "pii", "key": "HEM370136"}, {"db": "figshare", "key": "10.6084/m9.figshare.28053263"}], "notes": [], "created": "2025-09-08T07:07:08.984Z", "modified": "2025-09-08T07:07:09.087Z"}, {"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": "cc91895d782a4623b95f8d39c736a4cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc91895d782a4623b95f8d39c736a4cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc91895d782a4623b95f8d39c736a4cf"}}, "title": "Error Reduction in Leukemia Machine Learning Classification With Conformal Prediction.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M", "orcid": "0000-0002-0012-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/48850e5606b9470caa6b130286055388.json"}}, {"family": "Zachariah", "given": "Dave", "initials": "D", "orcid": "0000-0002-6698-0166", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdf118819f654f32ad53f994e83c227d.json"}}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2025-05-00", "journal": {"title": "JCO Clin Cancer Inform", "issn": "2473-4276", "volume": "9", "pages": "e2400324", "issn-l": null}, "abstract": "Recent advances in machine learning have led to the development of classifiers that predict molecular subtypes of acute lymphoblastic leukemia (ALL) using RNA-sequencing (RNA-seq) data. Although these models have shown promising results, they often lack robust performance guarantees. The aim of this study was three-fold: to quantify the uncertainty of these classifiers, to provide prediction sets that control the false-negative rate (FNR), and to perform implicit error reduction by transforming incorrect predictions into uncertain predictions.\n\nConformal prediction (CP) is a distribution-agnostic framework for generating statistically calibrated prediction sets whose size reflects model uncertainty. In this study, we applied an extension called conformal risk control to three RNA-seq ALL subtype classifiers. Leveraging RNA-seq data from 1,227 patient samples taken at diagnosis, we developed a multiclass conformal predictor ALLCoP, which generates statistically guaranteed FNR-controlled prediction sets.\n\nALLCoP was able to create prediction sets with specified FNR tolerances ranging from 7.5% to 30%. In a validation cohort, ALLCoP successfully reduced the FNR of the ALLIUM RNA-seq ALL subtype classifier from 8.95% to 3.5%. For patients whose subtype was not previously known, the use of ALLCoP was able to reduce the occurrence of empty predictions from 37% to 17%. Notably, up to 34% of the multiple-class prediction sets included the PAX5alt subtype, suggesting that increased prediction set size may reflect secondary aberrations and biological complexity, contributing to classifier uncertainty. Finally, ALLCoP was validated on two additional RNA-seq ALL subtype classifiers, ALLSorts and ALLCatchR.\n\nOur results highlight the potential of CP in enhancing the use of oncologic RNA-seq subtyping classifiers and also in uncovering additional molecular aberrations of potential clinical importance.", "doi": "10.1200/CCI-24-00324", "pmid": "40435436", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12133051"}], "notes": [], "created": "2025-11-07T07:27:00.813Z", "modified": "2025-11-14T11:08:56.250Z"}, {"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"}, "xrefs": [{"db": "pmc", "key": "PMC11992678"}, {"db": "pii", "key": "8112696"}], "notes": [], "created": "2025-04-16T07:03:31.301Z", "modified": "2025-09-08T11:29:59.901Z"}, {"entity": "publication", "iuid": "59b7b1a3171445408a05b3c342c2dc3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/59b7b1a3171445408a05b3c342c2dc3b"}}, "title": "Genome-wide comparison reveals large structural variants in cassava landraces.", "authors": [{"family": "Landi", "given": "Michael", "initials": "M"}, {"family": "Carluccio", "given": "Anna Vittoria", "initials": "AV"}, {"family": "Shah", "given": "Trushar", "initials": "T"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Stavolone", "given": "Livia", "initials": "L"}, {"family": "Falquet", "given": "Laurent", "initials": "L"}, {"family": "Gisel", "given": "Andreas", "initials": "A"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2025-04-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "362", "issn-l": "1471-2164"}, "abstract": "Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.\n\nWe validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.\n\nThis study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity.", "doi": "10.1186/s12864-025-11523-y", "pmid": "40211122", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11987339"}, {"db": "pii", "key": "10.1186/s12864-025-11523-y"}], "notes": [], "created": "2025-09-08T06:59:22.722Z", "modified": "2025-09-08T06:59:22.728Z"}, {"entity": "publication", "iuid": "a624b6ccad7b449fa079200d5b4a545f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a624b6ccad7b449fa079200d5b4a545f"}}, "title": "Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in Icelandic horses.", "authors": [{"family": "Sigur\u00f0ard\u00f3ttir", "given": "Hei\u00f0r\u00fan", "initials": "H"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Niazi", "given": "Adnan", "initials": "A"}, {"family": "Rhodin", "given": "Marie", "initials": "M"}, {"family": "Albertsd\u00f3ttir", "given": "Elsa", "initials": "E"}, {"family": "Kristjansson", "given": "Thorvaldur", "initials": "T"}, {"family": "Lindgren", "given": "Gabriella", "initials": "G"}], "type": "journal article", "published": "2025-04-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "11641", "issn-l": "2045-2322"}, "abstract": "Selection for performance in horse breeding benefits from precise genetic insights at a molecular level, but knowledge remains limited. This study used whole-genome sequences of 39 elite and non-elite Icelandic horses to identify candidate causal variants linked to previously identified haplotypes in the STAU2 and RELN genes affecting pace and other gaits. A frameshift variant in linkage disequilibrium with the previously identified haplotypes in the STAU2 gene (r2 = 0.85) was identified within a predicted STAU2 transcript. This variant alters the amino acid sequence and introduces a premature stop codon but does not appear harmful or disease-causing and is potentially unique to equine biology. A large portion of the RELN haplotype overlapped with an H3K27me3 modification mark, suggesting a regulatory role of this region. Despite the small sample size, the RELN haplotype's effects were validated for t\u00f6lt, trot, and canter/gallop. Additionally, the RELN haplotype significantly influenced the age at which horses were presented for breeding field tests, indicating a potential role of the region in precocity and trainability. Functional experiments are needed to further investigate the regions' influences on biological processes and their potential impact on horse performance.", "doi": "10.1038/s41598-025-95593-8", "pmid": "40185812", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11971302"}, {"db": "pii", "key": "10.1038/s41598-025-95593-8"}], "notes": [], "created": "2025-11-07T07:27:05.828Z", "modified": "2025-11-14T11:07:06.654Z"}, {"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": "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": "647d53b18b37408db896d3a565fec76c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/647d53b18b37408db896d3a565fec76c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/647d53b18b37408db896d3a565fec76c"}}, "title": "The DNA methylation landscape of primary triple-negative breast cancer.", "authors": [{"family": "Aine", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0851-5952", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec863fc84b064759b355272fa1be61ff.json"}}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/e484e25cfdf64d27842357355409dbfc.json"}}, {"family": "Arbajian", "given": "Elsa", "initials": "E", "orcid": "0000-0002-1484-0073", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9615e08a1a04fada47e805c27a29c61.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications.scilifelab.se/researcher/c203a0b3112f4f499ccc79db3e47b303.json"}}, {"family": "Karlsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-6974-5965", "researcher": {"href": "https://publications.scilifelab.se/researcher/016d7daf94304064a461e0df719112c5.json"}}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b8605b9a7c74b20986146f020cf4b8f.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fa1d04cb640858fe3534d04cd04d1.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications.scilifelab.se/researcher/127501d4e0854d14a4120acee9042bb7.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications.scilifelab.se/researcher/07acbd7f211e4809a8195e2ccf5faf57.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3041", "issn-l": "2041-1723"}, "abstract": "Triple-negative breast cancer (TNBC) is a clinically challenging and molecularly heterogenous breast cancer subgroup. Here, we investigate the DNA methylation landscape of TNBC. By analyzing tumor methylome profiles and accounting for the genomic context of CpG methylation, we divide TNBC into two epigenetic subtypes corresponding to a Basal and a non-Basal group, in which characteristic transcriptional patterns are correlated with DNA methylation of distal regulatory elements and epigenetic regulation of key steroid response genes and developmental transcription factors. Further subdivision of the Basal and non-Basal subtypes identifies subgroups transcending genetic and proposed TNBC mRNA subtypes, demonstrating widely differing immunological microenvironments, putative epigenetically-mediated immune evasion strategies, and a specific metabolic gene network in older patients that may be epigenetically regulated. Our study attempts to target the epigenetic backbone of TNBC, an approach that may inform future studies regarding tumor origins and the role of the microenvironment in shaping the cancer epigenome.", "doi": "10.1038/s41467-025-58158-x", "pmid": "40155623", "labels": {"Clinical Genomics Lund": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11953470"}, {"db": "pii", "key": "10.1038/s41467-025-58158-x"}], "notes": [], "created": "2025-04-14T12:30:37.267Z", "modified": "2025-09-08T06:57:25.392Z"}, {"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": "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": "94b833e1cf11498a8be10d219e3db160", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94b833e1cf11498a8be10d219e3db160.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94b833e1cf11498a8be10d219e3db160"}}, "title": "Genome Sequence Resources from Three Isolates of the Apple Canker Pathogen Neonectria ditissima Infecting Forest Trees", "authors": [{"family": "Bourras", "given": "Salim", "initials": "S", "orcid": "0000-0003-0855-5433", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6b49cf30d404c7ab7bbbe30bda39d1c.json"}}, {"family": "V\u00e9l\u00ebz", "given": "Heriberto", "initials": "H"}, {"family": "Ihrmark", "given": "Katarina", "initials": "K"}, {"family": "Corrales Guti\u00e9rrez", "given": "Miguel \u00c1ngel", "initials": "M\u00c1"}, {"family": "Elfstrand", "given": "Malin", "initials": "M", "orcid": "0000-0002-0214-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/2957dac173f4495a9245f0d8a9750606.json"}}, {"family": "Garkava-Gustavsson", "given": "Larisa", "initials": "L"}, {"family": "Falk", "given": "Kerstin Dalman", "initials": "KD"}], "type": "journal-article", "published": "2025-03-00", "journal": {"title": "PhytoFrontiers\u2122", "issn": "2690-5442", "volume": "5", "issue": "1", "pages": "117-119", "issn-l": null}, "abstract": null, "doi": "10.1094/phytofr-05-24-0055-a", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:54:44.172Z", "modified": "2025-09-08T06:54:44.391Z"}, {"entity": "publication", "iuid": "42d2bb44130c40a9a57616496fc17474", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42d2bb44130c40a9a57616496fc17474.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42d2bb44130c40a9a57616496fc17474"}}, "title": "Yellow barley xan-m mutants are deficient in the motor unit SECA1 of the SEC1 translocase system.", "authors": [{"family": "Stuart", "given": "David", "initials": "D"}, {"family": "Ivanova", "given": "Anastasiia", "initials": "A"}, {"family": "Zakhrabekova", "given": "Shakhira", "initials": "S"}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "Planta", "issn": "1432-2048", "volume": "261", "issue": "4", "pages": "68", "issn-l": "0032-0935"}, "abstract": "Chloroplast protein transport depends on the SEC1 translocase. Barley xan-m mutants, deficient in SECA1, lack chlorophyll and die as seedlings. Their yellow phenotype indicates that carotenoid chemistry is less SEC1-dependent. Chloroplast proteins encoded by genes located in the cell nucleus need to be transported across up to three chloroplast membranes to find its correct location. SEC1 is one of the major translocase systems. In plants, SEC1 consists of three proteins (SECA1, SECY1 and SECE1) and transports substrate proteins over the thylakoid membrane. SECA1 is an ATPase that delivers the substrate protein to the SECY1-SECE1 channel. In the present study, we analyzed five allelic barley xan-m mutants, which had been isolated between 1925 and 1957. The mutants belong to a larger collection of barley mutants deficient in chlorophyll biosynthesis and chloroplast development. Mutations in the xan-m gene are recessive and result in a yellow phenotype due to lack of chlorophyll and presence of carotenoids. Mutant seedlings die after approximately 10 days. We identified the defective gene in the xan-m mutants by a variant of bulk segregant analysis. The gene xan-m is an orthologue of SECA1 in Arabidopsis. Previously, only genes related to chlorophyll biosynthesis have been identified in the collection of barley xan mutants. The yellow phenotype of the mutants demonstrates that proteins responsible for carotenoid biosynthesis and storage are not or less dependent on an intact SEC1 translocase.", "doi": "10.1007/s00425-025-04654-9", "pmid": "40009246", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11865152"}, {"db": "pii", "key": "10.1007/s00425-025-04654-9"}], "notes": [], "created": "2025-09-08T06:54:56.835Z", "modified": "2025-11-14T11:05:42.039Z"}, {"entity": "publication", "iuid": "31cc2ec2f8a34c93b6d17050bec2d830", "links": {"self": {"href": "https://publications.scilifelab.se/publication/31cc2ec2f8a34c93b6d17050bec2d830.json"}, "display": {"href": "https://publications.scilifelab.se/publication/31cc2ec2f8a34c93b6d17050bec2d830"}}, "title": "Single-cell analysis of aplastic anemia reveals a convergence of NK and NK-like CD8+ T cells with a disease-associated TCR signature.", "authors": [{"family": "Lundgren", "given": "Sofie", "initials": "S", "orcid": "0000-0003-3146-9816", "researcher": {"href": "https://publications.scilifelab.se/researcher/3838050baa4847c5ad8edcd02b3b54e2.json"}}, {"family": "Huuhtanen", "given": "Jani", "initials": "J", "orcid": "0000-0003-2750-4033", "researcher": {"href": "https://publications.scilifelab.se/researcher/f982fef263e644799e27df3f31083d6c.json"}}, {"family": "Ker\u00e4nen", "given": "Mikko", "initials": "M", "orcid": "0000-0001-8027-499X", "researcher": {"href": "https://publications.scilifelab.se/researcher/065055dc206c4749b64c08e7414875b1.json"}}, {"family": "Feng", "given": "Xingmin", "initials": "X", "orcid": "0000-0001-8018-2366", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecf564243b464d919b534c054c6e5fee.json"}}, {"family": "Patel", "given": "Bhavisha A", "initials": "BA", "orcid": "0000-0002-2974-7701", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f42376804c4437fb68895915f369d39.json"}}, {"family": "Ryland", "given": "Georgina L", "initials": "GL", "orcid": "0000-0002-4990-0961", "researcher": {"href": "https://publications.scilifelab.se/researcher/891952aec8b442e1af79388838e73e05.json"}}, {"family": "Fox", "given": "Lucy C", "initials": "LC", "orcid": "0000-0002-3855-8232", "researcher": {"href": "https://publications.scilifelab.se/researcher/827f9263f0734c7ab1b757bc35758862.json"}}, {"family": "Bravo-Perez", "given": "Carlos", "initials": "C", "orcid": "0000-0001-9794-7847", "researcher": {"href": "https://publications.scilifelab.se/researcher/4260758112534ceba7efe94660a0a43e.json"}}, {"family": "Clemente", "given": "Michael", "initials": "M"}, {"family": "Kerr", "given": "Cassandra", "initials": "C"}, {"family": "Walldin", "given": "Gunilla", "initials": "G", "orcid": "0009-0005-6663-6540", "researcher": {"href": "https://publications.scilifelab.se/researcher/24fb888d0212421eaa2353ed6cc31ac7.json"}}, {"family": "Dufva", "given": "Olli", "initials": "O"}, {"family": "Zaimoku", "given": "Yoshitaka", "initials": "Y", "orcid": "0000-0002-4108-5245", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9bc97e77a35491197fa901757bd92f0.json"}}, {"family": "Tuononen", "given": "Tiina", "initials": "T", "orcid": "0009-0007-6677-3064", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c764c4bf7746fc9c6c468a51a5db52.json"}}, {"family": "Myllym\u00e4ki", "given": "Mikko", "initials": "M", "orcid": "0000-0002-8194-7356", "researcher": {"href": "https://publications.scilifelab.se/researcher/071c21748567437393dfb1b7c3bedad4.json"}}, {"family": "Ebeling", "given": "Freja", "initials": "F", "orcid": "0000-0002-7921-089X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5318f08e1aff4e988f961f1c7806d1bb.json"}}, {"family": "Jokinen", "given": "Emmi", "initials": "E", "orcid": "0000-0002-0060-6868", "researcher": {"href": "https://publications.scilifelab.se/researcher/8392afc052914d47ab93466ba898cbc8.json"}}, {"family": "Heinonen", "given": "Markus", "initials": "M", "orcid": "0000-0002-7741-2279", "researcher": {"href": "https://publications.scilifelab.se/researcher/8733ddf664b2445188aed518dab08873.json"}}, {"family": "Kasanen", "given": "Tiina", "initials": "T", "orcid": "0000-0002-5408-1948", "researcher": {"href": "https://publications.scilifelab.se/researcher/06fb270832244566bfc649d43f7e718c.json"}}, {"family": "Klievink", "given": "Jay", "initials": "J", "orcid": "0000-0002-4081-5840", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdad6fd259c749a5b3a770ae47c770cf.json"}}, {"family": "L\u00e4hteenm\u00e4ki", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6773-2677", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0cb9da3e4cb4430a779d4d4185e6652.json"}}, {"family": "Jaatinen", "given": "Taina", "initials": "T", "orcid": "0000-0001-7783-6189", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b981dc2e49a4731abc5ac1ee7bbfecf.json"}}, {"family": "Kyt\u00f6l\u00e4", "given": "Sari", "initials": "S", "orcid": "0000-0003-1649-8993", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8e0b29c15c24626b529b3b1cab1ca1a.json"}}, {"family": "Siitonen", "given": "Sanna", "initials": "S", "orcid": "0009-0001-2241-6731", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c6a7c0c04f3451086c3b32d74da6ffa.json"}}, {"family": "Dulau-Florea", "given": "Alina", "initials": "A", "orcid": "0000-0003-3512-4946", "researcher": {"href": "https://publications.scilifelab.se/researcher/480fa59b41ab400d8eca304bf23c3332.json"}}, {"family": "Braylan", "given": "Raul", "initials": "R", "orcid": "0000-0001-6733-5161", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1ec596e60c542238a5ada29bb62fc51.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}, {"family": "Nakao", "given": "Shinji", "initials": "S", "orcid": "0000-0002-9674-624X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab2d147043454ff2b403f70bd60136e6.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Maciejewski", "given": "Jaroslaw P", "initials": "JP"}, {"family": "Blombery", "given": "Piers", "initials": "P"}, {"family": "Young", "given": "Neal S", "initials": "NS"}, {"family": "L\u00e4hdesm\u00e4ki", "given": "Harri", "initials": "H"}, {"family": "Mustjoki", "given": "Satu", "initials": "S", "orcid": "0000-0002-0816-8241", "researcher": {"href": "https://publications.scilifelab.se/researcher/03cdbac477284e7093121bc3d35a6dfb.json"}}], "type": "journal article", "published": "2025-02-26", "journal": {"title": "Sci Transl Med", "issn": "1946-6242", "volume": "17", "issue": "787", "pages": "eadl6758", "issn-l": "1946-6234"}, "abstract": "Immune aplastic anemia (AA) is a life-threatening bone marrow failure disorder driven by an autoimmune T cell attack against hematopoietic stem and progenitor cells (HSPCs). However, the exact autoantigen targets and role of other immune cells in the pathogenesis of AA are unknown. Here, we analyzed a cohort of 218 patients with AA using single-cell RNA and T cell receptor (TCR) \u03b1\u03b2 sequencing, TCR\u03b2 sequencing, flow cytometry, and plasma cytokine profiling. We identified natural killer (NK) cells and CD8+ terminally differentiated effector T (TEMRA) cells expressing NK receptors with AA-associated TCR\u03b2 motifs as the most dysregulated immune cell populations in AA bone marrow. Functional coculture experiments using primary HSPCs and immune cells showed that NK cells cannot kill HSPCs alone but may sensitize HSPCs to CD8+ T cell-mediated killing through production of interferons. Furthermore, HSPCs induced activation of T cell clones with CD8+ TEMRA NK-like phenotype in coculture. Our results reveal a convergent phenotype of innate and adaptive immune cells that may drive AA.", "doi": "10.1126/scitranslmed.adl6758", "pmid": "40009697", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:23.304Z", "modified": "2025-09-08T11:37:24.704Z"}, {"entity": "publication", "iuid": "229f504c7e6941e88c6f4ae750d0bbcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/229f504c7e6941e88c6f4ae750d0bbcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/229f504c7e6941e88c6f4ae750d0bbcf"}}, "title": "Digital sequencing is improved by using structured unique molecular identifiers.", "authors": [{"family": "Micallef", "given": "Peter", "initials": "P"}, {"family": "Santamar\u00eda", "given": "Manuel Luna", "initials": "ML"}, {"family": "Escobar", "given": "Mandy", "initials": "M"}, {"family": "Andersson", "given": "Daniel", "initials": "D"}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T"}, {"family": "Mouhanna", "given": "Pia", "initials": "P"}, {"family": "Filges", "given": "Stefan", "initials": "S"}, {"family": "Johansson", "given": "Gustav", "initials": "G"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Vannas", "given": "Christoffer", "initials": "C"}, {"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": "2025-02-25", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "37", "issn-l": "1474-7596"}, "abstract": "Digital sequencing uses unique molecular identifiers (UMIs) to correct for polymerase induced errors and amplification biases. Here, we design 19 different structured UMIs to minimize the capacity of primers to form non-specific PCR products during library construction using SiMSen-Seq, a PCR-based digital sequencing approach with flexible multiplexing capabilities suitable for tumor-informed mutation analysis. All structured UMI designs demonstrate enhanced assay performance compared with an unstructured reference UMI. The best performing structured UMI design shows significant improvements in all tested aspects of assay and sequencing performance with the ability to reliable detect low variant allele frequencies.", "doi": "10.1186/s13059-025-03504-x", "pmid": "40001095", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11853513"}, {"db": "pii", "key": "10.1186/s13059-025-03504-x"}], "notes": [], "created": "2025-09-08T06:54:47.020Z", "modified": "2025-09-08T06:54:47.088Z"}, {"entity": "publication", "iuid": "e09133a40d7145b18f9bb8facb4dc96c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e09133a40d7145b18f9bb8facb4dc96c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e09133a40d7145b18f9bb8facb4dc96c"}}, "title": "Comprehensive Gene Expression Analysis in Papillary Thyroid Carcinoma Reveals a Transcriptional Profile Associated with Reduced Radioiodine Avidity.", "authors": [{"family": "Condello", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4569-5398", "researcher": {"href": "https://publications.scilifelab.se/researcher/09be613118f743bd992bba237b61ceb4.json"}}, {"family": "Marchettini", "given": "Carlotta", "initials": "C"}, {"family": "Ihre-Lundgren", "given": "Catharina", "initials": "C"}, {"family": "Nilsson", "given": "Joachim N", "initials": "JN", "orcid": "0000-0001-7496-9189", "researcher": {"href": "https://publications.scilifelab.se/researcher/47b5460e0a2444c49675506d7f028784.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": "2025-02-21", "journal": {"title": "Endocr. Pathol.", "issn": "1559-0097", "volume": "36", "issue": "1", "pages": "4", "issn-l": "1046-3976"}, "abstract": "Papillary thyroid carcinoma (PTC) is the most common form of well-differentiated thyroid cancer (WDTC) and generally has a favorable prognosis. However, subsets of these tumors can metastasize, leading to aggressive disease progression and poorer clinical outcomes. Radioactive iodine (RAI) therapy is routinely given in the adjuvant setting following thyroidectomy and lymph node dissection for WDTC. Nevertheless, its therapeutic efficacy is limited to tumors with high iodine avidity. Early post-surgical classification of thyroid cancers as either iodine-avid or refractory is crucial for enabling more personalized and effective treatment strategies. In this study, we aimed to identify transcriptomic determinants associated with RAI refractoriness (RAI-R) to improve prognostication. We collected clinicopathologic data and conducted RNA-seq on 36 tissue samples (18 high-avidity and 18 low-avidity), each uniquely characterized by ex vivo iodine concentration measurements taken directly from surgical specimens. Whole-transcriptomic analysis identified 63 differentially expressed genes, with six (S100A4, CRTC2, ANO1, WWTR1, DEPTOR, MT1G) showing consistent deregulation. The expression of ANO1, an established iodine transporter at the apical membrane of the thyroid follicular cells, correlated significantly with iodine avidity (r = 0.54). Validation via RT-qPCR confirmed differential expression trends. Gene ontology and pathway enrichment analyses highlighted thyroid hormone synthesis, PI3K-AKT, and MAPK signaling pathways as key regulators of RAI avidity. A refined multivariate predictive model incorporating ANO1 mRNA expression, histological subtypes, and sample type demonstrated strong predictive performance (adjusted R2 = 0.55). These findings suggest ANO1 as a promising biomarker for predicting iodine avidity in thyroid cancer.", "doi": "10.1007/s12022-025-09849-0", "pmid": "39982585", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11845550"}, {"db": "pii", "key": "10.1007/s12022-025-09849-0"}], "notes": [], "created": "2025-05-12T05:46:47.965Z", "modified": "2025-09-08T07:13:03.100Z"}, {"entity": "publication", "iuid": "d9bc92127ecf49ce8f19dabdd5e631a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9bc92127ecf49ce8f19dabdd5e631a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9bc92127ecf49ce8f19dabdd5e631a1"}}, "title": "Age-Dependent Pleomorphism in Mycobacterium monacense Cultures.", "authors": [{"family": "Ramesh", "given": "Malavika", "initials": "M", "orcid": "0000-0002-2353-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/e679c292f1904ecbb1dece92d5513d26.json"}}, {"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK", "orcid": "0000-0002-8810-6066", "researcher": {"href": "https://publications.scilifelab.se/researcher/711dae7f552146ac95d209bc8efab54e.json"}}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF", "orcid": "0009-0006-8579-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5d1d0f6732d4dee869861d57ce02cd7.json"}}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA", "orcid": "0000-0002-5092-512X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e80849a89d0043b0b4daff9804c67332.json"}}], "type": "journal article", "published": "2025-02-20", "journal": {"title": "Microorganisms", "issn": "2076-2607", "volume": "13", "issue": "3", "issn-l": "2076-2607"}, "abstract": "Changes in cell shape have been shown to be an integral part of the mycobacterial life cycle; however, systematic investigations into its patterns of pleomorphic behaviour in connection with stages or conditions of growth are scarce. We have studied the complete growth cycle of Mycobacterium monacense cultures, a Non-Tuberculous Mycobacterium (NTM), in solid as well as in liquid media. We provide data showing changes in cell shape from rod to coccoid and occurrence of refractive cells ranging from Phase Grey to phase Bright (PGB) in appearance upon ageing. Changes in cell shape could be correlated to the bi-phasic nature of the growth curves for M. monacense (and the NTM Mycobacterium boenickei) as measured by the absorbance of liquid cultures while growth measured by colony-forming units (CFU) on solid media showed a uniform exponential growth. Based on the complete M. monacense genome we identified genes involved in cell morphology, and analyses of their mRNA levels revealed changes at different stages of growth. One gene, dnaK_3 (encoding a chaperone), showed significantly increased transcript levels in stationary phase cells relative to exponentially growing cells. Based on protein domain architecture, we identified that the DnaK_3 N-terminus domain is an MreB-like homolog. Endogenous overexpression of M. monacense dnaK_3 in M. monacense was unsuccessful (appears to be lethal) while exogenous overexpression in Mycobacterium marinum resulted in morphological changes with an impact on the frequency of appearance of PGB cells. However, the introduction of an anti-sense \"gene\" targeting the M. marinum dnaK_3 did not show significant effects. Using dnaK_3-lacZ reporter constructs we also provide data suggesting that the morphological differences could be due to differences in the regulation of dnaK_3 in the two species. Together these data suggest that, although its regulation may vary between mycobacterial species, the dnaK_3 might have a direct or indirect role in the processes influencing mycobacterial cell shape.", "doi": "10.3390/microorganisms13030475", "pmid": "40142368", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11946739"}, {"db": "pii", "key": "microorganisms13030475"}], "notes": [], "created": "2025-08-19T13:27:17.755Z", "modified": "2025-09-08T07:17:25.329Z"}, {"entity": "publication", "iuid": "db0102f308044e068375eaab4e78dc48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db0102f308044e068375eaab4e78dc48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db0102f308044e068375eaab4e78dc48"}}, "title": "An Evolutionary Mosaic Challenges Traditional Monitoring of a Foundation Species in a Coastal Environment-The Baltic Fucus vesiculosus.", "authors": [{"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Kinnby", "given": "Alexandra", "initials": "A"}, {"family": "Le Moan", "given": "Alan", "initials": "A", "orcid": "0000-0002-9124-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/609a745ce1fb42fea85cc8d55db25acf.json"}}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O"}, {"family": "Jonsson", "given": "Per R", "initials": "PR"}, {"family": "Piarulli", "given": "Stefania", "initials": "S"}, {"family": "Pinder", "given": "Matthew I M", "initials": "MIM", "orcid": "0000-0003-4407-0214", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6d9f52178249f3995c3d276fbc2728.json"}}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C"}, {"family": "Knutsen", "given": "Halvor", "initials": "H", "orcid": "0000-0002-7627-7634", "researcher": {"href": "https://publications.scilifelab.se/researcher/a822f994fed046018a713105bc5e03a0.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": "2025-02-17", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17699", "issn-l": "0962-1083"}, "abstract": "During periods of environmental change, genetic diversity in foundation species is critical for ecosystem function and resilience, but it remains overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates. Ecological distribution models predict a significant loss of Baltic F. vesiculosus due to ocean warming, unless populations can adapt. Genetic variation and recombination during sexual reproduction are essential for adaptation, but studies have revealed large-scale clonal reproduction within the Baltic Sea. We analysed genome-wide single nucleotide polymorphism (SNP) data from the east Atlantic, the \"Transition zone,\" and the Baltic Sea, and found a mosaic of divergent lineages in the Baltic Sea, contrasting an outside dominance of a few genetic groups. We determined that the previously described endemic species Fucus radicans is predominantly a large female clone of F. vesiculosus in its northern Baltic distribution. In the two Estonian sites, however, individuals earlier referred to as F. radicans are sexually and reproductively isolated from Baltic F. vesiculosus, revealing a separate lineage that may have diverged long before the formation of the Baltic Sea. Monitoring Baltic Fucus without considering this genetic complexity will fail to prioritise populations with adaptive potential to new climate conditions. From our genomic data, we can extract informative and diagnostic genetic markers that differentiate major genetic entities. Such a SNP panel will provide a straightforward tool for spatial and temporal monitoring and informing management decisions and actions.", "doi": "10.1111/mec.17699", "pmid": "39957665", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-07T07:26:56.214Z", "modified": "2025-11-07T07:26:56.376Z"}, {"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": "12fa1b73f76d40158b12fc385a35aa1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12fa1b73f76d40158b12fc385a35aa1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12fa1b73f76d40158b12fc385a35aa1f"}}, "title": "Methodological aspects of investigating the resistome in pig farm environments.", "authors": [{"family": "Ladyhina", "given": "Valeriia", "initials": "V"}, {"family": "Rajala", "given": "Elisabeth", "initials": "E"}, {"family": "Sternberg-Lewerin", "given": "Susanna", "initials": "S"}, {"family": "Nasirzadeh", "given": "Leila", "initials": "L"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Dicksved", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "J Microbiol Methods", "issn": "1872-8359", "issn-l": null, "volume": "230-231", "issue": null, "pages": "107103"}, "abstract": "A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.", "doi": "10.1016/j.mimet.2025.107103", "pmid": "39954816", "labels": {"Clinical Genomics Link\u00f6ping": "Collaborative", "Clinical Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0167-7012(25)00019-3"}], "notes": [], "created": "2025-03-18T07:11:00.806Z", "modified": "2025-09-08T07:13:09.538Z"}, {"entity": "publication", "iuid": "67fe70a7254545e7b2be4a509f5ff479", "links": {"self": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479.json"}, "display": {"href": "https://publications.scilifelab.se/publication/67fe70a7254545e7b2be4a509f5ff479"}}, "title": "Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning.", "authors": [{"family": "Mazzaferro", "given": "Eugenia", "initials": "E"}, {"family": "Mujica", "given": "Endrina", "initials": "E"}, {"family": "Zhang", "given": "Hanqing", "initials": "H"}, {"family": "Emmanouilidou", "given": "Anastasia", "initials": "A"}, {"family": "Jenseit", "given": "Anne", "initials": "A"}, {"family": "Evcimen", "given": "Bade", "initials": "B"}, {"family": "Metzendorf", "given": "Christoph", "initials": "C"}, {"family": "Dethlefsen", "given": "Olga", "initials": "O"}, {"family": "Loos", "given": "Ruth Jf", "initials": "RJ"}, {"family": "Vienberg", "given": "Sara Gry", "initials": "SG"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "den Hoed", "given": "Marcel", "initials": "M"}], "type": "journal article", "published": "2025-02-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "5408"}, "abstract": "Hundreds of loci have been robustly associated with obesity-related traits, but functional characterization of candidate genes remains a bottleneck. Aiming to systematically characterize candidate genes for a role in accumulation of lipids in adipocytes and other cardiometabolic traits, we developed a pipeline using CRISPR/Cas9, non-invasive, semi-automated fluorescence imaging and deep learning-based image analysis in live zebrafish larvae. Results from a dietary intervention show that 5 days of overfeeding is sufficient to increase the odds of lipid accumulation in adipocytes by 10 days post-fertilization (dpf, n = 275). However, subsequent experiments show that across 12 to 16 established obesity genes, 10 dpf is too early to detect an effect of CRISPR/Cas9-induced mutations on lipid accumulation in adipocytes (n = 1014), and effects on food intake at 8 dpf (n = 1127) are inconsistent with earlier results from mammals. Despite this, we observe effects of CRISPR/Cas9-induced mutations on ectopic accumulation of lipids in the vasculature (sh2b1 and sim1b) and liver (bdnf); as well as on body size (pcsk1, pomca, irs1); whole-body LDLc and/or total cholesterol content (irs2b and sh2b1); and pancreatic beta cell traits and/or glucose content (pcsk1, pomca, and sim1a). Taken together, our results illustrate that CRISPR/Cas9- and image-based experiments in zebrafish larvae can highlight direct effects of obesity genes on cardiometabolic traits, unconfounded by their - not yet apparent - effect on excess adiposity.", "doi": "10.1038/s41598-025-89823-2", "pmid": "39948378", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11825957"}, {"db": "pii", "key": "10.1038/s41598-025-89823-2"}], "notes": [], "created": "2025-09-08T11:37:27.351Z", "modified": "2025-11-28T10:47:20.122Z"}, {"entity": "publication", "iuid": "ab8fa0c345a2433995ebac47f3ad0b58", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab8fa0c345a2433995ebac47f3ad0b58.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab8fa0c345a2433995ebac47f3ad0b58"}}, "title": "Rare and common single nucleotide variants in childhood-onset systemic lupus erythematosus.", "authors": [{"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML", "orcid": "0000-0002-8454-1351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162e060954d420e825884f254886dcd.json"}}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}, {"family": " DISSECT Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-02-11", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "12", "issue": "1", "issn-l": "2053-8790"}, "abstract": "SLE is a systemic autoimmune disease with a large number of common risk gene variants, but several rare gene variants can cause monogenic SLE. The relationship between common and rare variants in SLE is unclear. We therefore investigated the occurrence of rare deleterious variants in patients with childhood-onset SLE (cSLE) and adult-onset SLE (aSLE) and compared the frequency of these variants with their individual SLE polygenic risk score (PRS).\n\nTargeted sequencing of 1832 gene regions, including coding regions of 31 genes associated with monogenic SLE, was performed in 958 patients with SLE and 1026 healthy individuals. A total of 116 patients with SLE had disease onset before the age of 18 (cSLE). An SLE common variant PRS was created from 37 SLE genome-wide association study single nucleotide variants (SNVs).\n\nRare coding deleterious SNVs (RD SNVs) were observed in 23 of the monogenic SLE-associated genes. Six per cent of patients with cSLE, compared with 3.2% of controls and 4.6% of patients with aSLE, carried rare deleterious alleles. In cSLE, RD SNVs were observed in the C1S, DDX58, IFIH1, IKZF1, RNASEH2A and C8A genes. A PRS analysis showed that patients with cSLE with any of these gene variants had a similar average PRS as control individuals.\n\nRD SNVs were observed in a small proportion of cSLE and carriers of these RD SNVs had a PRS similar to healthy individuals, suggesting the importance of rare coding heterozygous variants in driving disease risk in a subset of children with SLE.", "doi": "10.1136/lupus-2024-001436", "pmid": "39933823", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "12/1/e001436"}], "notes": [], "created": "2025-02-12T13:49:33.306Z", "modified": "2025-03-24T08:21:29.400Z"}, {"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": "ae26270a2c64410591f4cbb23c632b69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae26270a2c64410591f4cbb23c632b69"}}, "title": "In vivo regulation of the monocyte phenotype by Mycobacterium marinum and the ESX-1 type VII secretion system.", "authors": [{"family": "Munke", "given": "Kristina", "initials": "K"}, {"family": "Wulff", "given": "Line", "initials": "L"}, {"family": "Lienard", "given": "Julia", "initials": "J"}, {"family": "Carlsson", "given": "Fredric", "initials": "F"}, {"family": "Agace", "given": "William W", "initials": "WW"}], "type": "journal article", "published": "2025-02-07", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4545", "issn-l": "2045-2322"}, "abstract": "Pathogenic mycobacteria require the conserved ESX-1 type VII secretion system to cause disease. In a murine Mycobacterium marinum infection model we previously demonstrated that infiltrating monocytes and neutrophils represent the major bacteria-harbouring cell populations in infected tissue. In the current study we use this model, in combination with scRNA sequencing, to assess the impact of M. marinum infection on the transcriptional profile of infiltrating Ly6C\u207aMHCII\u207a monocytes in vivo. Our findings demonstrate that infection of infiltrating monocytes with M. marinum alters their cytokine expression profile, induces glycolytic metabolism, hypoxia-mediated signaling, nitric oxide synthesis, tissue remodeling, and suppresses responsiveness to IFN\u03b3. We further show that the transcriptional response of bystander monocytes is influenced by ESX-1-dependent mechanisms, including a reduced responsiveness to IFN\u03b3. These findings suggest that mycobacterial infection has pleiotropic effects on monocyte phenotype, with potential implications in bacterial growth restriction and granuloma formation.", "doi": "10.1038/s41598-025-88212-z", "pmid": "39915532", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11802795"}, {"db": "pii", "key": "10.1038/s41598-025-88212-z"}], "notes": [], "created": "2025-09-08T11:29:57.395Z", "modified": "2025-09-08T11:29:57.400Z"}, {"entity": "publication", "iuid": "05dfc96807f64f37a3917f85f1198b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/05dfc96807f64f37a3917f85f1198b7e"}}, "title": "Whole genome sequencing in early onset advanced heart failure.", "authors": [{"family": "Linn\u00e9r", "given": "Erik", "initials": "E", "orcid": "0009-0004-6961-8957", "researcher": {"href": "https://publications.scilifelab.se/researcher/666959db0ed3435ab374dcbd50cb9925.json"}}, {"family": "Czuba", "given": "Tomasz", "initials": "T"}, {"family": "Gidl\u00f6f", "given": "Olof", "initials": "O", "orcid": "0000-0002-7402-3139", "researcher": {"href": "https://publications.scilifelab.se/researcher/83f5453e507041b995e0d69a74540c24.json"}}, {"family": "Lundgren", "given": "Jakob", "initials": "J", "orcid": "0000-0001-9338-2906", "researcher": {"href": "https://publications.scilifelab.se/researcher/c929a6ea1c6f4975ad0ec84da3a32f5e.json"}}, {"family": "Bollano", "given": "Entela", "initials": "E", "orcid": "0000-0003-3341-2434", "researcher": {"href": "https://publications.scilifelab.se/researcher/f486393025c0406bbf6c397b7d1b6f05.json"}}, {"family": "Hellberg", "given": "Maria", "initials": "M"}, {"family": "Celik", "given": "Selvi", "initials": "S", "orcid": "0000-0001-7032-3444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da057ac725d4fb0bdbaddbc06a8ea64.json"}}, {"family": "Pimpalwar", "given": "Neha", "initials": "N"}, {"family": "Rentzsch", "given": "Philipp", "initials": "P", "orcid": "0000-0002-0413-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/372fb956b5634de493dd639dae9e8158.json"}}, {"family": "Martorella", "given": "Molly", "initials": "M", "orcid": "0000-0002-3306-6650", "researcher": {"href": "https://publications.scilifelab.se/researcher/64e0f833822b463b9736178d9a25c861.json"}}, {"family": "Gummesson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0024-960X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb164de27f2846328bb675876922a5fe.json"}}, {"family": "Melander", "given": "Olle", "initials": "O", "orcid": "0000-0002-2581-484X", "researcher": {"href": "https://publications.scilifelab.se/researcher/868a7e41aa054097a85575aa1d9658cc.json"}}, {"family": "Albinsson", "given": "Sebastian", "initials": "S", "orcid": "0000-0001-6936-3967", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac577769c2d44ac7bd8ccc28f69045de.json"}}, {"family": "Dellgren", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0003-4961-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d5ee559ab58458197bab1d119a50824.json"}}, {"family": "Bor\u00e9n", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e85f6d287ce4c60a7b35b287efb4f79.json"}}, {"family": "Jeppsson", "given": "Anders", "initials": "A", "orcid": "0000-0003-2356-2295", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec361c8c3f84b25a44213af77f4ac31.json"}}, {"family": "Lumbers", "given": "R Thomas", "initials": "RT", "orcid": "0000-0002-9077-4741", "researcher": {"href": "https://publications.scilifelab.se/researcher/a53e4d6591db481f881ec6046d54535b.json"}}, {"family": "Shah", "given": "Sonia", "initials": "S", "orcid": "0000-0001-5860-4526", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6a8568b3cae476199b27818eeb19e4d.json"}}, {"family": "Nilsson", "given": "Johan", "initials": "J", "orcid": "0000-0001-6860-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/c07e3381e15b4806b77d1b575e4ddca2.json"}}, {"family": "Natarajan", "given": "Pradeep", "initials": "P", "orcid": "0000-0001-8402-7435", "researcher": {"href": "https://publications.scilifelab.se/researcher/85de5f6926c94fbd96bbc9428b6a384f.json"}}, {"family": "Lappalainen", "given": "Tuuli", "initials": "T", "orcid": "0000-0002-7746-8109", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f81f8a2e6f4f11ad4504746492fc41.json"}}, {"family": "Levin", "given": "Malin", "initials": "M", "orcid": "0000-0003-1069-5275", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d251e6a73fb49bcbd930f7ec8bd274c.json"}}, {"family": "Ehrencrona", "given": "Hans", "initials": "H", "orcid": "0000-0002-5589-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b89608a8ce941c3b9911630b4ff9720.json"}}, {"family": "Smith", "given": "J Gustav", "initials": "JG", "orcid": "0000-0001-6285-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/26e50df6bb7f4194a52546dbd5652e84.json"}}], "type": "journal article", "published": "2025-02-05", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "15", "issue": "1", "pages": "4306", "issn-l": "2045-2322"}, "abstract": "The genetic contributions to early onset heart failure (HF) are incompletely understood. Genetic testing in advanced HF patients undergoing heart transplantation (HTx) may yield clinical benefits, but data is limited. We performed deep-coverage whole genome sequencing (WGS) in 102 Swedish HTx recipients. Gene lists were compiled through a systematic literature review. Variants were prioritized for pathogenicity and classified manually. We also compared polygenic HF risk scores to a population-based cohort. We found a pathogenic (LP/P) variant in 34 individuals (34%). Testing yield was highest in hypertrophic (63% LP/P carriers), dilated (40%) and arrhythmogenic right ventricular (33%) cardiomyopathy and lower in ischemic cardiomyopathy (10%). A family history was more common in LP/P variant carriers than in non-carriers but was present in less than half of carriers (44% vs 13%, P < 0.001), whereas age was similar. Polygenic risk scores were similar in HTx recipients and the population cohort. In conclusion, we observed a high prevalence of pathogenic cardiomyopathy gene variants in individuals with early-onset advanced HF, which could not accurately be ruled out by family history and age. In contrast, we did not observe higher polygenic risk scores in early onset advanced HF cases than in the general population.", "doi": "10.1038/s41598-025-88465-8", "pmid": "39910139", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11799378"}, {"db": "pii", "key": "10.1038/s41598-025-88465-8"}], "notes": [], "created": "2025-02-11T07:01:17.258Z", "modified": "2025-02-11T07:01:20.425Z"}, {"entity": "publication", "iuid": "874f1c17b7aa431f977a1f680546f059", "links": {"self": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059.json"}, "display": {"href": "https://publications.scilifelab.se/publication/874f1c17b7aa431f977a1f680546f059"}}, "title": "Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice.", "authors": [{"family": "Jin", "given": "Yunkai", "initials": "Y"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Hu", "given": "Jia", "initials": "J"}, {"family": "Sun", "given": "Kai", "initials": "K"}, {"family": "Xue", "given": "Lihong", "initials": "L"}, {"family": "Bettembourg", "given": "Mathilde", "initials": "M"}, {"family": "Bedada", "given": "Girma", "initials": "G"}, {"family": "Hou", "given": "Pengfu", "initials": "P"}, {"family": "Hao", "given": "Peiying", "initials": "P"}, {"family": "Tang", "given": "Jintian", "initials": "J"}, {"family": "Ye", "given": "Zihong", "initials": "Z"}, {"family": "Liu", "given": "Chunlin", "initials": "C"}, {"family": "Li", "given": "Peng", "initials": "P"}, {"family": "Pan", "given": "Aihu", "initials": "A"}, {"family": "Weng", "given": "Lushui", "initials": "L"}, {"family": "Xiao", "given": "Guoying", "initials": "G"}, {"family": "Moazzami", "given": "Ali A", "initials": "AA"}, {"family": "Yu", "given": "Xiaoping", "initials": "X"}, {"family": "Wu", "given": "Jun", "initials": "J"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Sun", "given": "Chuanxin", "initials": "C"}], "type": "journal article", "published": "2025-02-03", "journal": {"title": "Mol Plant", "issn": "1752-9867", "issn-l": "1674-2052", "volume": "18", "issue": "2", "pages": "333-349"}, "abstract": "Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.", "doi": "10.1016/j.molp.2025.01.008", "pmid": "39904305", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service"}, "xrefs": [{"db": "pii", "key": "S1674-2052(25)00029-2"}], "notes": [], "created": "2025-09-08T11:37:21.068Z", "modified": "2025-11-21T12:24:20.380Z"}, {"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": "5959d8a1ef54451098a8e6ac640e7442", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5959d8a1ef54451098a8e6ac640e7442.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5959d8a1ef54451098a8e6ac640e7442"}}, "title": "Unraveling the Genetics of Shared Clinical and Serological Manifestations in Patients With Systemic Inflammatory Autoimmune Diseases.", "authors": [{"family": "Bianchi", "given": "Matteo", "initials": "M", "orcid": "0000-0003-3394-6495", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645ef0e04a245f0ac9e7d7498b2bd69.json"}}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Notarnicola", "given": "Antonella", "initials": "A", "orcid": "0000-0003-0272-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/42411ecc60cd4357930ff0e978b3fcd8.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Enocsson", "given": "Helena", "initials": "H", "orcid": "0000-0002-2125-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/e34f7f45437c404da069fe0e83bf11f6.json"}}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Bucher", "given": "Sara Magnusson", "initials": "SM"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Andersson", "given": "Helena", "initials": "H"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Diederichsen", "given": "Louise Pyndt", "initials": "LP"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M", "orcid": "0000-0002-0915-7245", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8451e7f5e6e4e4da0bace3dfafaeb38.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE", "orcid": "0000-0002-6068-9212", "researcher": {"href": "https://publications.scilifelab.se/researcher/40f6c8e761a944b78e67f0e04453f78b.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "with the DISSECT consortium and the ImmunoArray consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "77", "issue": "2", "pages": "212-225", "issn-l": "2326-5191"}, "abstract": "Systemic inflammatory autoimmune diseases (SIADs) such as systemic lupus erythematosus (SLE), primary Sj\u00f6gren disease (pSS), and idiopathic inflammatory myopathies (myositis) are complex conditions characterized by shared circulating autoantibodies and clinical manifestations, including skin rashes, among others. This study was aimed at elucidating the genetics underlying these common features.\n\nWe performed targeted DNA sequencing of coding and regulatory regions from approximately 1,900 immune-related genes in a large cohort of 2,292 well-characterized Scandinavian patients with SIADs with SLE, pSS, and myositis as well as 1,252 controls. A gene-based functionally weighted genetic score for aggregate testing of all genetic variants, including rare variants, was complemented by in silico functional analyses and in vitro reporter experiments.\n\nCase-control association analysis detected known and potentially novel genetic loci in agreement with previous genetic and transcriptomics findings linked to the SIAD autoimmune background. Intriguingly, case-case comparisons between patient subgroups with and without specific autoantibodies revealed that the subgroups defined by antinuclear antibodies and anti-double-stranded DNA antibodies have unique genetic profiles reflecting their heterogeneity. When focusing on clinical features, we overall showed that dual-specificity phosphatase 1 (DUSP1) protective genetic variants lead to increased gene expression and potentially to anti-inflammatory effects on the SIAD-associated skin phenotype. This is consistent with recent genetic findings on eczema and with the previously reported down-regulation of the MAPK signaling-related gene DUSP1 in other skin disorders.\n\nTogether, this suggests common molecular mechanisms potentially underlying overlapping clinical manifestations shared among different disorders and informs clinical heterogeneity, which could be translated to improve disease diagnostic and treatment, also in more generalized disease frameworks.", "doi": "10.1002/art.42988", "pmid": "39284741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI SNP genotyping": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11782108"}], "notes": [], "created": "2024-11-12T11:40:11.189Z", "modified": "2025-09-08T06:50:36.661Z"}, {"entity": "publication", "iuid": "c8f5dbcb52864b11a987807b315f87ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8f5dbcb52864b11a987807b315f87ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8f5dbcb52864b11a987807b315f87ed"}}, "title": "RNA Sequencing Reveals the Long Non-Coding RNA Signature in Psoriasis Keratinocytes and Identifies CYDAER as a Long Non-Coding RNA Regulating Epidermal Differentiation.", "authors": [{"family": "Freisenhausen", "given": "Jan Cedric", "initials": "JC", "orcid": "0000-0002-3078-0365", "researcher": {"href": "https://publications.scilifelab.se/researcher/74f596e44f3d4dd78d499469c9f0b04e.json"}}, {"family": "Luo", "given": "Longlong", "initials": "L", "orcid": "0000-0002-5931-0666", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa6310dd902342b4a74bac1efd4090c0.json"}}, {"family": "Kelemen", "given": "Evelyn", "initials": "E", "orcid": "0000-0002-8357-790X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f1c75b553304176b8cafa84815421e8.json"}}, {"family": "Elton", "given": "Jonathan", "initials": "J", "orcid": "0000-0003-4919-8065", "researcher": {"href": "https://publications.scilifelab.se/researcher/22bf1246696541abafd2c2ad902a3b84.json"}}, {"family": "Skoog", "given": "Viktor", "initials": "V", "orcid": "0009-0005-8862-1534", "researcher": {"href": "https://publications.scilifelab.se/researcher/160d22c12c9743e193a47f6ded86b7ad.json"}}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E", "orcid": "0000-0002-4909-5413", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c1ce318445d4b2bb586ac1f8ed8ed87.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Exp. Dermatol.", "issn": "1600-0625", "volume": "34", "issue": "2", "pages": "e70054", "issn-l": "0906-6705"}, "abstract": "Psoriasis is a common chronic inflammatory skin disease determined by genetic and environmental factors, resulting in the activation of IL-23/IL-17-mediated immune response, epidermal hyperproliferation, and keratinocyte activation. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts > 500 nucleotides with diverse regulatory functions; their role in epidermal dysfunction in psoriasis is poorly understood. To identify epidermal transcripts with potential roles in psoriasis, including lncRNAs, we performed RNA sequencing on keratinocytes from psoriasis and healthy skin. We identified 889 differentially expressed lncRNAs, many of which with yet unknown functions. RP11-295G20.2 was identified as a lncRNA significantly induced in psoriasis keratinocytes, and this was verified by qRT-PCR and by single-molecule in situ hybridisation. Analysis of subcellular fractions of epidermis revealed a cytoplasmic localisation in line with results of single molecule in situ hybridisation. We report that RP11-295G20.2 has a skin-enriched expression, and within skin it is mainly expressed in suprabasal epidermal layers. Moreover, RP11-295G20.2 is induced by the key psoriasis cytokine IL-17A and shows a dynamic regulation during keratinocyte differentiation with upregulation during early differentiation and downregulation in the late stage. Knockdown of RP11-295G20.2 in keratinocytes promotes terminal differentiation. Based on our findings, we named RP11-295G20.2 Cytoplasmic Differentiation-Associated Epidermal RNA, CYDAER. In summary, our study provides a comprehensive characterisation of the non-coding RNA landscape of psoriasis keratinocytes and identifies CYDAER as a skin-enriched lncRNA regulating keratinocyte differentiation. Our data suggest that overexpression of CYDAER may contribute to altered differentiation in psoriatic epidermis.", "doi": "10.1111/exd.70054", "pmid": "39953783", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11829188"}], "notes": [], "created": "2025-09-08T06:52:12.448Z", "modified": "2025-09-08T06:52:13.267Z"}, {"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": "9458971190ee41e099e40121d1866819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819"}}, "title": "Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.", "authors": [{"family": "J\u00f6nsson", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0709-2828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4b2eb9eef5496eb27e76fc9fca120a.json"}}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Kugelberg", "given": "Unn", "initials": "U"}, {"family": "Skog", "given": "Signe", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Axel", "initials": "A"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Ofori", "given": "Jones K", "initials": "JK"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "\u00d6st", "given": "Anita", "initials": "A"}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Epigenomics", "issn": "1750-192X", "volume": "17", "issue": "2", "pages": "89-104", "issn-l": null}, "abstract": "Dietary factors may regulate the epigenome. We aimed to explore whether a diet intervention, including excess sugar, affects the methylome in human sperm, and to describe the sperm methylome. We used Whole Genome Bisulfite Sequencing (WGBS) to analyze DNA methylation in sperm taken at three time points from 15 males during a diet intervention; i) at baseline, ii) after one week on a standardized diet, and iii) after an additional week on a high-sugar diet providing 150% of their estimated total energy expenditure.\n\nWe identified seven nominal diet-associated differentially methylated regions in sperm (p < 0.05). The diet was nominally associated with methylation of 143 sites linked to fertility (e.g. AHRR, GNAS, and HDAC4), 313 sites in imprinted genes (e.g. GLIS3, PEG10, PEG3, and SNURF), and 42 sites in top 1%-expressed genes (e.g. CHD2) (p < 0.05). In sperm, 3'UTRs and introns had the highest levels of methylation, while 5'UTRs and CpG islands had the lowest levels. Non-expressed genes in human sperm were hypomethylated in exons compared with transcribed genes.\n\nIn human sperm, DNA methylation levels were linked to gene expression, and excess sugar had modest effects on methylation on imprinted and highly expressed genes, and genes affecting fertility.", "doi": "10.1080/17501911.2024.2439782", "pmid": "39707713", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-03T07:41:54.349Z", "modified": "2025-02-03T07:41:54.880Z"}, {"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": "b7086e5f716e435090388237fe0eaeb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7086e5f716e435090388237fe0eaeb5"}}, "title": "Lack of ST2 aggravates glioma invasiveness, vascular abnormality, and immune suppression.", "authors": [{"family": "Wicher", "given": "Grzegorz", "initials": "G"}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Vaccaro", "given": "Alessandra", "initials": "A"}, {"family": "Vemuri", "given": "Kalyani", "initials": "K"}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M"}, {"family": "Olofsson", "given": "Tommie", "initials": "T"}, {"family": "Imbria", "given": "Rebeca-Noemi", "initials": "RN"}, {"family": "Belting", "given": "Mattias", "initials": "M"}, {"family": "Nilsson", "given": "Gunnar", "initials": "G"}, {"family": "Dimberg", "given": "Anna", "initials": "A"}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}], "type": "journal article", "published": "2025-01-27", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "7", "issue": "1", "pages": "vdaf010", "issn-l": null}, "abstract": "Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, characterized by aggressive growth and a dismal prognosis. Interleukin-33 (IL-33) and its receptor ST2 have emerged as regulators of glioma growth, but their exact function in tumorigenesis has not been deciphered. Indeed, previous studies on IL-33 in cancer have yielded somewhat opposing results as to whether it is pro- or anti-tumorigenic.\n\nIL-33 expression was assessed in a GBM tissue microarray and public databases. As in vivo models we used orthotopic xenografts of patient-derived GBM cells, and syngenic models with grafted mouse glioma cells.\n\nWe analyzed the role of IL-33 and its receptor ST2 in nonmalignant cells of the glioma microenvironment and found that IL-33 levels are increased in cells surrounding the tumor. Protein complexes of IL-33 and ST2 are mainly found outside of the tumor core. The IL-33-producing cells consist primarily of oligodendrocytes. To determine the function of IL-33 in the tumor microenvironment, we used mice lacking the ST2 receptor. When glioma cells were grafted to ST2-deficient mouse brains, the resulting tumors exhibited a more invasive growth pattern, and are associated with poorer survival, compared to wild-type mice. Tumors in ST2-deficient hosts are more invasive, with increased expression of extracellular matrix remodeling enzymes and enhanced tumor angiogenesis. Furthermore, the absence of ST2 leads to a more immunosuppressive environment.\n\nOur findings reveal that glia-derived IL-33 and its receptor ST2 participate in modulating tumor invasiveness, tumor vasculature, and immunosuppression in glioma.", "doi": "10.1093/noajnl/vdaf010", "pmid": "39931535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11808570"}, {"db": "pii", "key": "vdaf010"}], "notes": [], "created": "2025-09-08T11:37:18.675Z", "modified": "2025-09-08T11:37:18.685Z"}, {"entity": "publication", "iuid": "694184d0fedc41c3ba78ea06f31e7668", "links": {"self": {"href": "https://publications.scilifelab.se/publication/694184d0fedc41c3ba78ea06f31e7668.json"}, "display": {"href": "https://publications.scilifelab.se/publication/694184d0fedc41c3ba78ea06f31e7668"}}, "title": "Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K"}, {"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Akula", "given": "Srinivas", "initials": "S"}, {"family": "Wernersson", "given": "Sara", "initials": "S", "orcid": "0000-0003-3067-7875", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d03168eb2f54a91897b5b738e2c5137.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}], "type": "journal article", "published": "2025-01-24", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "20", "issue": "1", "pages": "e0317343", "issn-l": "1932-6203"}, "abstract": "Single-cell RNA sequencing (scRNA-seq) is a valuable tool for investigating cellular heterogeneity in diseases such as equine asthma (EA). This study evaluates the HIVE\u2122 scRNA-seq method, a pico-well-based technology, for processing bronchoalveolar lavage (BAL) cells from horses with EA. The HIVE method offers practical advantages, including compatibility with both field and clinical settings, as well as a gentle workflow suited for handling sensitive cells. Our results show that the major cell types in equine BAL were successfully identified; however, the proportions of T cells and macrophages deviated from cytological expectations, with macrophages being overrepresented and T cells underrepresented. Despite these limitations, the HIVE method confirmed previously identified T cell and macrophage subpopulations and defined other BAL cell subsets. However, compared to previous studies T helper subsets were less clearly defined. Additionally, consistent with previous scRNA-seq studies, the HIVE method detected fewer granulocytes and mast cells than anticipated in the total BAL samples. Nevertheless, applying the method to purified mast cells recovered an expected number of cells. A small set of eosinophils were also detected which have not been characterized in earlier studies. In summary these findings suggest that while the HIVE method shows promise for certain applications, further optimization is needed to improve the accuracy of cell type representation, particularly for granulocytes and mast cells, in BAL samples.", "doi": "10.1371/journal.pone.0317343", "pmid": "39854349", "labels": {"NGI Short read": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11760581"}, {"db": "pii", "key": "PONE-D-24-13492"}], "notes": [], "created": "2025-05-12T05:47:24.783Z", "modified": "2025-11-14T11:09:01.384Z"}, {"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": "0729e1b65266450092168ec789fee122", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0729e1b65266450092168ec789fee122.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0729e1b65266450092168ec789fee122"}}, "title": "Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest.", "authors": [{"family": "Burc", "given": "Estelle", "initials": "E"}, {"family": "Girard-Tercieux", "given": "Camille", "initials": "C"}, {"family": "Metz", "given": "Moa", "initials": "M"}, {"family": "Cazaux", "given": "Elise", "initials": "E"}, {"family": "Baur", "given": "Julian", "initials": "J", "orcid": "0000-0002-4739-2756", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e69e394b67145188a77f90365f3fe15.json"}}, {"family": "Koppik", "given": "Mareike", "initials": "M"}, {"family": "R\u00eago", "given": "Alexandre", "initials": "A"}, {"family": "Hart", "given": "Alex F", "initials": "AF"}, {"family": "Berger", "given": "David", "initials": "D", "orcid": "0000-0003-0196-6109", "researcher": {"href": "https://publications.scilifelab.se/researcher/c788f99e9df4435587f7e991eae4311e.json"}}], "type": "journal article", "published": "2025-01-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "827", "issn-l": "2041-1723"}, "abstract": "Climate change is affecting population growth rates of ectothermic pests with potentially dire consequences for agriculture and global food security. However, current projection models of pest impact typically overlook the potential for rapid genetic adaptation, making current forecasts uncertain. Here, we predict how climate change adaptation in life-history traits of insect pests affects their growth rates and impact on agricultural yields by unifying thermodynamics with classic theory on resource acquisition and allocation trade-offs between foraging, reproduction, and maintenance. Our model predicts that warming temperatures will favour resource allocation towards maintenance coupled with increased resource acquisition through larval foraging, and the evolution of this life-history strategy results in both increased population growth rates and per capita host consumption, causing a double-blow on agricultural yields. We find support for these predictions by studying thermal adaptation in life-history traits and gene expression in the wide-spread insect pest, Callosobruchus maculatus; with 5 years of evolution under experimental warming causing an almost two-fold increase in its predicted agricultural footprint. These results show that pest adaptation can offset current projections of agricultural impact and emphasize the need for integrating a mechanistic understanding of life-history evolution into forecasts of pest impact under climate change.", "doi": "10.1038/s41467-025-56177-2", "pmid": "39827176", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11743133"}, {"db": "pii", "key": "10.1038/s41467-025-56177-2"}], "notes": [], "created": "2025-09-08T11:37:34.656Z", "modified": "2025-09-08T11:37:34.821Z"}, {"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": "fd23b37917bf4c6f8b0bb095abb3235d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd23b37917bf4c6f8b0bb095abb3235d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd23b37917bf4c6f8b0bb095abb3235d"}}, "title": "The type of environment has a greater impact on the larval microbiota of Anopheles arabiensis than on the microbiota of their breeding water.", "authors": [{"family": "Assentato", "given": "Lorenzo", "initials": "L", "orcid": "0000-0003-3699-0483", "researcher": {"href": "https://publications.scilifelab.se/researcher/69a8069f62434b128fb5837b139dbb56.json"}}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "Brunius", "given": "Carl", "initials": "C", "orcid": "0000-0003-3957-870X", "researcher": {"href": "https://publications.scilifelab.se/researcher/560a5d14ee83421680058b00df2ac9e2.json"}}, {"family": "Feltelius", "given": "Vilhelm", "initials": "V"}, {"family": "Elleby", "given": "Rasmus", "initials": "R"}, {"family": "Hopkins", "given": "Richard J", "initials": "RJ"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2025-01-07", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "101", "issue": "1", "issn-l": "0168-6496"}, "abstract": "Mosquito larvae of the genus Anopheles develop entirely in water, frequently visiting the surface for air. The aquatic environment plays a key role in shaping their microbiota, but the connection between environmental characteristics of breeding sites and larval microbiota remains underexplored. This study focuses on Anopheles arabiensis, which inhabits the surface microlayer (SML) of breeding sites, a zone with high particle density. We hypothesized that the SML could allow us to capture the diversity of the surrounding environment, and in turn its influence on the larval microbial communities. To test this, we collected A. arabiensis larvae and SML samples from various breeding sites categorized by environmental features. Our results confirm that breeding site characteristics are significant drivers of the bacterial species present in mosquito larvae. Additionally, we found that the larval micro-environment selectively shapes its microbiota, highlighting a dynamic interplay between environmental and internal factors. Interestingly, specific bacterial families were associated with the presence or absence of larvae in breeding sites, suggesting potential ecological roles. These findings expand our understanding of vector-mosquito microbiota, emphasizing the importance of breeding site features in shaping larval microbial communities and providing a foundation for future research on mosquito ecology and control strategies.", "doi": "10.1093/femsec/fiae161", "pmid": "39694819", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11737318"}, {"db": "pii", "key": "7928135"}], "notes": [], "created": "2025-09-08T11:37:32.415Z", "modified": "2025-09-08T11:37:32.533Z"}, {"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": "36465c1e65bd499d940371185242fb06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36465c1e65bd499d940371185242fb06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36465c1e65bd499d940371185242fb06"}}, "title": "Hydrological regime of a continental river system predicts bacterial macroecological patterns.", "authors": [{"family": "Demeter", "given": "Katalin", "initials": "K", "orcid": "0000-0002-4260-3630", "researcher": {"href": "https://publications.scilifelab.se/researcher/5df5f47af9c9454bbf13ea30dfef4df3.json"}}, {"family": "Savio", "given": "Domenico", "initials": "D", "orcid": "0000-0001-5322-9536", "researcher": {"href": "https://publications.scilifelab.se/researcher/66c6378c7ebf41cca7c709a88fcf27c2.json"}}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AKT", "orcid": "0000-0002-9797-3073", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb459d6e22e4c39983578abae121f74.json"}}, {"family": "Reischer", "given": "Georg H", "initials": "GH", "orcid": "0000-0002-3962-8685", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1d9145cd724db1803aae7a6ff3319a.json"}}, {"family": "Kolarevic", "given": "Stoimir", "initials": "S"}, {"family": "Parajka", "given": "Juraj", "initials": "J", "orcid": "0000-0002-1177-5181", "researcher": {"href": "https://publications.scilifelab.se/researcher/2698181b5e734debaeb74650004ed055.json"}}, {"family": "Derx", "given": "Julia", "initials": "J", "orcid": "0000-0002-9931-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6845bf4cbe784c41b4efe52b87b887c1.json"}}, {"family": "Jakwerth", "given": "Stefan", "initials": "S"}, {"family": "Wurzbacher", "given": "Christian", "initials": "C", "orcid": "0000-0001-7418-0831", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fed784d185749498b07f7458c9ccfb6.json"}}, {"family": "Blaschke", "given": "Alfred P", "initials": "AP", "orcid": "0000-0001-8617-5802", "researcher": {"href": "https://publications.scilifelab.se/researcher/aa8d81f7cfcc4a82acce9690a4d6cffc.json"}}, {"family": "Mach", "given": "Robert L", "initials": "RL", "orcid": "0000-0003-2375-7244", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a53d6c16f2f4e978764b982ba485e97.json"}}, {"family": "Bl\u00f6schl", "given": "G\u00fcnter", "initials": "G", "orcid": "0000-0003-2227-8225", "researcher": {"href": "https://publications.scilifelab.se/researcher/8791191bfcb041d28768a3cda7206d16.json"}}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH", "orcid": "0000-0002-0542-5425", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f1019fab4eb42a8896e3aa2c2cced44.json"}}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "19", "issue": "1", "issn-l": "1751-7362"}, "abstract": "Modeling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S ribosomal RNA (rRNA) gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6000-21 000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged from 0.92 to 0.96 along the river, indicating an almost complete replacement of phylotypes with 2%-11% of headwater-associated amplicon sequence variants (ASVs) persisting under base-flow conditions. Richness declined gradually downstream at a rate of ~0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.", "doi": "10.1093/ismejo/wrag013", "pmid": "41626752", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "8454621"}, {"db": "pmc", "key": "PMC12927878"}], "notes": [], "created": "2026-02-24T19:07:12.652Z", "modified": "2026-02-24T19:07:14.084Z"}, {"entity": "publication", "iuid": "c42cf07b07844cabbe0ad109571234eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c42cf07b07844cabbe0ad109571234eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c42cf07b07844cabbe0ad109571234eb"}}, "title": "Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.", "authors": [{"family": "Jeevannavar", "given": "Aditya", "initials": "A"}, {"family": "Florenza", "given": "Javier", "initials": "J"}, {"family": "Divne", "given": "Anna-Maria", "initials": "A"}, {"family": "Tamminen", "given": "Manu", "initials": "M"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2025-01-02", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "19", "issue": "1", "pages": null}, "abstract": "Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.", "doi": "10.1093/ismejo/wraf046", "pmid": "40057978", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Single cell": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11973420"}, {"db": "pii", "key": "8064733"}], "notes": [], "created": "2025-09-08T06:54:54.550Z", "modified": "2025-11-21T14:35:21.491Z"}, {"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": "14530d7aa2004964a747e0dc46f3c5aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14530d7aa2004964a747e0dc46f3c5aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14530d7aa2004964a747e0dc46f3c5aa"}}, "title": "Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.", "authors": [{"family": "Kula\u0161", "given": "Antonija", "initials": "A", "orcid": "0000-0003-0619-4697", "researcher": {"href": "https://publications.scilifelab.se/researcher/08acba03d1b445a7b4d0571c287b723b.json"}}, {"family": "Lemonnier", "given": "Clarisse", "initials": "C"}, {"family": "Alric", "given": "Benjamin", "initials": "B"}, {"family": "Kahlert", "given": "Maria", "initials": "M"}, {"family": "Trobajo", "given": "Rosa", "initials": "R"}, {"family": "Udovi\u010d", "given": "Marija Gligora", "initials": "MG"}, {"family": "Rimet", "given": "Fr\u00e9d\u00e9ric", "initials": "F"}], "type": "journal article", "published": "2025-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "5", "issue": "1", "pages": "ycaf171", "issn-l": null}, "abstract": "Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.", "doi": "10.1093/ismeco/ycaf171", "pmid": "41104113", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12527276"}, {"db": "pii", "key": "ycaf171"}], "notes": [], "created": "2025-11-18T15:39:43.663Z", "modified": "2025-11-18T15:39:43.810Z"}, {"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": "94ab6b3617474bc092224f924b8f0d46", "links": {"self": {"href": "https://publications.scilifelab.se/publication/94ab6b3617474bc092224f924b8f0d46.json"}, "display": {"href": "https://publications.scilifelab.se/publication/94ab6b3617474bc092224f924b8f0d46"}}, "title": "The evolutionary history of metastatic pancreatic neuroendocrine tumours reveals a therapy driven route to high-grade transformation.", "authors": [{"family": "Backman", "given": "Samuel", "initials": "S"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Nord", "given": "Helena", "initials": "H", "orcid": "0000-0002-6098-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/22d8cc445c6b41b4a8488d620995d8c3.json"}}, {"family": "Ghosal", "given": "Suman", "initials": "S"}, {"family": "St\u00e5lberg", "given": "Peter", "initials": "P"}, {"family": "Juhlin", "given": "C Christofer", "initials": "CC", "orcid": "0000-0002-5945-9081", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb660e24421749d4acaaf6e9a90042f8.json"}}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1211-9821", "researcher": {"href": "https://publications.scilifelab.se/researcher/046904cd12eb4764bd2dcadc876f65d7.json"}}, {"family": "Sundin", "given": "Anders", "initials": "A", "orcid": "0000-0001-6615-2419", "researcher": {"href": "https://publications.scilifelab.se/researcher/b03a78e59f0845c5b68b372f2709dbf0.json"}}, {"family": "Zhang", "given": "Liang", "initials": "L"}, {"family": "Moens", "given": "Lotte", "initials": "L", "orcid": "0000-0002-5347-6526", "researcher": {"href": "https://publications.scilifelab.se/researcher/577b0c2d09e349d89ef8ae73efd8c5f7.json"}}, {"family": "Eriksson", "given": "Barbro", "initials": "B"}, {"family": "Welin", "given": "Staffan", "initials": "S"}, {"family": "Hellman", "given": "Per", "initials": "P"}, {"family": "Skogseid", "given": "Britt", "initials": "B"}, {"family": "Pacak", "given": "Karel", "initials": "K"}, {"family": "Mollazadegan", "given": "Kazhan", "initials": "K"}, {"family": "\u00c5kerstr\u00f6m", "given": "Tobias", "initials": "T"}, {"family": "Crona", "given": "Joakim", "initials": "J", "orcid": "0000-0003-0677-4894", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c601868a0c14b13a01b2868a4fb690e.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "J. Pathol.", "issn": "1096-9896", "volume": "264", "issue": "4", "pages": "357-370", "issn-l": "0022-3417"}, "abstract": "Tumour evolution with acquisition of more aggressive disease characteristics is a hallmark of disseminated cancer. Metastatic pancreatic neuroendocrine tumours (PanNETs) in particular may progress from a low/intermediate to a high-grade disease. The aim of this work was to understand the molecular mechanisms underlying metastatic progression as well as PanNET transformation from a low/intermediate to a high-grade disease. We performed multi-omics analysis (genome/exome sequencing, total RNA-sequencing and methylation array) of 32 longitudinal samples from six patients with metastatic low/intermediate grade PanNET. The clonal composition of tumour lesions and underlying phylogeny of each patient were determined with bioinformatics analyses. Findings were validated in post-alkylating chemotherapy samples from 24 patients with PanNET using targeted next generation sequencing. We validate the current PanNET evolutionary model with MEN1 inactivation that occurs very early in tumourigenesis. This was followed by pronounced genetic diversity on both spatial and temporal levels, with parallel and convergent tumour evolution involving the ATRX/DAXX and mechanistic target of the rapamycin (mTOR) pathways. Following alkylating chemotherapy treatment, some PanNETs developed mismatch repair deficiency and acquired a hypermutational phenotype. This was validated among 16 patients with PanNET who had high-grade progression after alkylating chemotherapy, of whom eight had a tumour mutational burden >50 (50%). In comparison, among the eight patients who did not show high-grade progression, 0 had a tumour mutational burden >50 (0%; odds ratio 'infinite', 95% confidence interval 1.8 to 'infinite', p = 0.02). Our findings contribute to broaden the understanding of metastatic/high-grade PanNETs and suggests that therapy driven disease evolution is an important hallmark of this disease. \u00a9 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.", "doi": "10.1002/path.6348", "pmid": "39360347", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Short read": "Service", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2024-11-12T11:41:11.475Z", "modified": "2025-04-07T07:28:57.040Z"}, {"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": "281525954deb43569a3aeab075748d9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/281525954deb43569a3aeab075748d9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/281525954deb43569a3aeab075748d9c"}}, "title": "Genomics of severe and treatment-resistant obsessive-compulsive disorder treated with deep brain stimulation: A preliminary investigation.", "authors": [{"family": "Chen", "given": "Long Long", "initials": "LL"}, {"family": "Naesstr\u00f6m", "given": "Matilda", "initials": "M"}, {"family": "Halvorsen", "given": "Matthew", "initials": "M"}, {"family": "Fytagoridis", "given": "Anders", "initials": "A"}, {"family": "Crowley", "given": "Stephanie B", "initials": "SB"}, {"family": "Mataix-Cols", "given": "David", "initials": "D"}, {"family": "R\u00fcck", "given": "Christian", "initials": "C"}, {"family": "Crowley", "given": "James J", "initials": "JJ", "orcid": "0000-0001-9051-1557", "researcher": {"href": "https://publications.scilifelab.se/researcher/14ecad66262b47dcadebcc8c7e759024.json"}}, {"family": "Pascal", "given": "Diana", "initials": "D"}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn": "1552-485X", "issn-l": "1552-4841", "volume": "195", "issue": "8", "pages": "e32983"}, "abstract": "Individuals with severe and treatment-resistant obsessive-compulsive disorder (trOCD) represent a small but severely disabled group of patients. Since trOCD cases eligible for deep brain stimulation (DBS) probably comprise the most severe end of the OCD spectrum, we hypothesize that they may be more likely to have a strong genetic contribution to their disorder. Therefore, while the worldwide population of DBS-treated cases may be small (~300), screening these individuals with modern genomic methods may accelerate gene discovery in OCD. As such, we have begun to collect DNA from trOCD cases who qualify for DBS, and here we report results from whole exome sequencing and microarray genotyping of our first five cases. All participants had previously received DBS in the bed nucleus of stria terminalis (BNST), with two patients responding to the surgery and one showing a partial response. Our analyses focused on gene-disruptive rare variants (GDRVs; rare, predicted-deleterious single-nucleotide variants or copy number variants overlapping protein-coding genes). Three of the five cases carried a GDRV, including a missense variant in the ion transporter domain of KCNB1, a deletion at 15q11.2, and a duplication at 15q26.1. The KCNB1 variant (hg19 chr20-47991077-C-T, NM_004975.3:c.1020G>A, p.Met340Ile) causes substitution of methionine for isoleucine in the trans-membrane region of neuronal potassium voltage-gated ion channel KV2.1. This KCNB1 substitution (Met340Ile) is located in a highly constrained region of the protein where other rare missense variants have previously been associated with neurodevelopmental disorders. The patient carrying the Met340Ile variant responded to DBS, which suggests that genetic factors could potentially be predictors of treatment response in DBS for OCD. In sum, we have established a protocol for recruiting and genomically characterizing trOCD cases. Preliminary results suggest that this will be an informative strategy for finding risk genes in OCD.", "doi": "10.1002/ajmg.b.32983", "pmid": "38650085", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1984060"}, {"db": "pmc", "key": "PMC11493841"}], "notes": "Pre-print available:\r\nDOI: 10.1101/2023.04.15.23288623", "created": "2024-11-12T10:39:23.334Z", "modified": "2024-11-19T10:09:44.036Z"}, {"entity": "publication", "iuid": "ba82c88779c94bd8ae035c075c26214b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba82c88779c94bd8ae035c075c26214b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba82c88779c94bd8ae035c075c26214b"}}, "title": "Genomic signals of adaptation to a natural CO2 gradient over a striking microgeographic scale", "authors": [{"family": "Gonz\u00e1lez-Delgado", "given": "Sara", "initials": "S"}, {"family": "P\u00e9rez-Portela", "given": "Roc\u00edo", "initials": "R"}, {"family": "Ortega-Mart\u00ednez", "given": "Olga", "initials": "O", "orcid": "0000-0003-2734-6434", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc84f54ca2cc49bc869cd23adeffc7ac.json"}}, {"family": "Alfonso", "given": "Beatriz", "initials": "B"}, {"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Hern\u00e1ndez", "given": "Jos\u00e9 Carlos", "initials": "JC"}], "type": "journal-article", "published": "2024-12-00", "journal": {"title": "Marine Pollution Bulletin", "issn": "0025-326X", "volume": "209", "pages": "117225", "issn-l": null}, "abstract": null, "doi": "10.1016/j.marpolbul.2024.117225", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:38:54.128Z", "modified": "2025-04-07T07:31:21.426Z"}, {"entity": "publication", "iuid": "b63ebec5607f49219d63cb4bcce20f95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b63ebec5607f49219d63cb4bcce20f95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b63ebec5607f49219d63cb4bcce20f95"}}, "title": "Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations", "authors": [{"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Hagen", "given": "\u00d8rjan", "initials": "\u00d8"}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Janhunen", "given": "Matti", "initials": "M"}, {"family": "Kause", "given": "Antti", "initials": "A"}], "type": "journal-article", "published": "2024-12-00", "journal": {"title": "Aquaculture Reports", "issn": "2352-5134", "volume": "39", "pages": "102495", "issn-l": "2352-5134"}, "abstract": null, "doi": "10.1016/j.aqrep.2024.102495", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:39:01.587Z", "modified": "2025-12-04T19:36:52.855Z"}, {"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": "3b78200d104a464e92c79279e034bb9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b78200d104a464e92c79279e034bb9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b78200d104a464e92c79279e034bb9f"}}, "title": "Perfluorooctanesulfonic acid (PFOS) induced cancer related DNA methylation alterations in human breast cells: A whole genome methylome study.", "authors": [{"family": "Pierozan", "given": "Paula", "initials": "P"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Theodoropoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Karlsson", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2024-11-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "949", "pages": "174864", "issn-l": "0048-9697"}, "abstract": "DNA methylation plays a pivotal role in cancer. The ubiquitous contaminant perfluorooctanesulfonic acid (PFOS) has been epidemiologically associated with breast cancer, and can induce proliferation and malignant transformation of normal human breast epithelial cells (MCF-10A), but the information about its effect on DNA methylation is sparse. The aim of this study was to characterize the whole-genome methylome effects of PFOS in our breast cell model and compare the findings with previously demonstrated DNA methylation alterations in breast tumor tissues. The DNA methylation profile was assessed at single CpG resolution in MCF-10A cells treated with 1 \u03bcM PFOS for 72 h by using Enzymatic Methyl sequencing (EM-seq). We found 12,591 differentially methylated CpG-sites and 13,360 differentially methylated 100 bp tiles in the PFOS exposed breast cells. These differentially methylated regions (DMRs) overlapped with 2406 genes of which 494 were long non-coding RNA and 1841 protein coding genes. We identified 339 affected genes that have been shown to display altered DNA methylation in breast cancer tissue and several other genes related to cancer development. This includes hypermethylation of GACAT3, DELEC1, CASC2, LCIIAR, MUC16, SYNE1 and hypomethylation of TTN and KMT2C. DMRs were also found in estrogen receptor genes (ESR1, ESR2, ESRRG, ESRRB, GREB1) and estrogen responsive genes (GPER1, EEIG1, RERG). The gene ontology analysis revealed pathways related to cancer phenotypes such as cell adhesion and growth. These findings improve the understanding of PFOS's potential role in breast cancer and illustrate the value of whole-genome methylome analysis in uncovering mechanisms of chemical effects, identifying biomarker candidates, and strengthening epidemiological associations, potentially impacting risk assessment.", "doi": "10.1016/j.scitotenv.2024.174864", "pmid": "39032741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(24)05013-7"}], "notes": [], "created": "2024-10-21T11:15:52.243Z", "modified": "2025-02-28T14:12:59.071Z"}, {"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": "ff82f6f4bfb34c93a66ea6b5c6e6a9f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ff82f6f4bfb34c93a66ea6b5c6e6a9f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ff82f6f4bfb34c93a66ea6b5c6e6a9f0"}}, "title": "The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia.", "authors": [{"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Oder", "given": "Bla\u017e", "initials": "B", "orcid": "0000-0001-7984-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9851f9fc65fc44aea55d0c1567be7887.json"}}, {"family": "Cortese", "given": "Diego", "initials": "D"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Binzer-Panchal", "given": "Amrei", "initials": "A", "orcid": "0000-0002-0472-0609", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b6fe18ad8f8495a97d9322cac3201da.json"}}, {"family": "\u00d6sterholm", "given": "Cecilia", "initials": "C"}, {"family": "Del Peso Santos", "given": "Teresa", "initials": "T"}, {"family": "Rabbani", "given": "Leily", "initials": "L"}, {"family": "Asl", "given": "Hassan Foroughi", "initials": "HF"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Lundholm", "given": "August", "initials": "A"}, {"family": "Koutroumani", "given": "Maria", "initials": "M"}, {"family": "Haider", "given": "Zahra", "initials": "Z"}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Mollstedt", "given": "John", "initials": "J"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Plevova", "given": "Karla", "initials": "K"}, {"family": "Agathangelidis", "given": "Andreas", "initials": "A", "orcid": "0000-0002-8467-7945", "researcher": {"href": "https://publications.scilifelab.se/researcher/79eb64984ac1494094f8c632b18bc793.json"}}, {"family": "Scarf\u00f2", "given": "Lydia", "initials": "L", "orcid": "0000-0002-0844-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/47c4c336efb24d86b41c872d03836c78.json"}}, {"family": "Armand", "given": "Marine", "initials": "M", "orcid": "0000-0001-8906-3128", "researcher": {"href": "https://publications.scilifelab.se/researcher/8d2e8c325db8415cb723a9718d49ae78.json"}}, {"family": "Muggen", "given": "Alice F", "initials": "AF"}, {"family": "Kay", "given": "Neil E", "initials": "NE", "orcid": "0000-0002-5951-5055", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef074d0fdb0b4070b5216be063317bf8.json"}}, {"family": "Shanafelt", "given": "Tait", "initials": "T"}, {"family": "Rossi", "given": "Davide", "initials": "D"}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4e49a93b0143db88059c4d1e9fdc59.json"}}, {"family": "Pospisilova", "given": "Sarka", "initials": "S", "orcid": "0000-0001-7136-2680", "researcher": {"href": "https://publications.scilifelab.se/researcher/241cf7f1344c4016b40dfcf439c0b43d.json"}}, {"family": "Barylyuk", "given": "Konstantin", "initials": "K", "orcid": "0000-0002-3580-0345", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5db39fce380438e82060c586e230ee6.json"}}, {"family": "Davi", "given": "Frederic", "initials": "F"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Langerak", "given": "Anton W", "initials": "AW", "orcid": "0000-0002-2078-3220", "researcher": {"href": "https://publications.scilifelab.se/researcher/769a5b06013b43d6af8d3e13804cd50c.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Ghia", "given": "Paolo", "initials": "P", "orcid": "0000-0003-3750-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f24783739d44c7b73a1be28c344a35.json"}}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}, {"family": "Sutton", "given": "Lesley-Ann", "initials": "LA"}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications.scilifelab.se/researcher/b570128e641140fb964ae3241414f510.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "38", "issue": "11", "pages": "2429-2442", "issn-l": "0887-6924"}, "abstract": "SF3B1 mutations are recurrent in chronic lymphocytic leukemia (CLL), particularly enriched in clinically aggressive stereotyped subset #2. To investigate their impact, we conducted RNA-sequencing of 18 SF3B1MUT and 17 SF3B1WT subset #2 cases and identified 80 significant alternative splicing events (ASEs). Notable ASEs concerned exon inclusion in the non-canonical BAF (ncBAF) chromatin remodeling complex subunit, BRD9, and splice variants in eight additional ncBAF complex interactors. Long-read RNA-sequencing confirmed the presence of splice variants, and extended analysis of 139 CLL cases corroborated their association with SF3B1 mutations. Overexpression of SF3B1K700E induced exon inclusion in BRD9, resulting in a novel splice isoform with an alternative C-terminus. Protein interactome analysis of the BRD9 splice isoform revealed augmented ncBAF complex interaction, while exhibiting decreased binding of auxiliary proteins, including SPEN, BRCA2, and CHD9. Additionally, integrative multi-omics analysis identified a ncBAF complex-bound gene quartet on chromosome 1 with higher expression levels and more accessible chromatin in SF3B1MUT CLL. Finally, Cancer Dependency Map analysis and BRD9 inhibition displayed BRD9 dependency and sensitivity in cell lines and primary CLL cells. In conclusion, spliceosome dysregulation caused by SF3B1 mutations leads to multiple ASEs and an altered ncBAF complex interactome, highlighting a novel pathobiological mechanism in SF3B1MUT CLL.", "doi": "10.1038/s41375-024-02379-4", "pmid": "39261602", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11518989"}, {"db": "pii", "key": "10.1038/s41375-024-02379-4"}], "notes": [], "created": "2024-11-12T10:55:28.718Z", "modified": "2025-02-28T14:13:56.146Z"}, {"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": "63f6cd69ef3c4f43981d68e75f2d426a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63f6cd69ef3c4f43981d68e75f2d426a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63f6cd69ef3c4f43981d68e75f2d426a"}}, "title": "Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.", "authors": [{"family": "Vera-Ponce de Le\u00f3n", "given": "Arturo", "initials": "A", "orcid": "0000-0003-4085-5700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd53e0d4a23147acbf207767ed5f930f.json"}}, {"family": "Hensen", "given": "Tim", "initials": "T"}, {"family": "Hoetzinger", "given": "Matthias", "initials": "M"}, {"family": "Gupta", "given": "Shashank", "initials": "S"}, {"family": "Weston", "given": "Bronson", "initials": "B"}, {"family": "Johnsen", "given": "Sander M", "initials": "SM"}, {"family": "Rasmussen", "given": "Jacob A", "initials": "JA", "orcid": "0000-0002-7710-8912", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce676b0101c645e086c4144f309616f0.json"}}, {"family": "Clausen", "given": "Cecilie Gr\u00f8nlund", "initials": "CG"}, {"family": "Pless", "given": "Louisa", "initials": "L"}, {"family": "Ver\u00edssimo", "given": "Ana Raquel Andrade", "initials": "ARA"}, {"family": "Rudi", "given": "Knut", "initials": "K"}, {"family": "Snipen", "given": "Lars", "initials": "L"}, {"family": "Karlsen", "given": "Christian Ren\u00e9", "initials": "CR"}, {"family": "Limborg", "given": "Morten T", "initials": "MT", "orcid": "0000-0002-7718-6531", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccc405b9a4d44155b2d36b0cb7cf05ce.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Thiele", "given": "Ines", "initials": "I"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR", "orcid": "0000-0001-6097-2539", "researcher": {"href": "https://publications.scilifelab.se/researcher/987fbb5763c74f6895bee64630528d8d.json"}}, {"family": "Sandve", "given": "Simen R", "initials": "SR"}, {"family": "Pope", "given": "Phillip B", "initials": "PB", "orcid": "0000-0002-2067-4059", "researcher": {"href": "https://publications.scilifelab.se/researcher/606fbc0320664a1890b7b6ad0b5f0d68.json"}}, {"family": "La Rosa", "given": "Sabina Leanti", "initials": "SL", "orcid": "0000-0003-3527-8101", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b9163383f4c437495b90bd8f2fb72df.json"}}], "type": "journal article", "published": "2024-11-00", "journal": {"title": "Nat Microbiol", "issn": "2058-5276", "volume": "9", "issue": "11", "pages": "3059-3074", "issn-l": "2058-5276"}, "abstract": "To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.", "doi": "10.1038/s41564-024-01830-7", "pmid": "39402236", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41564-024-01830-7"}], "notes": [], "created": "2024-11-12T10:39:11.102Z", "modified": "2025-02-28T14:15:24.513Z"}, {"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": "a2fdff49e57d4d3b943d89f689136860", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2fdff49e57d4d3b943d89f689136860.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2fdff49e57d4d3b943d89f689136860"}}, "title": "Characterization of Pediatric Acute Myeloid Leukemia With t(7;12)(q36;p13)", "authors": [{"family": "\u00d6stlund", "given": "Anders", "initials": "A"}, {"family": "Waraky", "given": "Ahmed", "initials": "A"}, {"family": "Staffas", "given": "Anna", "initials": "A"}, {"family": "Sj\u00f6gren", "given": "Helene", "initials": "H", "orcid": "0000-0003-2592-1239", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cb19c7d5b8c4611ae0ba909897603ca.json"}}, {"family": "De\u00a0Moerloose", "given": "Barbara", "initials": "B"}, {"family": "Arad\u2010Cohen", "given": "Nira", "initials": "N"}, {"family": "Cheuk", "given": "Daniel", "initials": "D"}, {"family": "Navarro", "given": "Jose Maria Fernandez", "initials": "JMF"}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K", "orcid": "0000-0001-9296-2028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec8cc2ae60a245e4807ce50c05273ded.json"}}, {"family": "Kaspers", "given": "Gertjan J L", "initials": "GJL"}, {"family": "Kovalova", "given": "Zhanna", "initials": "Z"}, {"family": "Pasauliene", "given": "Ramune", "initials": "R"}, {"family": "Saks", "given": "Kadri", "initials": "K"}, {"family": "Zeller", "given": "Bernward", "initials": "B"}, {"family": "Nor\u00e9n\u2010Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Hasle", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3976-9231", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bd29fb163f9461d92b50157101bf384.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Palmqvist", "given": "Lars", "initials": "L", "orcid": "0000-0001-9274-360X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e50c0057dcb47f39e085b16580806c2.json"}}], "type": "journal-article", "published": "2024-11-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1045-2257", "volume": "63", "issue": "11", "pages": "e70003", "issn-l": null}, "abstract": "Acute myeloid leukemia (AML) with t(7;12)(q36;p13) is a recurrent translocation in AML in infants or very young children and was recently included in the World Health Organization (WHO) Classification of Hematolymphoid Tumors. AML with t(7;12) is reported to involve MNX1 and ETV6 signaling; however, the mechanism of leukemogenesis is not well understood, and the presence of MNX1::ETV6 fusion transcripts has only been confirmed in approximately 50% of cases. In contrast, high expression of MNX1 has been seen in all investigated cases. In this study, we investigated the clinical as well as biological characteristics of 12 pediatric AML with t(7;12) and performed whole transcriptome (WTS) and whole genome sequencing (WGS) on six of these. There was no significant difference in event-free survival or overall survival of these t(7;12) AML patients compared with other AML in the same age group. Interestingly, WTS identified several fusion transcripts involving ETV6 but not together with MNX1. WGS identified the genomic breakpoints and revealed that a common fusion partner on chromosome 7 was NOM1. Principal component analysis (PCA) of the WTS data showed that all t(7;12) AML cases cluster together, separate from all other pediatric AML subtypes; all cases had high expression of MNX1, MNX1-AS1, and MNX1-AS2. Hence, t(7;12) AML, despite expressing different fusion transcripts and with varying translocation breakpoints, constitutes a phenotypically homogenous subgroup. This underlines that the leukemia-driving event most likely is ectopic expression of MNX1 and that this therefore should be the defining Classifying criteria of this type of AML.", "doi": "10.1002/gcc.70003", "pmid": "39508359", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:38:57.208Z", "modified": "2025-12-04T19:33:55.324Z"}, {"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": "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": "34b3ab08d6fb428d9a51611e76936c20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34b3ab08d6fb428d9a51611e76936c20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34b3ab08d6fb428d9a51611e76936c20"}}, "title": "High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae.", "authors": [{"family": "Khan", "given": "Faheema Kalsoom", "initials": "FK", "orcid": "0000-0002-4891-953X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3d13492ee8f4ad1b69ce59f21b09155.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "volume": "244", "issue": "1", "pages": "219-234", "issn-l": "0028-646X"}, "abstract": "The genomes of ectomycorrhizal (ECM) fungi have a reduced number of genes encoding Carbohydrate-Active EnZymes (CAZymes), expansions in transposable elements (TEs) and small secreted proteins (SSPs) compared with saprotrophs. Fewer genes for specific peptidases and lipases in ECM fungi are also reported. It is unclear whether these changes occur at the shift to the ECM habit or are more gradual throughout the evolution of ECM lineages. We generated a genomic dataset of 20 species in the ECM lineage Inocybaceae and compared them with six saprotrophic species. Inocybaceae genomes have fewer CAZymes, peptidases, lipases, secondary metabolite clusters and SSPs and higher TE content than their saprotrophic relatives. There was an increase in the rate of gene family evolution along the branch with the transition to the ECM lifestyle. This branch had very high rate of evolution in CAZymes and had the largest number of contractions. Other significant changes along this branch included expansions in transporters, transposons-related genes and communication genes such as fungal kinases. There is a high concentration of changes in proximity to the transition to the ECM lifestyle, which correspond to the identified key changes for the gain of this lifestyle.", "doi": "10.1111/nph.20007", "pmid": "39113397", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-09-17T11:56:17.664Z", "modified": "2025-02-28T14:20:41.968Z"}, {"entity": "publication", "iuid": "7a3541f280af4c2284e0b872bff2d2b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a3541f280af4c2284e0b872bff2d2b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a3541f280af4c2284e0b872bff2d2b6"}}, "title": "Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days.", "authors": [{"family": "Resj\u00f6", "given": "Svante", "initials": "S"}, {"family": "Willforss", "given": "Jakob", "initials": "J"}, {"family": "Large", "given": "Annabel", "initials": "A"}, {"family": "Siino", "given": "Valentina", "initials": "V"}, {"family": "Alexandersson", "given": "Erik", "initials": "E"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Andreasson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Plant Physiol Biochem", "issn": "1873-2690", "volume": "215", "pages": "109032", "issn-l": null}, "abstract": "There are limited molecular data and few biomarkers available for studies of field-grown plants, especially for plants grown during extremely long days. In this study we present quantitative proteomics data from 3 years of field trials on potato, conducted in northern and southern Sweden and analyze over 3000 proteins per year of the study and complement the proteomic analysis with metabolomic and transcriptomic analyses. Small but consistent differences linked to the longer days (an average of four more hours of light per day) in northern Sweden (20 h light/day) compared to southern Sweden can be observed, with a high correlation between the mRNA determined by RNA-seq and protein abundances. The majority of the proteins with differential abundances between northern and southern Sweden could be divided into three groups: metabolic enzymes (especially GABA metabolism), proteins involved in redox metabolism, and hydrolytic enzymes. The observed differences in metabolic enzyme abundances corresponded well with untargeted metabolite data determined by GC and LC mass-spectrometry. We also analyzed differences in protein abundance between potato varieties that performed relatively well in northern Sweden in terms of yield with those that performed relatively less well. This comparison indicates that the proteins with higher abundance in the high-yield quotient group are more anabolic in their character, whereas the proteins with lower abundance are more catabolic. Our results create a base of information about potato \"field-omics\" for improved understanding of physiological and molecular processes in field-grown plants, and our data indicate that the potato plant is not generally stressed by extremely long days.", "doi": "10.1016/j.plaphy.2024.109032", "pmid": "39181085", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "S0981-9428(24)00700-9"}], "notes": [], "created": "2024-10-21T11:17:16.284Z", "modified": "2025-10-17T13:03:13.007Z"}, {"entity": "publication", "iuid": "46bc0cd9439d4cffbec0472e91aa975b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46bc0cd9439d4cffbec0472e91aa975b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46bc0cd9439d4cffbec0472e91aa975b"}}, "title": "\"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems\".", "authors": [{"family": "Zheng", "given": "Dan", "initials": "D", "orcid": "0000-0002-8680-432X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a36d31143d764232898009845c059013.json"}}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}, {"family": "\u00d6berg", "given": "Ola", "initials": "O"}, {"family": "Wik", "given": "Torsten", "initials": "T"}, {"family": "Modin", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "26", "issue": "10", "pages": "e16696", "issn-l": "1462-2912"}, "abstract": "Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.", "doi": "10.1111/1462-2920.16696", "pmid": "39379175", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-12T10:39:04.883Z", "modified": "2025-02-28T14:19:59.973Z"}, {"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": "e17d4a0e0e434723a36f929e80935cd5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e17d4a0e0e434723a36f929e80935cd5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e17d4a0e0e434723a36f929e80935cd5"}}, "title": "The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.", "authors": [{"family": "Mc Cartney", "given": "Ann M", "initials": "AM"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Mouton", "given": "Alice", "initials": "A"}, {"family": "De Panis", "given": "Diego", "initials": "D"}, {"family": "Marins", "given": "Lu\u00edsa S", "initials": "LS"}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG"}, {"family": "Diedericks", "given": "Genevieve", "initials": "G"}, {"family": "Kirangwa", "given": "Joseph", "initials": "J"}, {"family": "Morselli", "given": "Marco", "initials": "M"}, {"family": "Salces-Ortiz", "given": "Judit", "initials": "J"}, {"family": "Escudero", "given": "Nuria", "initials": "N"}, {"family": "Iannucci", "given": "Alessio", "initials": "A"}, {"family": "Natali", "given": "Chiara", "initials": "C"}, {"family": "Svardal", "given": "Hannes", "initials": "H"}, {"family": "Fern\u00e1ndez", "given": "Rosa", "initials": "R"}, {"family": "De Pooter", "given": "Tim", "initials": "T"}, {"family": "Joris", "given": "Geert", "initials": "G"}, {"family": "Strazisar", "given": "Mojca", "initials": "M"}, {"family": "Wood", "given": "Jonathan M D", "initials": "JMD"}, {"family": "Herron", "given": "Katie E", "initials": "KE"}, {"family": "Seehausen", "given": "Ole", "initials": "O"}, {"family": "Watts", "given": "Phillip C", "initials": "PC"}, {"family": "Shaw", "given": "Felix", "initials": "F"}, {"family": "Davey", "given": "Robert P", "initials": "RP"}, {"family": "Minotto", "given": "Alice", "initials": "A"}, {"family": "Fern\u00e1ndez", "given": "Jos\u00e9 M", "initials": "JM"}, {"family": "B\u00f6hne", "given": "Astrid", "initials": "A"}, {"family": "Alegria", "given": "Carla", "initials": "C"}, {"family": "Alioto", "given": "Tyler", "initials": "T"}, {"family": "Alves", "given": "Paulo C", "initials": "PC"}, {"family": "Amorim", "given": "Isabel R", "initials": "IR"}, {"family": "Aury", "given": "Jean-Marc", "initials": "J"}, {"family": "Backstrom", "given": "Niclas", "initials": "N"}, {"family": "Baldrian", "given": "Petr", 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"Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Guerin", "given": "Thomas", "initials": "T"}, {"family": "Guiglielmoni", "given": "Nadege", "initials": "N"}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Haesler", "given": "Marcel P", "initials": "MP"}, {"family": "Hahn", "given": "Christoph", "initials": "C"}, {"family": "Halpern", "given": "Balint", "initials": "B"}, {"family": "Harrison", "given": "Peter W", "initials": "PW"}, {"family": "Heintz", "given": "Julia", "initials": "J"}, {"family": "Hindrikson", "given": "Maris", "initials": "M"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Howe", "given": "Kerstin", "initials": "K"}, {"family": "Hughes", "given": "Graham M", "initials": "GM"}, {"family": "Istace", "given": "Benjamin", "initials": "B"}, {"family": "Cock", "given": "Mark J", "initials": "MJ"}, {"family": "Jan\u017eekovi\u010d", "given": "Franc", "initials": "F"}, {"family": "Jonsson", "given": "Zophonias O", "initials": "ZO"}, {"family": "Joye-Dind", "given": "Sagane", "initials": "S"}, {"family": "Koskim\u00e4ki", "given": "Janne J", "initials": "JJ"}, {"family": "Krystufek", "given": "Boris", "initials": "B"}, {"family": "Kubacka", "given": "Justyna", "initials": "J"}, {"family": "Kuhl", "given": "Heiner", "initials": "H"}, {"family": "Kusza", "given": "Szilvia", "initials": "S"}, {"family": "Labadie", "given": "Karine", "initials": "K"}, {"family": "L\u00e4hteenaro", "given": "Meri", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Lavrinienko", "given": "Anton", "initials": "A"}, {"family": "Lecl\u00e8re", "given": "Lucas", "initials": "L"}, {"family": "Lopes", "given": "Ricardo Jorge", "initials": "RJ"}, {"family": "Madsen", "given": "Ole", "initials": "O"}, {"family": "Magdelenat", "given": "Ghislaine", "initials": "G"}, {"family": "Magoga", "given": "Giulia", "initials": "G"}, {"family": "Manousaki", "given": "Tereza", "initials": "T"}, {"family": "Mappes", "given": "Tapio", "initials": "T"}, {"family": "Marques", "given": "Joao Pedro", "initials": "JP"}, {"family": "Redondo", "given": "Gemma I Martinez", "initials": "GIM"}, {"family": "Maumus", "given": "Florian", "initials": "F"}, {"family": "McCarthy", "given": "Shane A", "initials": "SA"}, {"family": "Megens", "given": "Hendrik-Jan", "initials": "H"}, {"family": "Melo-Ferreira", "given": "Jose", "initials": "J"}, {"family": "Mendes", "given": "Sofia L", "initials": "SL"}, {"family": "Montagna", "given": "Matteo", "initials": "M"}, {"family": "Moreno", "given": "Joao", "initials": "J"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Moura", "given": "M\u00f3nica", "initials": "M"}, {"family": "Musilova", "given": "Zuzana", "initials": "Z"}, {"family": "Myers", "given": "Eugene", "initials": "E"}, {"family": "Nash", "given": "Will J", "initials": "WJ"}, {"family": "Nater", "given": "Alexander", "initials": "A"}, {"family": "Nicholson", "given": "Pamela", "initials": "P"}, {"family": "Niell", "given": "Manuel", "initials": "M"}, {"family": "Nijland", "given": "Reindert", "initials": "R"}, {"family": "Noel", "given": "Benjamin", "initials": "B"}, {"family": "Noren", "given": "Karin", "initials": "K"}, {"family": "Oliveira", "given": "Pedro H", "initials": "PH"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "R"}, {"family": "Ometto", "given": "Lino", "initials": "L"}, {"family": "Oomen", "given": "Rebekah A", "initials": "RA"}, {"family": "Ossowski", "given": "Stephan", "initials": "S"}, {"family": "Palinauskas", "given": "Vaidas", "initials": "V"}, {"family": "Palsson", "given": "Snaebjorn", "initials": "S"}, {"family": "Panibe", "given": "Jerome P", "initials": "JP"}, {"family": "Pauperio", "given": "Joana", "initials": "J"}, {"family": "Pavlek", "given": "Martina", "initials": "M"}, {"family": "Payen", "given": "Emilie", "initials": "E"}, {"family": "Pawlowska", "given": "Julia", "initials": "J"}, {"family": "Pellicer", "given": "Jaume", "initials": "J"}, {"family": "Pesole", "given": "Graziano", "initials": "G"}, {"family": "Pimenta", "given": "Joao", "initials": "J"}, {"family": "Pippel", "given": "Martin", "initials": "M"}, {"family": "Pirttil\u00e4", "given": "Anna Maria", "initials": "AM"}, {"family": "Poulakakis", "given": "Nikos", "initials": "N"}, {"family": "Rajan", "given": "Jeena", "initials": "J"}, {"family": "M C Rego", "given": "R\u00faben", "initials": "R"}, {"family": "Resendes", "given": "Roberto", "initials": "R"}, {"family": "Resl", "given": "Philipp", "initials": "P"}, {"family": "Riesgo", "given": "Ana", "initials": "A"}, {"family": "Rodin-Morch", "given": "Patrik", "initials": "P"}, {"family": "Soares", "given": "Andre E R", "initials": "AER"}, {"family": "Fernandes", "given": "Carlos Rodriguez", "initials": "CR"}, {"family": "Romeiras", "given": "Maria M", "initials": "MM"}, {"family": "Roxo", "given": "Guilherme", "initials": "G"}, {"family": "R\u00fcber", "given": "Lukas", "initials": "L"}, {"family": "Ruiz-Lopez", "given": "Maria Jose", "initials": "MJ"}, {"family": "Saarma", "given": "Urmas", "initials": "U"}, {"family": "da Silva", "given": "Luis P", "initials": "LP"}, {"family": "Sim-Sim", "given": "Manuela", "initials": "M"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Sousa", "given": "Vitor C", "initials": "VC"}, {"family": "Santos", "given": "Carla Sousa", "initials": "CS"}, {"family": "Spada", "given": "Alberto", "initials": "A"}, {"family": "Stefanovic", "given": "Milomir", "initials": "M"}, {"family": "Steger", "given": "Viktor", "initials": "V"}, {"family": "Stiller", "given": "Josefin", "initials": "J"}, {"family": "St\u00f6ck", "given": "Matthias", "initials": "M"}, {"family": "Struck", "given": "Torsten H", "initials": "TH"}, {"family": "Sudasinghe", "given": "Hiranya", "initials": "H"}, {"family": "Tapanainen", "given": "Riikka", "initials": "R"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "Trindade", "given": "Helena", "initials": "H"}, {"family": "Tukalenko", "given": "Yevhen", "initials": "Y"}, {"family": "Urso", "given": "Ilenia", "initials": "I"}, {"family": "Vacherie", "given": "Benoit", "initials": "B"}, {"family": "Van Belleghem", "given": "Steven M", "initials": "SM"}, {"family": "Van Oers", "given": "Kees", "initials": "K"}, {"family": "Vargas-Chavez", "given": "Carlos", "initials": "C"}, {"family": "Velickovic", "given": "Nevena", "initials": "N"}, {"family": "Vella", "given": "Noel", "initials": "N"}, {"family": "Vella", "given": "Adriana", "initials": "A"}, {"family": "Vernesi", "given": "Cristiano", "initials": "C"}, {"family": "Vicente", "given": "Sara", "initials": "S"}, {"family": "Villa", "given": "Sara", "initials": "S"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Volckaert", "given": "Filip A M", "initials": "FAM"}, {"family": "Voros", "given": "Judit", "initials": "J"}, {"family": "Wincker", "given": "Patrick", "initials": "P"}, {"family": "Winkler", "given": "Sylke", "initials": "S"}, {"family": "Ciofi", "given": "Claudio", "initials": "C"}, {"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Mazzoni", "given": "Camila J", "initials": "CJ"}], "type": "journal article", "published": "2024-09-17", "journal": {"title": "NPJ Biodivers", "issn": "2731-4243", "issn-l": null, "volume": "3", "issue": "1", "pages": "28"}, "abstract": "A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.", "doi": "10.1038/s44185-024-00054-6", "pmid": "39289538", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11408602"}, {"db": "pii", "key": "10.1038/s44185-024-00054-6"}], "notes": [], "created": "2024-10-28T09:59:00.105Z", "modified": "2024-11-12T11:36:01.896Z"}, {"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": "da70971f10de48a2a607c9b51dc45c38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/da70971f10de48a2a607c9b51dc45c38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/da70971f10de48a2a607c9b51dc45c38"}}, "title": "Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells.", "authors": [{"family": "Jhamat", "given": "Naveed", "initials": "N", "orcid": "0009-0002-9876-4262", "researcher": {"href": "https://publications.scilifelab.se/researcher/e95627ce396b48f3828f038706cad7ac.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y", "orcid": "0000-0002-5057-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/8040d6c76eb6467585d054d55a1965fe.json"}}, {"family": "Han", "given": "Jilong", "initials": "J", "orcid": "0000-0001-9747-8163", "researcher": {"href": "https://publications.scilifelab.se/researcher/6849bbc1472c447a82af373ca5a44e21.json"}}, {"family": "Humblot", "given": "Patrice", "initials": "P", "orcid": "0000-0002-5292-1798", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d74c76f33864331ab7c72614ae855f0.json"}}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}], "type": "journal article", "published": "2024-09-11", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "18", "issn-l": null}, "abstract": "Endometritis is an inflammatory disease that negatively influences fertility and is common in milk-producing cows. An in vitro model for bovine endometrial inflammation was used to identify enrichment of cis-acting regulatory elements in differentially methylated regions (DMRs) in the genome of in vitro-cultured primary bovine endometrial epithelial cells (bEECs) before and after treatment with lipopolysaccharide (LPS) from E. coli, a key player in the development of endometritis. The enriched regulatory elements contain binding sites for transcription factors with established roles in inflammation and hypoxia including NFKB and Hif-1\u03b1. We further showed co-localization of certain enriched cis-acting regulatory motifs including ARNT, Hif-1\u03b1, and NRF1. Our results show an intriguing interplay between increased mRNA levels in LPS-treated bEECs of the mRNAs encoding the key transcription factors such as AHR, EGR2, and STAT1, whose binding sites were enriched in the DMRs. Our results demonstrate an extraordinary cis-regulatory complexity in these DMRs having binding sites for both inflammatory and hypoxia-dependent transcription factors. Obtained data using this in vitro model for bacterial-induced endometrial inflammation have provided valuable information regarding key transcription factors relevant for clinical endometritis in both cattle and humans.", "doi": "10.3390/ijms25189832", "pmid": "39337320", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "ijms25189832"}, {"db": "pmc", "key": "PMC11432661"}], "notes": [], "created": "2024-09-30T06:07:03.182Z", "modified": "2024-09-30T06:07:04.535Z"}, {"entity": "publication", "iuid": "73cad3816af2484e851c50eb262486d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73cad3816af2484e851c50eb262486d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73cad3816af2484e851c50eb262486d1"}}, "title": "Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference.", "authors": [{"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Fernandez", "given": "Carola", "initials": "C"}, {"family": "Correa Muler", "given": "Ana Iris", "initials": "AI"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Fabrik", "given": "Ivo", "initials": "I"}, {"family": "Huynh", "given": "Hang T", "initials": "HT"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Poyraz", "given": "Melis", "initials": "M"}, {"family": "H\u00e4rtlova", "given": "Anetta", "initials": "A"}, {"family": "Benhalevy", "given": "Daniel", "initials": "D"}, {"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": "2024-09-09", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "52", "issue": "16", "pages": "9917-9935"}, "abstract": "In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.", "doi": "10.1093/nar/gkae589", "pmid": "38994560", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "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": "pmc", "key": "PMC11381323"}, {"db": "pii", "key": "7712617"}], "notes": [], "created": "2024-10-21T11:21:54.725Z", "modified": "2025-02-28T14:19:11.123Z"}, {"entity": "publication", "iuid": "411c02d828c14370a99a8a2b57b28e22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/411c02d828c14370a99a8a2b57b28e22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/411c02d828c14370a99a8a2b57b28e22"}}, "title": "Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Ponnikas", "given": "Suvi", "initials": "S", "orcid": "0000-0003-3526-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddd324bbfbb4833b25ba6dfe4c7dcb4.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2024-09-04", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "14", "issue": "9", "issn-l": "2160-1836"}, "abstract": "Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyze the genomes of 12 great reed warblers (Acrocephalus arundinaceus) in a 3-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated toward the telomeric ends of the chromosomes. Apart from this major pattern in the recombination landscape, we found significantly higher frequencies of crossovers in genic compared with intergenic regions, and in exons compared with introns. Moreover, while the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared with maternal chromosomes. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias toward the sub-telomeric regions, particularly on the paternal side. These findings emphasize the importance of thoroughly screening the entire length of chromosomes to characterize the recombination landscape and uncover potential sex-biases in recombination.", "doi": "10.1093/g3journal/jkae150", "pmid": "38985659", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11373659"}, {"db": "pii", "key": "7710635"}], "notes": [], "created": "2024-10-21T11:19:13.917Z", "modified": "2024-11-25T10:23:45.131Z"}, {"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": "74e6bcf9f810455aafeb36c2253b4848", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74e6bcf9f810455aafeb36c2253b4848.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74e6bcf9f810455aafeb36c2253b4848"}}, "title": "Gene-based association analysis of a large patient cohort provides insights into genetics of atypical femur fractures.", "authors": [{"family": "Zhou", "given": "Wei", "initials": "W", "orcid": "0000-0002-6748-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f7e9b3a6ffa45dba854cb6acf59739b.json"}}, {"family": "\u00c5s", "given": "Joel", "initials": "J"}, {"family": "Shore-Lorenti", "given": "Catherine", "initials": "C"}, {"family": "Nguyen", "given": "Hanh H", "initials": "HH", "orcid": "0000-0002-8846-6168", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a4cb30d23e54b8c8b328859ead81ba7.json"}}, {"family": "van de Laarschot", "given": "Denise M", "initials": "DM"}, {"family": "Sztal-Mazer", "given": "Shoshana", "initials": "S"}, {"family": "Grill", "given": "Vivian", "initials": "V"}, {"family": "Girgis", "given": "Christian M", "initials": "CM"}, {"family": "Stricker", "given": "Bruno H Ch", "initials": "BHC"}, {"family": "van der Eerden", "given": "Bram C J", "initials": "BCJ"}, {"family": "Thakker", "given": "Rajesh V", "initials": "RV"}, {"family": "Appelman-Dijkstra", "given": "Natasha M", "initials": "NM", "orcid": "0000-0001-5035-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f26fbf2e8d14f8ebf65acd9e22d7b41.json"}}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "Clifton-Bligh", "given": "Roderick J", "initials": "RJ"}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}, {"family": "Verkerk", "given": "Annemieke J M H", "initials": "AJMH"}, {"family": "van Rooij", "given": "Jeroen G J", "initials": "JGJ"}, {"family": "Ebeling", "given": "Peter R", "initials": "PR"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC", "orcid": "0000-0001-9186-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c71c257a4de4ac7b59381237a0fa500.json"}}], "type": "journal article", "published": "2024-09-02", "journal": {"title": "J. Bone Miner. Res.", "issn": "1523-4681", "volume": "39", "issue": "9", "pages": "1315-1326", "issn-l": "0884-0431"}, "abstract": "Several small genetic association studies have been conducted for atypical femur fracture (AFF) without replication of results. We assessed previously implicated and novel genes associated with AFFs in a larger set of unrelated AFF cases using whole exome sequencing (WES). We performed gene-based association analysis on 139 European AFF cases and 196 controls matched for bisphosphonate use. We tested all rare, protein-altering variants using both candidate gene and hypothesis-free approaches. In the latter, genes suggestively associated with AFFs (uncorrected p-values <.01) were investigated in a Swedish whole-genome sequencing replication study and assessed in 46 non-European cases. In the candidate gene analysis, PLOD2 showed a suggestive signal. The hypothesis-free approach revealed 10 tentative associations, with XRN2, SORD, and PLOD2 being the most likely candidates for AFF. XRN2 and PLOD2 showed consistent direction of effect estimates in the replication analysis, albeit not statistically significant. Three SNPs associated with SORD expression according to the GTEx portal were in linkage disequilibrium (R2 \u2265 0.2) with an SNP previously reported in a genome-wide association study of AFF. The prevalence of carriers of variants for both PLOD2 and SORD was higher in Asian versus European cases. While we did not identify genes enriched for damaging variants, we found suggestive evidence of a role for XRN2, PLOD2, and SORD, which requires further investigation. Our findings indicate that genetic factors responsible for AFFs are not widely shared among AFF cases. The study provides a stepping-stone for future larger genetic studies of AFF.", "doi": "10.1093/jbmr/zjae122", "pmid": "39126371", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11371903"}, {"db": "pii", "key": "7731319"}], "notes": [], "created": "2024-10-21T11:12:51.933Z", "modified": "2024-10-21T11:13:04.359Z"}, {"entity": "publication", "iuid": "04e23b32f608475991bc284705d024a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e23b32f608475991bc284705d024a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e23b32f608475991bc284705d024a8"}}, "title": "Transcriptomic and functional analyses on a Botrytis cinerea multidrug-resistant (MDR) strain provides new insights into the potential molecular mechanisms of MDR and fitness.", "authors": [{"family": "Sofianos", "given": "Georgios", "initials": "G", "orcid": "0009-0002-2678-7158", "researcher": {"href": "https://publications.scilifelab.se/researcher/6caa00e6738e4dfaa70832c456ddc6e6.json"}}, {"family": "Piombo", "given": "Edoardo", "initials": "E", "orcid": "0000-0003-2830-1967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff26b84d14643f3ae4e45a23cd2107b.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Karlsson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-6098-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34e4b8bad4e34912b011f2ead759b422.json"}}, {"family": "Karaoglanidis", "given": "George", "initials": "G", "orcid": "0000-0002-7413-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/477fa9557e904366aabb7d7b6b53e4d6.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "volume": "25", "issue": "9", "pages": "e70004", "issn-l": null}, "abstract": "Botrytis cinerea is a notorious pathogen causing pre- and post-harvest spoilage in many economically important crops. Excessive application of site-specific fungicides to control the pathogen has led to the selection of strains possessing target site alterations associated with resistance to these fungicides and/or strains overexpressing efflux transporters associated with multidrug resistance (MDR). MDR in B. cinerea has been correlated with the overexpression of atrB and mfsM2, encoding an ATP-binding cassette (ABC) and a major facilitator superfamily (MFS) transporter, respectively. However, it remains unknown whether other transporters may also contribute to the MDR phenotype. In the current study, the transcriptome of a B. cinerea multidrug-resistant (MDR) field strain was analysed upon exposure to the fungicide fludioxonil, and compared to the B05.10 reference strain. The transcriptome of this field strain displayed significant differences as compared to B05.10, including genes involved in sugar membrane transport, toxin production and virulence. Among the induced genes in the field strain, even before exposure to fludioxonil, were several putatively encoding ABC and MFS transmembrane transporters. Overexpression of a highly induced MFS transporter gene in the B05.10 strain led to an increased tolerance to the fungicides fluopyram and boscalid, indicating an involvement in efflux transport of these compounds. Overall, the data from this study give insights towards better understanding the molecular mechanisms involved in MDR and fitness cost, contributing to the development of more efficient control strategies against this pathogen.", "doi": "10.1111/mpp.70004", "pmid": "39244735", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11380696"}], "notes": [], "created": "2024-10-21T11:12:58.472Z", "modified": "2024-10-21T11:13:08.829Z"}, {"entity": "publication", "iuid": "41ddca0947d04600adb7ac6263f21f5c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41ddca0947d04600adb7ac6263f21f5c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41ddca0947d04600adb7ac6263f21f5c"}}, "title": "Species-genetic diversity correlation in a metacommunity of urban pond invertebrates", "authors": [{"family": "Johansson", "given": "Frank", "initials": "F"}, {"family": "Yildirim", "given": "Yeserin", "initials": "Y"}, {"family": "Hyseni", "given": "Chaz", "initials": "C", "orcid": "0000-0003-2567-8013", "researcher": {"href": "https://publications.scilifelab.se/researcher/7327304d59cb41a7a97cdcba953f9cdc.json"}}, {"family": "Heino", "given": "Jani", "initials": "J"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Bini", "given": "Luis Mauricio", "initials": "LM", "orcid": "0000-0003-3398-9399", "researcher": {"href": "https://publications.scilifelab.se/researcher/490cfde8f1824571a07f21bf11ea61f0.json"}}], "type": "journal-article", "published": "2024-09-00", "journal": {"title": "Basic and Applied Ecology", "issn": "1439-1791", "volume": "79", "pages": "114-122", "issn-l": null}, "abstract": null, "doi": "10.1016/j.baae.2024.07.002", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:15:57.869Z", "modified": "2024-10-21T11:15:58.840Z"}, {"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": "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": "a3c5e0204138422aa03a305231f99f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3c5e0204138422aa03a305231f99f89"}}, "title": "An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Hodge", "given": "McKaela", "initials": "M"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "Beckman", "given": "Madeleine", "initials": "M"}, {"family": "Bellone", "given": "Rebecca R", "initials": "RR", "orcid": "0000-0001-8838-7227", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c3235fb9bc24da59f4b2685ab0924a4.json"}}, {"family": "Kallenberg", "given": "Angelica", "initials": "A", "orcid": "0000-0001-7993-6597", "researcher": {"href": "https://publications.scilifelab.se/researcher/b86eca5b3e87464ca2e00fc0f1ad44e0.json"}}, {"family": "J'Usrey", "given": "Stephanie", "initials": "S"}, {"family": "Ohmura", "given": "Hajime", "initials": "H"}, {"family": "Seki", "given": "Kazuhiro", "initials": "K"}, {"family": "Furukawa", "given": "Risako", "initials": "R", "orcid": "0009-0002-4673-0845", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5000c3c34a44dcebe85e6c8418b065e.json"}}, {"family": "Ohnuma", "given": "Aoi", "initials": "A"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Tozaki", "given": "Teruaki", "initials": "T", "orcid": "0000-0001-8797-6644", "researcher": {"href": "https://publications.scilifelab.se/researcher/8246b65d8481438885db4d4be0691aaa.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.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": "2024-08-29", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7510", "issn-l": "2041-1723"}, "abstract": "The Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two different Grey alleles, G2 carrying two tandem copies of the duplicated sequence and G3 carrying three. The latter is by far the most common allele, probably due to strong selection for the striking white phenotype. Our results reveal a remarkable dosage effect where the G3 allele is associated with fast greying and high incidence of melanoma whereas G2 is associated with slow greying and low incidence of melanoma. The copy number expansion transforms a weak enhancer to a strong melanocyte-specific enhancer that underlies hair greying (G2 and G3) and a drastically elevated risk of melanoma (G3 only). Our direct pedigree-based observation of the origin of a G2 allele from a G3 allele by copy number contraction demonstrates the dynamic evolution of this locus and provides the ultimate evidence for causality of the copy number variation of the 4.6 kb intronic sequence.", "doi": "10.1038/s41467-024-51898-2", "pmid": "39209879", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11362437"}, {"db": "pii", "key": "10.1038/s41467-024-51898-2"}], "notes": [], "created": "2024-10-21T11:17:13.688Z", "modified": "2024-11-25T10:17:52.816Z"}, {"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": "47741b433ff341d898259372903d7f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47741b433ff341d898259372903d7f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47741b433ff341d898259372903d7f89"}}, "title": "Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips.", "authors": [{"family": "Aguirre Rivera", "given": "J", "initials": "J", "orcid": "0000-0002-5263-3577", "researcher": {"href": "https://publications.scilifelab.se/researcher/f164778943f24897a1fa31ac3c6fd2ce.json"}}, {"family": "Mao", "given": "G", "initials": "G", "orcid": "0000-0001-5841-0991", "researcher": {"href": "https://publications.scilifelab.se/researcher/827d755ddbd24c2ca839364c9e139965.json"}}, {"family": "Sabantsev", "given": "A", "initials": "A", "orcid": "0000-0002-8559-8894", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae73150df15e4730be688fc5137a1389.json"}}, {"family": "Panfilov", "given": "M", "initials": "M", "orcid": "0000-0003-2875-7315", "researcher": {"href": "https://publications.scilifelab.se/researcher/58d227ea91aa4b90915a7e2afeb9283e.json"}}, {"family": "Hou", "given": "Q", "initials": "Q", "orcid": "0009-0007-9296-4788", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1048338ae024e9fbc9d82d79f61ffee.json"}}, {"family": "Lindell", "given": "M", "initials": "M"}, {"family": "Chanez", "given": "C", "initials": "C", "orcid": "0000-0002-3432-4375", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce66636fd1344819df3518ffa6406ce.json"}}, {"family": "Ritort", "given": "F", "initials": "F", "orcid": "0000-0002-4869-5003", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7a34940c8ae42f1a2381b0b48fe06be.json"}}, {"family": "Jinek", "given": "M", "initials": "M", "orcid": "0000-0002-7601-210X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b86b5f94bbf4b87849dd4d8cebf80f8.json"}}, {"family": "Deindl", "given": "S", "initials": "S", "orcid": "0000-0001-6807-8654", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e45e8288a3445e2b346f29b73141738.json"}}], "type": "journal article", "published": "2024-08-23", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "385", "issue": "6711", "pages": "892-898"}, "abstract": "Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.", "doi": "10.1126/science.adn5371", "pmid": "39172826", "labels": {"NGI Short read": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development"}, "xrefs": [], "notes": [], "created": "2024-08-23T12:11:46.194Z", "modified": "2024-11-05T18:25:16.868Z"}, {"entity": "publication", "iuid": "5b55070b76c24485b9ebf1088919dd92", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b55070b76c24485b9ebf1088919dd92.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b55070b76c24485b9ebf1088919dd92"}}, "title": "CDK8 of the mediator kinase module connects leaf development to the establishment of correct stomata patterning by regulating the levels of the transcription factor SPEECHLESS (SPCH).", "authors": [{"family": "Hermida-Carrera", "given": "Carmen", "initials": "C", "orcid": "0000-0003-3272-3054", "researcher": {"href": "https://publications.scilifelab.se/researcher/2623d07dbfa54495aa50ddb18c8fd77a.json"}}, {"family": "Vergara", "given": "Alexander", "initials": "A"}, {"family": "Cervela-Cardona", "given": "Luis", "initials": "L", "orcid": "0000-0002-7293-4473", "researcher": {"href": "https://publications.scilifelab.se/researcher/3afcbfea5e0d4fc0bb91e2954105a29e.json"}}, {"family": "Jin", "given": "Xu", "initials": "X"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S"}, {"family": "Strand", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0001-6664-0471", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6cf82047f9d47bd863874878c1d0b2a.json"}}], "type": "journal article", "published": "2024-08-23", "journal": {"title": "Plant Cell Environ.", "issn": "1365-3040", "issn-l": "0140-7791"}, "abstract": "The components of the mediator kinase module are highly conserved across all eukaryotic lineages, and cyclin-dependent kinase 8 (CDK8) is essential for correct cell proliferation and differentiation in diverse eukaryotic systems. We show that CDK8 couples leaf development with the establishment of correct stomata patterning for prevailing CO2 conditions. In Arabidopsis, the basic helix-loop-helix (bHLH) transcription factor SPEECHLESS (SPCH) controls cellular entry into the stomatal cell lineage, and CDK8 interacts with and phosphorylates SPCH, controlling SPCH protein levels and thereby also expression of the SPCH target genes encoding key regulators of cell fate and asymmetric cell divisions. The lack of the CDK8-mediated control of SPCH results in an increased number of meristemoid and guard mother cells, and increased stomata index in the cdk8 mutants. Increasing atmospheric CO2 concentrations trigger a developmental programme controlling cell entry into stomatal lineage by limiting the asymmetric divisions. In cdk8, the number of meristemoids and guard mother cells remains the same under ambient and high CO2 concentrations, as the accumulated levels of SPCH caused by the lack of CDK8 appear to override the negative regulation of increased CO2. Thus, our work provides novel mechanistic understanding of how plants alter critical leaf properties in response to increasing atmospheric CO2.", "doi": "10.1111/pce.15102", "pmid": "39177450", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:25:58.331Z", "modified": "2024-10-21T11:25:58.481Z"}, {"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": "69d3c968e92644688b9b1341bc588cc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69d3c968e92644688b9b1341bc588cc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69d3c968e92644688b9b1341bc588cc9"}}, "title": "Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species.", "authors": [{"family": "Fetsiukh", "given": "Anastasiia", "initials": "A"}, {"family": "Pall", "given": "Taavi", "initials": "T"}, {"family": "Timmusk", "given": "Salme", "initials": "S"}], "type": "journal article", "published": "2024-08-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "18806", "issn-l": "2045-2322"}, "abstract": "Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed.", "doi": "10.1038/s41598-024-68123-1", "pmid": "39138231", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11322436"}, {"db": "pii", "key": "10.1038/s41598-024-68123-1"}], "notes": [], "created": "2024-10-21T11:17:11.546Z", "modified": "2024-10-21T11:17:11.551Z"}, {"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": "629725b0fd4d4f85bd4cbe31d33f7570", "links": {"self": {"href": "https://publications.scilifelab.se/publication/629725b0fd4d4f85bd4cbe31d33f7570.json"}, "display": {"href": "https://publications.scilifelab.se/publication/629725b0fd4d4f85bd4cbe31d33f7570"}}, "title": "Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.", "authors": [{"family": "Skytte Af S\u00e4tra", "given": "J", "initials": "J", "orcid": "0000-0002-2827-4842", "researcher": {"href": "https://publications.scilifelab.se/researcher/00b323220517477eb3c4acda1bb64c81.json"}}, {"family": "Garkava-Gustavsson", "given": "L", "initials": "L"}, {"family": "Ingvarsson", "given": "P K", "initials": "PK", "orcid": "0000-0001-9225-7521", "researcher": {"href": "https://publications.scilifelab.se/researcher/52a2c210ff754465a69f839b40fe8312.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "133", "issue": "2", "pages": "67-77", "issn-l": "0018-067X"}, "abstract": "Good understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into 'hardy' and 'not hardy' cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the 'hardy' group. Using phased genotypic data from the 20 K apple Infinium\u00ae SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.", "doi": "10.1038/s41437-024-00693-2", "pmid": "38834867", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11286948"}, {"db": "pii", "key": "10.1038/s41437-024-00693-2"}], "notes": [], "created": "2024-10-21T11:08:23.983Z", "modified": "2024-11-25T10:15:45.034Z"}, {"entity": "publication", "iuid": "7cdd71fc9b3a4e96bbece5625ab29d9e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7cdd71fc9b3a4e96bbece5625ab29d9e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7cdd71fc9b3a4e96bbece5625ab29d9e"}}, "title": "Selection against domestication alleles in introduced rabbit populations.", "authors": [{"family": "Andrade", "given": "Pedro", "initials": "P", "orcid": "0000-0003-2540-2471", "researcher": {"href": "https://publications.scilifelab.se/researcher/beb2336f18d94c57bbf9089dd6d06ccf.json"}}, {"family": "Alves", "given": "Joel M", "initials": "JM", "orcid": "0000-0001-6138-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/118178b7f76e4b5ba3ec39914aee7b57.json"}}, {"family": "Pereira", "given": "Paulo", "initials": "P", "orcid": "0000-0001-9519-7691", "researcher": {"href": "https://publications.scilifelab.se/researcher/c8913fec8d89466480fa55e47e47e2ce.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Silva", "given": "Eug\u00e9nio", "initials": "E", "orcid": "0000-0002-9680-3494", "researcher": {"href": "https://publications.scilifelab.se/researcher/099c8fd4d8324c5f8e39f8798d680e29.json"}}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Enbody", "given": "Erik", "initials": "E", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Afonso", "given": "Sandra", "initials": "S", "orcid": "0000-0001-7212-991X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ced62caf88e446c796ad9b022517442c.json"}}, {"family": "Faria", "given": "Rui", "initials": "R"}, {"family": "Zhang", "given": "Yexin", "initials": "Y", "orcid": "0000-0001-8253-4951", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5f20139428b4ebf93a8c478dd969264.json"}}, {"family": "Bonino", "given": "Never", "initials": "N"}, {"family": "Duckworth", "given": "Janine A", "initials": "JA"}, {"family": "Garreau", "given": "Herv\u00e9", "initials": "H", "orcid": "0000-0001-6195-1457", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9687c1ad7c04774aadaeb3f22abb034.json"}}, {"family": "Letnic", "given": "Mike", "initials": "M"}, {"family": "Strive", "given": "Tanja", "initials": "T", "orcid": "0000-0003-2971-8406", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0155b46301d490d974c8045f43ba4f6.json"}}, {"family": "Thulin", "given": "Carl-Gustaf", "initials": "CG", "orcid": "0000-0001-6543-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71a9794d2f94bdea1793abe41790d69.json"}}, {"family": "Queney", "given": "Guillaume", "initials": "G"}, {"family": "Villafuerte", "given": "Rafael", "initials": "R"}, {"family": "Jiggins", "given": "Francis M", "initials": "FM", "orcid": "0000-0001-7470-8157", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3992869d5e249968d550b75307fdc4a.json"}}, {"family": "Ferrand", "given": "Nuno", "initials": "N"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Carneiro", "given": "Miguel", "initials": "M", "orcid": "0000-0001-9882-7775", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1d62d41fce4469b878ea399d2d0abbf.json"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "8", "issue": "8", "pages": "1543-1555", "issn-l": "2397-334X"}, "abstract": "Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.", "doi": "10.1038/s41559-024-02443-3", "pmid": "38907020", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-024-02443-3"}], "notes": [], "created": "2024-11-12T10:54:12.925Z", "modified": "2024-11-25T10:19:02.495Z"}, {"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": "8b0ca8d9347d4e589bbd155951bd924a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b0ca8d9347d4e589bbd155951bd924a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b0ca8d9347d4e589bbd155951bd924a"}}, "title": "Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T"}, {"family": "Zhang", "given": "Zebin", "initials": "Z"}, {"family": "Genete", "given": "Mathieu", "initials": "M"}, {"family": "Poux", "given": "C\u00e9line", "initials": "C"}, {"family": "Sicard", "given": "Adrien", "initials": "A", "orcid": "0000-0002-4104-6844", "researcher": {"href": "https://publications.scilifelab.se/researcher/559469d6cd9a4435beffc526f2655c5c.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V"}, {"family": "Vekemans", "given": "Xavier", "initials": "X"}], "type": "journal article", "published": "2024-08-00", "journal": {"issn": "2056-3744", "title": "Evolution Letters", "volume": "8", "issue": "4", "pages": "550-560", "issn-l": "2056-3744"}, "abstract": "The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, SCR and SRK, tightly linked within the S-locus. A series of small non-coding RNAs also encoded within the S-locus regulates the transcriptional activity of SCR alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing Capsella orientalis and outcrossing Capsella grandiflora to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between S-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the SCR gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between S-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between S-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.", "doi": "10.1093/evlett/qrae011", "pmid": "39100231", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11291619"}, {"db": "pii", "key": "qrae011"}, {"db": "figshare", "key": "10.6084/m9.figshare.22567558.v2"}], "notes": [], "created": "2024-05-16T06:32:00.828Z", "modified": "2025-02-28T14:17:25.871Z"}, {"entity": "publication", "iuid": "92996e534bd244ad802a06aba40392a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92996e534bd244ad802a06aba40392a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92996e534bd244ad802a06aba40392a9"}}, "title": "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M", "orcid": "0000-0002-0012-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/48850e5606b9470caa6b130286055388.json"}}, {"family": "Arvidsson", "given": "Gustav", "initials": "G", "orcid": "0000-0001-7396-1820", "researcher": {"href": "https://publications.scilifelab.se/researcher/29beb4f9dd8b460382eab4f916fc1072.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}}, {"family": "Gezelius", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6242-6344", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad329767af94f9f9ad2c96771ff01d9.json"}}, {"family": "Bremer", "given": "Anna", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"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"}}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "7", "issue": "8", "pages": null}, "abstract": "The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.", "doi": "10.26508/lsa.202302481", "pmid": "38777370", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "NGI Short read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11111970"}, {"db": "pii", "key": "7/8/e202302481"}], "notes": [], "created": "2024-08-02T11:59:07.510Z", "modified": "2025-02-28T14:23:51.125Z"}, {"entity": "publication", "iuid": "4a894ab59574495e857e2b2155acc78b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a894ab59574495e857e2b2155acc78b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a894ab59574495e857e2b2155acc78b"}}, "title": "A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene.", "authors": [{"family": "Stuart", "given": "David", "initials": "D", "orcid": "0000-0001-5624-3608", "researcher": {"href": "https://publications.scilifelab.se/researcher/a18828bd03f04188b454b5ffc62ad106.json"}}, {"family": "Zakhrabekova", "given": "Shakhira", "initials": "S", "orcid": "0000-0002-5309-5459", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ebd0fe7ba0a48d1bb1d7e34a13b6c36.json"}}, {"family": "J\u00f8rgensen", "given": "Morten Egevang", "initials": "ME", "orcid": "0000-0001-6503-0495", "researcher": {"href": "https://publications.scilifelab.se/researcher/569eabce9b404d04adc3d85120140adc.json"}}, {"family": "Dockter", "given": "Christoph", "initials": "C", "orcid": "0000-0001-5923-3667", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7c36daf65a3443aace9f0803a4b1a62.json"}}, {"family": "Hansson", "given": "Mats", "initials": "M", "orcid": "0000-0002-0168-9968", "researcher": {"href": "https://publications.scilifelab.se/researcher/63440c24a3874af18614b26ac550e5cc.json"}}], "type": "journal article", "published": "2024-07-31", "journal": {"title": "Plant Physiol.", "issn": "1532-2548", "volume": "195", "issue": "4", "pages": "2877-2890", "issn-l": "0032-0889"}, "abstract": "Thousands of barley (Hordeum vulgare L.) mutants have been isolated over the last century, and many are stored in gene banks across various countries. In the present work, we developed a pipeline to efficiently identify causal mutations in barley. The pipeline is also efficient for mutations located in centromeric regions. Through bulked segregant analyses using whole genome sequencing of pooled F2 seedlings, we mapped 2 mutations and identified a limited number of candidate genes. We applied the pipeline on F2 mapping populations made from xan-j.59 (unknown mutation) and xan-l.82 (previously known). The Xantha-j (xan-j) gene was identified as encoding chlorophyll synthase, which catalyzes the last step in the chlorophyll biosynthetic pathway: the addition of a phytol moiety to the propionate side chain of chlorophyllide. Key amino acid residues in the active site, including the binding sites of the isoprenoid and chlorophyllide substrates, were analyzed in an AlphaFold2-generated structural model of the barley chlorophyll synthase. Three allelic mutants, xan-j.19, xan-j.59, and xan-j.64, were characterized. While xan-j.19 is a 1 base pair deletion and xan-j.59 is a nonsense mutation, xan-j.64 causes an S212F substitution in chlorophyll synthase. Our analyses of xan-j.64 and treatment of growing barley with clomazone, an inhibitor of chloroplastic isoprenoid biosynthesis, suggest that binding of the isoprenoid substrate is a prerequisite for the stable maintenance of chlorophyll synthase in the plastid. We further suggest that chlorophyll synthase is a sensor for coordinating chlorophyll and isoprenoid biosynthesis.", "doi": "10.1093/plphys/kiae218", "pmid": "38630859", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11288739"}, {"db": "pii", "key": "7649211"}], "notes": [], "created": "2024-11-12T10:48:23.148Z", "modified": "2024-11-25T10:25:51.770Z"}, {"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": "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": "cb40d036f76546bcaf773bb135db83a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb40d036f76546bcaf773bb135db83a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb40d036f76546bcaf773bb135db83a3"}}, "title": "The rate of W chromosome degeneration across multiple avian neo-sex chromosomes.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Downing", "given": "Philip A", "initials": "PA", "orcid": "0000-0002-5286-3153", "researcher": {"href": "https://publications.scilifelab.se/researcher/e004ff0660ee411cb310ab108f29c171.json"}}, {"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2024-07-17", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "16548", "issn-l": "2045-2322"}, "abstract": "When sex chromosomes evolve recombination suppression, the sex-limited chromosome (Y/W) commonly degenerate by losing functional genes. The rate of Y/W degeneration is believed to slow down over time as the most essential genes are maintained by purifying selection, but supporting data are scarce especially for ZW systems. Here, we study W degeneration in Sylvioidea songbirds where multiple autosomal translocations to the sex chromosomes, and multiple recombination suppression events causing separate evolutionary strata, have occurred during the last ~ 28.1-4.5 million years (Myr). We show that the translocated regions have maintained 68.3-97.7% of their original gene content, compared to only 4.2% on the much older ancestral W chromosome. By mapping W gene losses onto a dated phylogeny, we estimate an average gene loss rate of 1.0% per Myr, with only moderate variation between four independent lineages. Consistent with previous studies, evolutionarily constrained and haploinsufficient genes were preferentially maintained on W. However, the gene loss rate did not show any consistent association with strata age or with the number of W genes at strata formation. Our study provides a unique account on the pace of W gene loss and reinforces the significance of purifying selection in maintaining essential genes on sex chromosomes.", "doi": "10.1038/s41598-024-66470-7", "pmid": "39020011", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11255319"}, {"db": "pii", "key": "10.1038/s41598-024-66470-7"}], "notes": [], "created": "2024-10-21T11:21:49.931Z", "modified": "2024-11-25T10:21:24.059Z"}, {"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": "95e57751a0274736bc6b15540a8e4885", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95e57751a0274736bc6b15540a8e4885.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95e57751a0274736bc6b15540a8e4885"}}, "title": "DNA methylation of exercise-responsive genes differs between trained and untrained men.", "authors": [{"family": "Geiger", "given": "Carla", "initials": "C"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Emanuelsson", "given": "Eric B", "initials": "EB"}, {"family": "Norrbom", "given": "Jessica", "initials": "J"}, {"family": "Steindorf", "given": "Karen", "initials": "K"}, {"family": "Sundberg", "given": "Carl Johan", "initials": "CJ"}, {"family": "Reitzner", "given": "Stefan M", "initials": "SM"}, {"family": "Lindholm", "given": "Malene E", "initials": "ME", "orcid": "0000-0002-5763-7833", "researcher": {"href": "https://publications.scilifelab.se/researcher/f06626001b0e4fc5a81e0801720d6aaf.json"}}], "type": "journal article", "published": "2024-07-04", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "22", "issue": "1", "pages": "147", "issn-l": "1741-7007"}, "abstract": "Physical activity is well known for its multiple health benefits and although the knowledge of the underlying molecular mechanisms is increasing, our understanding of the role of epigenetics in long-term training adaptation remains incomplete. In this intervention study, we included individuals with a history of > 15 years of regular endurance or resistance training compared to age-matched untrained controls performing endurance or resistance exercise. We examined skeletal muscle DNA methylation of genes involved in key adaptation processes, including myogenesis, gene regulation, angiogenesis and metabolism.\n\nA greater number of differentially methylated regions and differentially expressed genes were identified when comparing the endurance group with the control group than in the comparison between the strength group and the control group at baseline. Although the cellular composition of skeletal muscle samples was generally consistent across groups, variations were observed in the distribution of muscle fiber types. Slow-twitch fiber type genes MYH7 and MYL3 exhibited lower promoter methylation and elevated expression in endurance-trained athletes, while the same group showed higher methylation in transcription factors such as FOXO3, CREB5, and PGC-1\u03b1. The baseline DNA methylation state of those genes was associated with the transcriptional response to an acute bout of exercise. Acute exercise altered very few of the investigated CpG sites.\n\nEndurance- compared to resistance-trained athletes and untrained individuals demonstrated a different DNA methylation signature of selected skeletal muscle genes, which may influence transcriptional dynamics following a bout of acute exercise. Skeletal muscle fiber type distribution is associated with methylation of fiber type specific genes. Our results suggest that the baseline DNA methylation landscape in skeletal muscle influences the transcription of regulatory genes in response to an acute exercise bout.", "doi": "10.1186/s12915-024-01938-6", "pmid": "38965555", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11225400"}, {"db": "pii", "key": "10.1186/s12915-024-01938-6"}], "notes": [], "created": "2024-11-12T10:39:08.137Z", "modified": "2024-11-12T10:39:08.230Z"}, {"entity": "publication", "iuid": "0477d212635a4177b3e68b39e3fa2f20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0477d212635a4177b3e68b39e3fa2f20"}}, "title": "Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.", "authors": [{"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Besnier", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Deng", "given": "Qiaoling", "initials": "Q"}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Kvamme", "given": "Cecilie", "initials": "C"}, {"family": "Bekkevold", "given": "Dorte", "initials": "D", "orcid": "0000-0002-5297-032X", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c62afa02e94554ba1c3afcfc622555.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "MB"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Lille-Lang\u00f8y", "given": "Roger", "initials": "R"}, {"family": "Leonori", "given": "Iole", "initials": "I", "orcid": "0000-0001-7673-1684", "researcher": {"href": "https://publications.scilifelab.se/researcher/abf52b64cdde43838c36347af47ea670.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Glover", "given": "Kevin A", "initials": "KA"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.", "doi": "10.1093/gbe/evae133", "pmid": "38918882", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11226789"}, {"db": "pii", "key": "7699122"}], "notes": [], "created": "2024-11-04T20:50:27.197Z", "modified": "2024-11-25T10:24:21.553Z"}, {"entity": "publication", "iuid": "c8247c4a542e4c94ae4a3ee22db83900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900"}}, "title": "Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (\u03c9) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall \u03c9 values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with \u03c9 values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.", "doi": "10.1093/gbe/evae143", "pmid": "38941482", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11251426"}, {"db": "pii", "key": "7701342"}], "notes": [], "created": "2024-11-12T10:52:28.961Z", "modified": "2024-11-25T10:24:28.390Z"}, {"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": "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": "c119e76b14514e52b934f2411b16aff8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c119e76b14514e52b934f2411b16aff8"}}, "title": "Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Jerlstr\u00f6m-Hultqvist", "given": "Jon", "initials": "J"}, {"family": "Koskiniemi", "given": "Sanna", "initials": "S"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "dataset", "published": "2024-06-22", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "11", "issue": "1", "pages": "678", "issn-l": "2052-4463"}, "abstract": "Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.", "doi": "10.1038/s41597-024-03513-8", "pmid": "38909042", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11193728"}, {"db": "pii", "key": "10.1038/s41597-024-03513-8"}], "notes": [], "created": "2024-06-28T06:39:46.481Z", "modified": "2024-11-25T10:20:11.383Z"}, {"entity": "publication", "iuid": "c9468bade168413f9365ee51ab1da260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c9468bade168413f9365ee51ab1da260"}}, "title": "Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.", "authors": [{"family": "Kellgren", "given": "Therese", "initials": "T", "orcid": "0000-0002-4911-7037", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c7a5a8c5024d5186f1a4d7385778e2.json"}}, {"family": "Dwibedi", "given": "Chinmay", "initials": "C", "orcid": "0000-0001-6416-4440", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b0dbf807be449da1856c0c018f13a3.json"}}, {"family": "Widerstr\u00f6m", "given": "Micael", "initials": "M", "orcid": "0000-0002-1483-4255", "researcher": {"href": "https://publications.scilifelab.se/researcher/563f129fdb4e468395de5df2a7e80ee4.json"}}, {"family": "Sundell", "given": "David", "initials": "D", "orcid": "0000-0002-6269-0217", "researcher": {"href": "https://publications.scilifelab.se/researcher/084bd7876637499b929007562d5ac03a.json"}}, {"family": "\u00d6hrman", "given": "Caroline", "initials": "C", "orcid": "0000-0003-0516-7523", "researcher": {"href": "https://publications.scilifelab.se/researcher/a347bde191ef42a98a8aaba829adb553.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Monsen", "given": "Tor", "initials": "T", "orcid": "0000-0001-8489-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/804b654aa0be4d7a9ecdf113487fe443.json"}}, {"family": "Ryd\u00e9n", "given": "Patrik", "initials": "P", "orcid": "0000-0002-0577-123X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65e733a3351940749605f054834eebef.json"}}, {"family": "Johansson", "given": "Anders", "initials": "A", "orcid": "0000-0003-0548-5943", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4cd5b852fab4d5da3231939f060e3f5.json"}}], "type": "journal article", "published": "2024-06-19", "journal": {"title": "BMC Microbiol.", "issn": "1471-2180", "volume": "24", "issue": "1", "pages": "215", "issn-l": "1471-2180"}, "abstract": "A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.\n\nWe completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.\n\nThis study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.", "doi": "10.1186/s12866-024-03367-5", "pmid": "38890594", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11186124"}, {"db": "pii", "key": "10.1186/s12866-024-03367-5"}], "notes": [], "created": "2024-06-28T06:39:22.789Z", "modified": "2024-11-25T10:30:17.631Z"}, {"entity": "publication", "iuid": "caa37fd92a5c432fbea7349ddc016e59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/caa37fd92a5c432fbea7349ddc016e59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/caa37fd92a5c432fbea7349ddc016e59"}}, "title": "Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.", "authors": [{"family": "Lobo", "given": "Vivian", "initials": "V"}, {"family": "Shcherbinina", "given": "Evgeniia", "initials": "E"}, {"family": "Westholm", "given": "Jakub O", "initials": "JO"}, {"family": "Nowak", "given": "Iwona", "initials": "I"}, {"family": "Huang", "given": "Hsiang-Chi", "initials": "HC"}, {"family": "Angeletti", "given": "Davide", "initials": "D", "orcid": "0000-0002-5256-1972", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae59c12bf82b4ad9a8d9ad8603d03d9c.json"}}, {"family": "Anastasakis", "given": "Dimitrios G", "initials": "DG"}, {"family": "Sarshad", "given": "Aishe A", "initials": "AA", "orcid": "0000-0001-7153-5959", "researcher": {"href": "https://publications.scilifelab.se/researcher/42c62bd8dbe34b5da39de17d6a2a06ab.json"}}], "type": "dataset", "published": "2024-06-12", "journal": {"title": "Sci Data", "issn": "2052-4463", "issn-l": "2052-4463", "volume": "11", "issue": "1", "pages": "617"}, "abstract": "In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.", "doi": "10.1038/s41597-024-03465-z", "pmid": "38866801", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Glycoproteomics and MS Proteomics": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11169490"}, {"db": "pii", "key": "10.1038/s41597-024-03465-z"}], "notes": [], "created": "2024-06-14T17:35:54.427Z", "modified": "2024-11-27T15:37:51.552Z"}, {"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": "0f7252933b2540c4a11ca7fcc3c1e960", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0f7252933b2540c4a11ca7fcc3c1e960.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0f7252933b2540c4a11ca7fcc3c1e960"}}, "title": "Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198.", "authors": [{"family": "Manyara", "given": "David", "initials": "D", "orcid": "0000-0002-8370-2651", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132548af20445b2b0561fa38b8f8b89.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M"}, {"family": "Montoliu-Nerin", "given": "Merce", "initials": "M"}, {"family": "Rosling", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2024-06-05", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "14", "issue": "6", "issn-l": "2160-1836"}, "abstract": "Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.", "doi": "10.1093/g3journal/jkae074", "pmid": "38656424", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11152072"}, {"db": "pii", "key": "7657467"}], "notes": [], "created": "2024-06-28T06:37:32.605Z", "modified": "2025-02-28T14:17:52.446Z"}, {"entity": "publication", "iuid": "85509550f8a04133b34f785895ed87e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7"}}, "title": "Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.", "authors": [{"family": "Larsson", "given": "Martin N A", "initials": "MNA"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Pan", "given": "Li", "initials": "L"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kivikero", "given": "Hanna", "initials": "H"}, {"family": "Kantanen", "given": "Juha", "initials": "J", "orcid": "0000-0001-6350-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd2d0b84728048f39df9c1153300252a.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"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": "2024-06-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "6", "issn-l": "1759-6653"}, "abstract": "Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and \u00c5land, dating from the Late Neolithic (\u223c4,100 cal BP) to historical times (\u223c1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.", "doi": "10.1093/gbe/evae114", "pmid": "38795367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11162877"}, {"db": "pii", "key": "7682331"}], "notes": [], "created": "2024-07-01T06:11:08.407Z", "modified": "2025-02-28T14:18:19.091Z"}, {"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": "be8e2e67fa824f9da9b80e1a8d9e15c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be8e2e67fa824f9da9b80e1a8d9e15c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be8e2e67fa824f9da9b80e1a8d9e15c2"}}, "title": "Expedient Bayesian prediction of subfossil bone protein content using portable ATR-FTIR data", "authors": [{"family": "Hixon", "given": "Sean", "initials": "S", "orcid": "0000-0001-6147-7118", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b38fdd8b3424dcca122a3faf0f9d4b7.json"}}, {"family": "Roberts", "given": "Patrick", "initials": "P"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "Rossoni-Notter", "given": "Elena", "initials": "E", "orcid": "0000-0002-3437-9923", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a6f9285c47c4d919bb9333735d87f42.json"}}, {"family": "Notter", "given": "Olivier", "initials": "O", "orcid": "0000-0002-1068-7649", "researcher": {"href": "https://publications.scilifelab.se/researcher/688e704c28184e2d9ac2cf94a9e11ef9.json"}}, {"family": "Raimondeau", "given": "Pauline", "initials": "P"}, {"family": "Besnard", "given": "Guillaume", "initials": "G", "orcid": "0000-0003-2275-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6f10e15f5a40f8b64bc6b2ba3e4ab8.json"}}, {"family": "Paust", "given": "Enrico", "initials": "E", "orcid": "0000-0001-6150-7196", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5741617fbe34163a3eff32797795886.json"}}, {"family": "Lucas", "given": "Mary", "initials": "M"}, {"family": "Lagia", "given": "Anna", "initials": "A", "orcid": "0000-0003-4158-8296", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1105178630f4a3ea6378e995e449044.json"}}, {"family": "Fernandes", "given": "Ricardo", "initials": "R"}], "type": "journal-article", "published": "2024-06-00", "journal": {"title": "Quaternary International", "issn": "1040-6182", "volume": "694", "pages": "1-12", "issn-l": null}, "abstract": null, "doi": "10.1016/j.quaint.2024.05.002", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:19:03.673Z", "modified": "2024-10-21T11:19:18.929Z"}, {"entity": "publication", "iuid": "33f838f6e3d2497fa4b6fd9a71cd282a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a"}}, "title": "An endothelial regulatory module links blood pressure regulation with elite athletic performance.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K", "orcid": "0000-0002-6428-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f232e1deee984344a57c88f550020e61.json"}}, {"family": "Rosengren", "given": "Maria K", "initials": "MK", "orcid": "0000-0003-0144-7034", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b771ed57d3e4c409c2a208173945786.json"}}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1335-3927", "researcher": {"href": "https://publications.scilifelab.se/researcher/50a91636c1064a0c944f7d794ba6ec72.json"}}, {"family": "Jouni", "given": "Ahmad", "initials": "A"}, {"family": "Velie", "given": "Brandon D", "initials": "BD"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Egner", "given": "Beate", "initials": "B"}, {"family": "Mattsson", "given": "C Mikael", "initials": "CM", "orcid": "0000-0002-0642-4838", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ca360922eb047129f945ec3ca5f59e3.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "6", "pages": "e1011285", "issn-l": "1553-7390"}, "abstract": "The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.", "doi": "10.1371/journal.pgen.1011285", "pmid": "38885195", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11182536"}, {"db": "pii", "key": "PGENETICS-D-23-00898"}], "notes": [], "created": "2024-10-21T11:19:11.160Z", "modified": "2024-11-25T10:31:46.138Z"}, {"entity": "publication", "iuid": "2f35c9b1f5d04d34b625afe231498b38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2f35c9b1f5d04d34b625afe231498b38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2f35c9b1f5d04d34b625afe231498b38"}}, "title": "Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids.", "authors": [{"family": "Boman", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0537-8219", "researcher": {"href": "https://publications.scilifelab.se/researcher/669c974e6e284e94bfb6009f49ffc06d.json"}}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Mugal", "given": "Carina F", "initials": "CF"}], "type": "journal article", "published": "2024-05-29", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "22", "issue": "1", "pages": "124", "issn-l": "1741-7007"}, "abstract": "Regulation of transcription by DNA methylation in 5'-CpG-3' context is a widespread mechanism allowing differential expression of genetically identical cells to persist throughout development. Consequently, differences in DNA methylation can reinforce variation in gene expression among cells, tissues, populations, and species. Despite a surge in studies on DNA methylation, we know little about the importance of DNA methylation in population differentiation and speciation. Here we investigate the regulatory and evolutionary impact of DNA methylation in five tissues of two Ficedula flycatcher species and their naturally occurring F1 hybrids.\n\nWe show that the density of CpG in the promoters of genes determines the strength of the association between DNA methylation and gene expression. The impact of DNA methylation on gene expression varies among tissues with the brain showing unique patterns. Differentially expressed genes between parental species are predicted by genetic and methylation differentiation in CpG-rich promoters. However, both these factors fail to predict hybrid misexpression suggesting that promoter mismethylation is not a main determinant of hybrid misexpression in Ficedula flycatchers. Using allele-specific methylation estimates in hybrids, we also determine the genome-wide contribution of cis- and trans effects in DNA methylation differentiation. These distinct mechanisms are roughly balanced in all tissues except the brain, where trans differences predominate.\n\nOverall, this study provides insight on the regulatory and evolutionary impact of DNA methylation in songbirds.", "doi": "10.1186/s12915-024-01920-2", "pmid": "38807214", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11134931"}, {"db": "pii", "key": "10.1186/s12915-024-01920-2"}], "notes": [], "created": "2024-10-21T11:21:52.507Z", "modified": "2024-11-25T10:30:43.234Z"}, {"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": "0b47a1ccf6df45f189be4688ab57ff66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b47a1ccf6df45f189be4688ab57ff66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b47a1ccf6df45f189be4688ab57ff66"}}, "title": "Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.", "authors": [{"family": "C\u00e1mara", "given": "Elena", "initials": "E", "orcid": "0000-0003-4271-7555", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b95845cfd0040449c13682905f082d4.json"}}, {"family": "Mormino", "given": "Maurizio", "initials": "M", "orcid": "0000-0003-2055-5081", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bfdb794959c4feeb11d6e12d68efc06.json"}}, {"family": "Siewers", "given": "Verena", "initials": "V", "orcid": "0000-0002-9502-9804", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4d2f2bc4e6a4ce29372afbc86cefda0.json"}}, {"family": "Nyg\u00e5rd", "given": "Yvonne", "initials": "Y", "orcid": "0000-0001-6117-0343", "researcher": {"href": "https://publications.scilifelab.se/researcher/a136743764bc4dc4aa4d363c5a930592.json"}}], "type": "journal article", "published": "2024-05-21", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "issn-l": "0099-2240", "volume": "90", "issue": "5", "pages": "e0233023"}, "abstract": "Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness.\r\n\r\nThe need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.", "doi": "10.1128/aem.02330-23", "pmid": "38587374", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11107148"}], "notes": [], "created": "2024-11-12T10:46:30.209Z", "modified": "2024-11-12T10:49:33.922Z"}, {"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": "1edd0b0187124503928edd662f1beb87", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1edd0b0187124503928edd662f1beb87.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1edd0b0187124503928edd662f1beb87"}}, "title": "Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing.", "authors": [{"family": "Engvall", "given": "Kristina", "initials": "K", "orcid": "0000-0002-7291-7227", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d42004025f8455e9ea979abff4bd7c3.json"}}, {"family": "Uvdal", "given": "Hanna", "initials": "H", "orcid": "0009-0009-3191-495X", "researcher": {"href": "https://publications.scilifelab.se/researcher/76a13b46df5040da93bf5f1e9c8f31bb.json"}}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N", "orcid": "0000-0001-6806-4527", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39cecc1714f4331b08a47f1f1bbe7ac.json"}}, {"family": "\u00c5vall-Lundqvist", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-7274-1770", "researcher": {"href": "https://publications.scilifelab.se/researcher/088f2c4f20ca4b3cb20490abeec77700.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}], "type": "journal article", "published": "2024-05-16", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "8", "issue": "1", "pages": "102", "issn-l": null}, "abstract": "Persistent taxane-induced peripheral neuropathy (TIPN) is highly prevalent among early-stage breast cancer survivors (ESBCS) and has detrimental effect on quality of life. We leveraged logistic regression models to develop and validate polygenic prediction models to estimate the risk of persistent PN symptoms in a training cohort and validation cohort taking clinical risk factors into account. Based on 337 whole-exome sequenced ESBCS two of five prediction models for individual PN symptoms obtained AUC results above 60% when validated. Using the model for numbness in feet (35 SNVs) in the test cohort, 73% survivors were correctly predicted. For tingling in feet (55 SNVs) 70% were correctly predicted. Both models included SNVs from the ADAMTS20, APT6V0A2, CCDC88C, CYP2C8, EPHA5, NR1H3, PSKH2/APTV0D2, and SCN10A genes. For cramps in feet, difficulty climbing stairs and difficulty opening a jar the validation was unsuccessful. Polygenic prediction models including clinical risk factors can estimate the risk of persistent taxane-induced numbness in feet and tingling in feet in ESBCS.", "doi": "10.1038/s41698-024-00594-x", "pmid": "38755266", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11099113"}, {"db": "pii", "key": "10.1038/s41698-024-00594-x"}], "notes": [], "created": "2024-10-21T11:10:16.668Z", "modified": "2025-02-28T14:16:00.044Z"}, {"entity": "publication", "iuid": "be905f5215af4f5daa928c5e4dd48155", "links": {"self": {"href": "https://publications.scilifelab.se/publication/be905f5215af4f5daa928c5e4dd48155.json"}, "display": {"href": "https://publications.scilifelab.se/publication/be905f5215af4f5daa928c5e4dd48155"}}, "title": "Complex genetic architecture of the chicken Growth1 QTL region.", "authors": [{"family": "Ou", "given": "Jen-Hsiang", "initials": "JH", "orcid": "0000-0001-9305-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccf5baf37c03451e95d76c42731f1490.json"}}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}, {"family": "Honaker", "given": "Christa Ferst", "initials": "CF"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}], "type": "journal article", "published": "2024-05-13", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "19", "issue": "5", "pages": "e0295109", "issn-l": "1932-6203"}, "abstract": "The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.", "doi": "10.1371/journal.pone.0295109", "pmid": "38739572", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11090294"}, {"db": "pii", "key": "PONE-D-23-37785"}], "notes": [], "created": "2024-06-28T06:38:07.479Z", "modified": "2024-11-25T10:32:02.110Z"}, {"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": "8115a4dd80094d05a57d1e654e0122b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8115a4dd80094d05a57d1e654e0122b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8115a4dd80094d05a57d1e654e0122b2"}}, "title": "Growth and mortality rates of picophytoplankton in the Baltic Sea Proper", "authors": [{"family": "Alegria Zufia", "given": "J", "initials": "J"}, {"family": "Laber", "given": "CP", "initials": "C"}, {"family": "Legrand", "given": "C", "initials": "C"}, {"family": "Lindehoff", "given": "E", "initials": "E"}, {"family": "Farnelid", "given": "H", "initials": "H"}], "type": "journal-article", "published": "2024-05-02", "journal": {"title": "Mar. Ecol. Prog. Ser.", "issn": "0171-8630", "volume": "735", "pages": "63-76", "issn-l": null}, "abstract": null, "doi": "10.3354/meps14572", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-05-16T06:30:12.035Z", "modified": "2024-11-25T10:32:58.447Z"}, {"entity": "publication", "iuid": "859f1ea1d197479ebdf6b48216eba94c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/859f1ea1d197479ebdf6b48216eba94c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/859f1ea1d197479ebdf6b48216eba94c"}}, "title": "Sex-biased gene expression during neural differentiation of human embryonic stem cells.", "authors": [{"family": "Pottmeier", "given": "Philipp", "initials": "P"}, {"family": "Nikolantonaki", "given": "Danai", "initials": "D"}, {"family": "Lanner", "given": "Fredrik", "initials": "F"}, {"family": "Peuckert", "given": "Christiane", "initials": "C"}, {"family": "Jazin", "given": "Elena", "initials": "E"}], "type": "journal article", "published": "2024-05-01", "journal": {"title": "Front Cell Dev Biol", "issn": "2296-634X", "volume": "12", "pages": "1341373", "issn-l": null}, "abstract": "Sex differences in the developing human brain are primarily attributed to hormonal influence. Recently however, genetic differences and their impact on the developing nervous system have attracted increased attention. To understand genetically driven sexual dimorphisms in neurodevelopment, we investigated genome-wide gene expression in an in vitro differentiation model of male and female human embryonic stem cell lines (hESC), independent of the effects of human sex hormones. Four male and four female-derived hESC lines were differentiated into a population of mixed neurons over 37 days. Differential gene expression and gene set enrichment analyses were conducted on bulk RNA sequencing data. While similar differentiation tendencies in all cell lines demonstrated the robustness and reproducibility of our differentiation protocol, we found sex-biased gene expression already in undifferentiated ESCs at day 0, but most profoundly after 37 days of differentiation. Male and female cell lines exhibited sex-biased expression of genes involved in neurodevelopment, suggesting that sex influences the differentiation trajectory. Interestingly, the highest contribution to sex differences was found to arise from the male transcriptome, involving both Y chromosome and autosomal genes. We propose 13 sex-biased candidate genes (10 upregulated in male cell lines and 3 in female lines) that are likely to affect neuronal development. Additionally, we confirmed gene dosage compensation of X/Y homologs escaping X chromosome inactivation through their Y homologs and identified a significant overexpression of the Y-linked demethylase UTY and KDM5D in male hESC during neuron development, confirming previous results in neural stem cells. Our results suggest that genetic sex differences affect neuronal differentiation trajectories, which could ultimately contribute to sex biases during human brain development.", "doi": "10.3389/fcell.2024.1341373", "pmid": "38764741", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11101176"}, {"db": "pii", "key": "1341373"}], "notes": [], "created": "2024-05-16T06:33:09.053Z", "modified": "2025-12-04T17:14:46.303Z"}, {"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": "9b508c1fd9064736b2a6e61b2a90718a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9b508c1fd9064736b2a6e61b2a90718a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9b508c1fd9064736b2a6e61b2a90718a"}}, "title": "Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics.", "authors": [{"family": "Gustafsson", "given": "Malin", "initials": "M"}, {"family": "Strand", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-9029-4123", "researcher": {"href": "https://publications.scilifelab.se/researcher/9702edaf28fe4a56b9d345f0045d6165.json"}}, {"family": "Laugen", "given": "Ane T", "initials": "AT", "orcid": "0000-0001-6196-8304", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed598dee082844f8b057abe7c4902ab3.json"}}, {"family": "Albretsen", "given": "Jon", "initials": "J", "orcid": "0000-0001-5863-2439", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc5786b0b2f64052a1288038dc5a6310.json"}}, {"family": "Andr\u00e9", "given": "Carl", "initials": "C", "orcid": "0000-0003-4404-7292", "researcher": {"href": "https://publications.scilifelab.se/researcher/66e1d059567644a7b7080eb10d209723.json"}}, {"family": "Brostr\u00f6m", "given": "G\u00f6ran", "initials": "G"}, {"family": "Jorde", "given": "Per Erik", "initials": "PE", "orcid": "0000-0001-5515-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/0466e9d7fdff40718e81e9bd530510f9.json"}}, {"family": "Knutsen", "given": "Halvor", "initials": "H", "orcid": "0000-0002-7627-7634", "researcher": {"href": "https://publications.scilifelab.se/researcher/a822f994fed046018a713105bc5e03a0.json"}}, {"family": "Ortega-Martinez", "given": "Olga", "initials": "O", "orcid": "0000-0003-2734-6434", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc84f54ca2cc49bc869cd23adeffc7ac.json"}}, {"family": "Sodeland", "given": "Marte", "initials": "M", "orcid": "0000-0001-6703-3972", "researcher": {"href": "https://publications.scilifelab.se/researcher/577d007c219b48f3919ca2d62c3303d3.json"}}, {"family": "Waern", "given": "Malin", "initials": "M", "orcid": "0000-0002-2459-040X", "researcher": {"href": "https://publications.scilifelab.se/researcher/15f48c8e09ab4b0880b4ed44feacbd87.json"}}, {"family": "Wrange", "given": "Anna-Lisa", "initials": "AL", "orcid": "0000-0002-3574-1779", "researcher": {"href": "https://publications.scilifelab.se/researcher/359e203f84144c26878b1dcbf1657dda.json"}}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}], "type": "journal article", "published": "2024-05-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "17", "issue": "5", "pages": "e13704", "issn-l": "1752-4571"}, "abstract": "Knowledge of functional dispersal barriers in the marine environment can be used to inform a wide variety of management actions, such as marine spatial planning, restoration efforts, fisheries regulations, and invasive species management. Locations and causes of dispersal barriers can be studied through various methods, including movement tracking, biophysical modeling, demographic models, and genetics. Combining methods illustrating potential dispersal, such as biophysical modeling, with realized dispersal through, e.g., genetic connectivity estimates, provides particularly useful information for teasing apart potential causes of observed barriers. In this study, we focus on blue mussels (Mytilus edulis) in the Skagerrak-a marginal sea connected to the North Sea in Northern Europe-and combine biophysical models of larval dispersal with genomic data to infer locations and causes of dispersal barriers in the area. Results from both methods agree; patterns of ocean currents are a major structuring factor in the area. We find a complex pattern of source-sink dynamics with several dispersal barriers and show that some areas can be isolated despite an overall high dispersal capability. Finally, we translate our finding into management advice that can be used to sustainably manage this ecologically and economically important species in the future.", "doi": "10.1111/eva.13704", "pmid": "38770102", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11104481"}, {"db": "pii", "key": "EVA13704"}], "notes": [], "created": "2024-10-21T11:15:54.793Z", "modified": "2024-11-25T10:26:53.880Z"}, {"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": "1d87703f951040d3ba20c90a98d45a20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d87703f951040d3ba20c90a98d45a20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d87703f951040d3ba20c90a98d45a20"}}, "title": "Fluorescently labeled prey surrogates in combination with fluorescence\u2010activated cell sorting successfully discriminate actively feeding mixotrophs in a lake water sample", "authors": [{"family": "Florenza", "given": "Javier", "initials": "J", "orcid": "0000-0002-3284-3702", "researcher": {"href": "https://publications.scilifelab.se/researcher/45ee0fc9406f4a9ea7c6b0d3b7740183.json"}}, {"family": "Divne", "given": "Anna\u2010Maria", "initials": "A"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}], "type": "journal-article", "published": "2024-05-00", "journal": {"title": "Limnol Oceanogr", "issn": "0024-3590", "volume": "69", "issue": "5", "pages": "1030-1044", "issn-l": null}, "abstract": null, "doi": "10.1002/lno.12545", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-10-21T11:25:54.028Z", "modified": "2024-10-21T11:25:54.050Z"}, {"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": "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": "7a0719a5a1cc4cef963a4832ec073fd7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7a0719a5a1cc4cef963a4832ec073fd7"}}, "title": "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.", "authors": [{"family": "Edelbroek", "given": "Bart", "initials": "B", "orcid": "0000-0002-5184-0873", "researcher": {"href": "https://publications.scilifelab.se/researcher/164d0bef1b3e48668e136dbe0d2e8736.json"}}, {"family": "Kjellin", "given": "Jonas", "initials": "J", "orcid": "0000-0002-3830-7046", "researcher": {"href": "https://publications.scilifelab.se/researcher/daf9964b08fa498e9c0eb3540a0aa1fa.json"}}, {"family": "Biryukova", "given": "Inna", "initials": "I", "orcid": "0000-0003-0701-2808", "researcher": {"href": "https://publications.scilifelab.se/researcher/47d787e9d8e14b8fa598d8c3e82e4058.json"}}, {"family": "Liao", "given": "Zhen", "initials": "Z"}, {"family": "Lundberg", "given": "Torgny", "initials": "T"}, {"family": "Noegel", "given": "Angelika A", "initials": "AA"}, {"family": "Eichinger", "given": "Ludwig", "initials": "L", "orcid": "0000-0003-1594-6117", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2b977ccf8604c2a9a048b21878fc828.json"}}, {"family": "Friedl\u00e4nder", "given": "Marc R", "initials": "MR", "orcid": "0000-0001-6577-4363", "researcher": {"href": "https://publications.scilifelab.se/researcher/744f7c6d0a884d9daa2e7303ed1779b8.json"}}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3616-3509", "researcher": {"href": "https://publications.scilifelab.se/researcher/4952b493871a4970a089074117bb303f.json"}}], "type": "journal article", "published": "2024-04-12", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "52", "issue": "6", "pages": "3121-3136", "issn-l": "0305-1048"}, "abstract": "MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.", "doi": "10.1093/nar/gkae109", "pmid": "38375870", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11014262"}, {"db": "pii", "key": "7611030"}], "notes": [], "created": "2024-10-22T07:38:55.161Z", "modified": "2024-11-25T10:25:30.684Z"}, {"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": "577c244ab9fc4be88fafc3a8861cee93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/577c244ab9fc4be88fafc3a8861cee93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/577c244ab9fc4be88fafc3a8861cee93"}}, "title": "Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD.", "authors": [{"family": "Pagano", "given": "L", "initials": "L"}, {"family": "Simonetti", "given": "L", "initials": "L"}, {"family": "Pennacchietti", "given": "V", "initials": "V"}, {"family": "Toto", "given": "A", "initials": "A"}, {"family": "Malagrin\u00f2", "given": "F", "initials": "F"}, {"family": "Ivarsson", "given": "Y", "initials": "Y"}, {"family": "Gianni", "given": "S", "initials": "S"}], "type": "journal article", "published": "2024-04-09", "journal": {"title": "Biochem. Biophys. Res. Commun.", "issn": "1090-2104", "volume": "703", "pages": "149658", "issn-l": "0006-291X"}, "abstract": "Adaptor proteins play a pivotal role in cellular signaling mediating a multitude of protein-protein interaction critical for cellular homeostasis. Dysregulation of these interactions has been linked to the onset of various cancer pathologies and exploited by viral pathogens during host cell takeover. CrkL is an adaptor protein composed of an N-terminal SH2 domain followed by two SH3 domains that mediate interactions with diverse partners through the recognition of specific binding motifs. In this study, we employed proteomic peptide-phage display (ProP-PD) to comprehensively explore the short linear motif (SLiM)-based interactions of CrkL. Furthermore, we scrutinized how the binding affinity for selected peptides was influenced in the context of the full-length CrkL versus the isolated N-SH3 domain. Importantly, our results provided insights into SLiM-binding sites within previously reported interactors, as well as revealing novel human and viral ligands, expanding our understanding of the interactions mediated by CrkL and highlighting the significance of SLiM-based interactions in mediating adaptor protein function, with implications for cancer and viral pathologies.", "doi": "10.1016/j.bbrc.2024.149658", "pmid": "38387229", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0006-291X(24)00194-3"}], "notes": [], "created": "2024-03-21T09:26:15.858Z", "modified": "2024-03-21T09:26:15.862Z"}, {"entity": "publication", "iuid": "a82091c31c4d4910869e7a8476a5f298", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a82091c31c4d4910869e7a8476a5f298.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a82091c31c4d4910869e7a8476a5f298"}}, "title": "Treatment Monitoring of a Patient with Synchronous Metastatic Angiosarcoma and Breast Cancer Using ctDNA.", "authors": [{"family": "Vannas", "given": "Christoffer", "initials": "C", "orcid": "0000-0002-1029-0393", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0e2981f2d6d4da586bf9f02abdfa539.json"}}, {"family": "Escobar", "given": "Mandy", "initials": "M", "orcid": "0000-0002-9095-1429", "researcher": {"href": "https://publications.scilifelab.se/researcher/84cd7b6436cf4b5585c0c53370d88728.json"}}, {"family": "\u00d6sterlund", "given": "Tobias", "initials": "T", "orcid": "0000-0002-7870-8645", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd452c3f815846eba9a0da736ed6b252.json"}}, {"family": "Andersson", "given": "Daniel", "initials": "D", "orcid": "0000-0002-4564-6652", "researcher": {"href": "https://publications.scilifelab.se/researcher/655089dbe08b4b2283c3bf81a3db3abc.json"}}, {"family": "Mouhanna", "given": "Pia", "initials": "P", "orcid": "0009-0000-2722-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/17cb3367a55f432ba11e67badc6178b8.json"}}, {"family": "Soom\u00e4gi", "given": "Amanda", "initials": "A"}, {"family": "Molin", "given": "Claes", "initials": "C"}, {"family": "Wennergren", "given": "David", "initials": "D"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "St\u00e5hlberg", "given": "Anders", "initials": "A", "orcid": "0000-0003-4243-0191", "researcher": {"href": "https://publications.scilifelab.se/researcher/05306b130d6543eea88a4f518085981e.json"}}], "type": "case reports", "published": "2024-04-04", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "25", "issue": "7", "issn-l": null}, "abstract": "Angiosarcoma is a rare and aggressive type of soft-tissue sarcoma with high propensity to metastasize. For patients with metastatic angiosarcoma, prognosis is dismal and treatment options are limited. To improve the outcomes, identifying patients with poor treatment response at an earlier stage is imperative, enabling alternative therapy. Consequently, there is a need for improved methods and biomarkers for treatment monitoring. Quantification of circulating tumor-DNA (ctDNA) is a promising approach for patient-specific monitoring of treatment response. In this case report, we demonstrate that quantification of ctDNA using SiMSen-Seq was successfully utilized to monitor a patient with metastatic angiosarcoma. By quantifying ctDNA levels using 25 patient-specific mutations in blood plasma throughout surgery and palliative chemotherapy, we predicted the outcome and monitored the clinical response to treatment. This was accomplished despite the additional complexity of the patient having a synchronous breast cancer. The levels of ctDNA showed a superior correlation to the clinical outcome compared with the radiological evaluations. Our data propose a promising approach for personalized biomarker analysis to monitor treatment in angiosarcomas, with potential applicability to other cancers and for patients with synchronous malignancies.", "doi": "10.3390/ijms25074023", "pmid": "38612833", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11012383"}, {"db": "pii", "key": "ijms25074023"}], "notes": [], "created": "2024-05-16T06:28:56.803Z", "modified": "2024-05-16T06:28:57.902Z"}, {"entity": "publication", "iuid": "63e7b29f92a149148163f3d5af923fbd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63e7b29f92a149148163f3d5af923fbd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63e7b29f92a149148163f3d5af923fbd"}}, "title": "The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A"}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Ronnblom", "given": "Lars", "initials": "L"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-9588-0260", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6edb43a7da34bf9af85c876b1b8974a.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}], "type": "journal article", "published": "2024-04-04", "journal": {"title": "RMD Open", "issn": "2056-5933", "volume": "10", "issue": "2", "issn-l": "2056-5933"}, "abstract": "The antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV) are inflammatory disorders with ANCA autoantibodies recognising either proteinase 3 (PR3-AAV) or myeloperoxidase (MPO-AAV). PR3-AAV and MPO-AAV have been associated with distinct loci in the human leucocyte antigen (HLA) region. While the association between MPO-AAV and HLA has been well characterised in East Asian populations where MPO-AAV is more common, studies in populations of European descent are limited. The aim of this study was to thoroughly characterise associations to the HLA region in Scandinavian patients with PR3-AAV as well as MPO-AAV.\n\nGenotypes of single-nucleotide polymorphisms (SNPs) located in the HLA region were extracted from a targeted exome-sequencing dataset comprising Scandinavian AAV cases and controls. Classical HLA alleles were called using xHLA. After quality control, association analyses were performed of a joint SNP/classical HLA allele dataset for cases with PR3-AAV (n=411) and MPO-AAV (n=162) versus controls (n=1595). Disease-associated genetic variants were analysed for association with organ involvement, age at diagnosis and relapse, respectively.\n\nPR3-AAV was significantly associated with both HLA-DPB1*04:01 and rs1042335 at the HLA-DPB1 locus, also after stepwise conditional analysis. MPO-AAV was significantly associated with HLA-DRB1*04:04. Neither carriage of HLA-DPB1*04:01 alleles in PR3-AAV nor of HLA-DRB1*04:04 alleles in MPO-AAV were associated with organ involvement, age at diagnosis or relapse.\n\nThe association to the HLA region was distinct in Scandinavian cases with MPO-AAV compared with cases of East Asian descent. In PR3-AAV, the two separate signals of association to the HLD-DPB1 region mediate potentially different functional effects.", "doi": "10.1136/rmdopen-2023-004039", "pmid": "38580345", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "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": "PMC11002376"}, {"db": "pii", "key": "rmdopen-2023-004039"}], "notes": [], "created": "2024-04-15T06:10:27.649Z", "modified": "2024-11-25T10:28:43.870Z"}, {"entity": "publication", "iuid": "433fbcdbe4af4353acf3eda9ea1ddc67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/433fbcdbe4af4353acf3eda9ea1ddc67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/433fbcdbe4af4353acf3eda9ea1ddc67"}}, "title": "Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures.", "authors": [{"family": "Hellman", "given": "Maria", "initials": "M"}, {"family": "Juhanson", "given": "Jaanis", "initials": "J"}, {"family": "Walln\u00e4s", "given": "Felicia", "initials": "F"}, {"family": "Herbert", "given": "Roger B", "initials": "RB"}, {"family": "Hallin", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "356", "pages": "120607", "issn-l": null}, "abstract": "Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.", "doi": "10.1016/j.jenvman.2024.120607", "pmid": "38537471", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(24)00593-0"}], "notes": [], "created": "2024-05-16T06:31:09.458Z", "modified": "2024-05-16T06:31:09.461Z"}, {"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": "d95f4f6b8ceb4ca7b80714ec7fcb18f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d95f4f6b8ceb4ca7b80714ec7fcb18f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d95f4f6b8ceb4ca7b80714ec7fcb18f4"}}, "title": "Identification and surveillance of rare relapse-initiating stem cells during complete remission after transplantation.", "authors": [{"family": "Dimitriou", "given": "Marios", "initials": "M", "orcid": "0000-0001-8362-2099", "researcher": {"href": "https://publications.scilifelab.se/researcher/531c153359bb400fb48c7324a3bd69ad.json"}}, {"family": "Mortera-Blanco", "given": "Teresa", "initials": "T"}, {"family": "Tobiasson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3633-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/37b88e8e02af4145b95cc379c68ebee9.json"}}, {"family": "Mazzi", "given": "Stefania", "initials": "S"}, {"family": "Lehander", "given": "Madeleine", "initials": "M", "orcid": "0009-0005-0114-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad724c37fc354c209b21b9b60431bf8e.json"}}, {"family": "H\u00f6gstrand", "given": "Kari", "initials": "K"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"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"}, {"family": "Vonlanthen", "given": "Sofie", "initials": "S", "orcid": "0000-0002-6215-7631", "researcher": {"href": "https://publications.scilifelab.se/researcher/376695e4d6f54d1caf6e776bf537864b.json"}}, {"family": "Ljungman", "given": "Per", "initials": "P", "orcid": "0000-0002-8281-3245", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e5e4220ae354a2e99cd69797638a529.json"}}, {"family": "Langemeijer", "given": "Saskia", "initials": "S"}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T", "orcid": "0000-0003-4283-2983", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6f499e339d2444b817a81ab2712b9e5.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"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": "2024-03-14", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "143", "issue": "11", "pages": "953-966", "issn-l": "0006-4971"}, "abstract": "Relapse after complete remission (CR) remains the main cause of mortality after allogeneic stem cell transplantation for hematological malignancies and, therefore, improved biomarkers for early prediction of relapse remains a critical goal toward development and assessment of preemptive relapse treatment. Because the significance of cancer stem cells as a source of relapses remains unclear, we investigated whether mutational screening for persistence of rare cancer stem cells would enhance measurable residual disease (MRD) and early relapse prediction after transplantation. In a retrospective study of patients who relapsed and patients who achieved continuous-CR with myelodysplastic syndromes and related myeloid malignancies, combined flow cytometric cell sorting and mutational screening for persistence of rare relapse-initiating stem cells was performed in the bone marrow at multiple CR time points after transplantation. In 25 CR samples from 15 patients that later relapsed, only 9 samples were MRD-positive in mononuclear cells (MNCs) whereas flowcytometric-sorted hematopoietic stem and progenitor cells (HSPCs) were MRD-positive in all samples, and always with a higher variant allele frequency than in MNCs (mean, 97-fold). MRD-positivity in HSPCs preceded MNCs in multiple sequential samples, in some cases preceding relapse by >2 years. In contrast, in 13 patients in long-term continuous-CR, HSPCs remained MRD-negative. Enhanced MRD sensitivity was also observed in total CD34+ cells, but HSPCs were always more clonally involved (mean, 8-fold). In conclusion, identification of relapse-initiating cancer stem cells and mutational MRD screening for their persistence consistently enhances MRD sensitivity and earlier prediction of relapse after allogeneic stem cell transplantation.", "doi": "10.1182/blood.2023022851", "pmid": "38096358", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10950475"}, {"db": "pii", "key": "S0006-4971(23)14644-1"}], "notes": [], "created": "2024-10-21T11:19:06.816Z", "modified": "2024-10-21T11:19:21.211Z"}, {"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": "c033e6d550b3493f91cfc42d9b9ebccd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c033e6d550b3493f91cfc42d9b9ebccd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c033e6d550b3493f91cfc42d9b9ebccd"}}, "title": "Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France.", "authors": [{"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG", "orcid": "0000-0002-6119-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/eea5b7ccd8f84d44b2e0be03f5c4e762.json"}}, {"family": "Peyroteo-Stjerna", "given": "Rita", "initials": "R", "orcid": "0000-0002-3309-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6a9ae2a39e94beba21b461ef827ce17.json"}}, {"family": "Marchand", "given": "Gr\u00e9gor", "initials": "G"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "Vialet", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Chetty", "given": "Darshan", "initials": "D", "orcid": "0000-0003-4668-1182", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a9c8096ccbc4b4e943373d9a3acd5b1.json"}}, {"family": "Ala\u00e7aml\u0131", "given": "Erkin", "initials": "E", "orcid": "0009-0009-0702-3313", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb8084ce6634c9c8e33cc29e98f8252.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Bouquin", "given": "Denis", "initials": "D"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Garmond", "given": "Nicolas", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.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": "2024-03-05", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "121", "issue": "10", "pages": "e2310545121", "issn-l": "0027-8424"}, "abstract": "Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic fa\u00e7ade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and T\u00e9viec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, T\u00e9viec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.", "doi": "10.1073/pnas.2310545121", "pmid": "38408241", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10927518"}], "notes": [], "created": "2024-02-27T13:17:58.460Z", "modified": "2024-11-25T10:22:31.622Z"}, {"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": "6dad922586f84341baf632ac55a61367", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dad922586f84341baf632ac55a61367"}}, "title": "High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Hartmann", "given": "Fanny E", "initials": "FE", "orcid": "0000-0002-9365-4008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac8e717031aa4621925ab90684adecdc.json"}}, {"family": "Gautier", "given": "Val\u00e9rie", "initials": "V"}, {"family": "Silar", "given": "Philippe", "initials": "P", "orcid": "0000-0003-0104-987X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a40756e83bc493ebc1d98d8c5c374da.json"}}, {"family": "Giraud", "given": "Tatiana", "initials": "T"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2024-03-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "3", "issn-l": "1759-6653"}, "abstract": "The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.", "doi": "10.1093/gbe/evae034", "pmid": "38386982", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10936905"}, {"db": "pii", "key": "7612620"}], "notes": [], "created": "2024-08-02T12:17:18.611Z", "modified": "2025-02-28T14:18:08.086Z"}, {"entity": "publication", "iuid": "0d08036c5f154cf0b2c0036250a0fa7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e"}}, "title": "The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A", "orcid": "0000-0002-1130-374X", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a484451caf40f2a1a196b36bb9c423.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM"}, {"family": "Martinez-Barrio", "given": "Alvaro", "initials": "A", "orcid": "0000-0001-5064-2093", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ff319fe64340f2bb2350121848ecff.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "3", "pages": "e1010719", "issn-l": "1553-7390"}, "abstract": "DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.", "doi": "10.1371/journal.pgen.1010719", "pmid": "38457441", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "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": "PMC10954189"}, {"db": "pii", "key": "PGENETICS-D-23-00328"}], "notes": [], "created": "2024-11-12T10:39:26.077Z", "modified": "2024-11-25T10:31:41.001Z"}, {"entity": "publication", "iuid": "8d17e70e0b5b4f70bad804ace9812eb2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d17e70e0b5b4f70bad804ace9812eb2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d17e70e0b5b4f70bad804ace9812eb2"}}, "title": "Sorption of pharmaceuticals to foam and aerobic granular sludge with different morphologies", "authors": [{"family": "Burzio", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-3887-2720", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ce542ce47d54ef88fb4306b282aacf8.json"}}, {"family": "Mohammadi", "given": "Amir Saeid", "initials": "AS", "orcid": "0000-0002-4600-773X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ed821235675423489a4cefa067f4800.json"}}, {"family": "Smith", "given": "Sanne", "initials": "S"}, {"family": "Abadikhah", "given": "Marie", "initials": "M", "orcid": "0000-0002-4270-3340", "researcher": {"href": "https://publications.scilifelab.se/researcher/94d7106a506f42b7bffcce6ffe6b455a.json"}}, {"family": "Svahn", "given": "Ola", "initials": "O"}, {"family": "Modin", "given": "Oskar", "initials": "O", "orcid": "0000-0002-9232-6096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1cfa2dd97cc472c9307498a65b5a8c6.json"}}, {"family": "Persson", "given": "Frank", "initials": "F", "orcid": "0000-0002-0269-9375", "researcher": {"href": "https://publications.scilifelab.se/researcher/40290cae1a7e44c1939801323653b31c.json"}}, {"family": "Wil\u00e9n", "given": "Britt Marie", "initials": "BM"}], "type": "journal-article", "published": "2024-03-00", "journal": {"title": "Resources, Environment and Sustainability", "issn": "2666-9161", "volume": "15", "pages": "100149", "issn-l": null}, "abstract": null, "doi": "10.1016/j.resenv.2024.100149", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T09:00:42.585Z", "modified": "2025-12-04T19:40:39.711Z"}, {"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": "c301b4d4c3a547c0b128bb82f1379493", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c301b4d4c3a547c0b128bb82f1379493.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c301b4d4c3a547c0b128bb82f1379493"}}, "title": "Gustavson syndrome is caused by an in-frame deletion in RBMX associated with potentially disturbed SH3 domain interactions.", "authors": [{"family": "Johansson", "given": "Josefin", "initials": "J", "orcid": "0000-0002-5152-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/e568827124304b769a3f336d76b6954e.json"}}, {"family": "Lid\u00e9us", "given": "Sarah", "initials": "S"}, {"family": "Frykholm", "given": "Carina", "initials": "C"}, {"family": "Gunnarsson", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-9474-6820", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed1a42fede5f4f6d87c20d6bb9f694de.json"}}, {"family": "Mihalic", "given": "Filip", "initials": "F", "orcid": "0000-0002-6840-2319", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f57a961e98e4e15b1b96ec8efc95d4f.json"}}, {"family": "Gudmundsson", "given": "Sanna", "initials": "S", "orcid": "0000-0002-2332-074X", "researcher": {"href": "https://publications.scilifelab.se/researcher/adb097c987504b2ca309e5f4e1cea5d2.json"}}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Molin", "given": "Anna-Maja", "initials": "AM"}, {"family": "Pham", "given": "Mai", "initials": "M"}, {"family": "Vihinen", "given": "Mauno", "initials": "M", "orcid": "0000-0002-9614-7976", "researcher": {"href": "https://publications.scilifelab.se/researcher/250999f129ad4b4cb6e7e14c96988db9.json"}}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Jemth", "given": "Per", "initials": "P"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Wilbe", "given": "Maria", "initials": "M"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML", "orcid": "0000-0002-3391-5341", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bcb92e271664d9a83e618d5f3e43200.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "issn-l": "1018-4813", "volume": "32", "issue": "3", "pages": "333-341"}, "abstract": "RNA binding motif protein X-linked (RBMX) encodes the heterogeneous nuclear ribonucleoprotein G (hnRNP G) that regulates splicing, sister chromatid cohesion and genome stability. RBMX knock down experiments in various model organisms highlight the gene's importance for brain development. Deletion of the RGG/RG motif in hnRNP G has previously been associated with Shashi syndrome, however involvement of other hnRNP G domains in intellectual disability remain unknown. In the current study, we present the underlying genetic and molecular cause of Gustavson syndrome. Gustavson syndrome was first reported in 1993 in a large Swedish five-generation family presented with profound X-linked intellectual disability and an early death. Extensive genomic analyses of the family revealed hemizygosity for a novel in-frame deletion in RBMX in affected individuals (NM_002139.4; c.484_486del, p.(Pro162del)). Carrier females were asymptomatic and presented with skewed X-chromosome inactivation, indicating silencing of the pathogenic allele. Affected individuals presented minor phenotypic overlap with Shashi syndrome, indicating a different disease-causing mechanism. Investigation of the variant effect in a neuronal cell line (SH-SY5Y) revealed differentially expressed genes enriched for transcription factors involved in RNA polymerase II transcription. Prediction tools and a fluorescence polarization assay imply a novel SH3-binding motif of hnRNP G, and potentially a reduced affinity to SH3 domains caused by the deletion. In conclusion, we present a novel in-frame deletion in RBMX segregating with Gustavson syndrome, leading to disturbed RNA polymerase II transcription, and potentially reduced SH3 binding. The results indicate that disruption of different protein domains affects the severity of RBMX-associated intellectual disabilities.", "doi": "10.1038/s41431-023-01392-y", "pmid": "37277488", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Service", "Clinical Genomics Stockholm": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10923852"}, {"db": "pii", "key": "10.1038/s41431-023-01392-y"}], "notes": [], "created": "2023-08-15T07:12:40.774Z", "modified": "2024-11-25T10:15:29.202Z"}, {"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": "48838c48da18481db8283614f606bee7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48838c48da18481db8283614f606bee7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48838c48da18481db8283614f606bee7"}}, "title": "Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening.", "authors": [{"family": "Gezelius", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6242-6344", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad329767af94f9f9ad2c96771ff01d9.json"}}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP", "orcid": "0000-0001-6505-4198", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51093d7e7b14d5d859502c535117aad.json"}}, {"family": "Lundmark", "given": "Anders", "initials": "A", "orcid": "0000-0003-2611-1772", "researcher": {"href": "https://publications.scilifelab.se/researcher/52d2e64456104adcba388414d4197a35.json"}}, {"family": "\u00c5berg", "given": "Martin", "initials": "M"}, {"family": "Blom", "given": "Kristin", "initials": "K"}, {"family": "Rudfeldt", "given": "Jakob", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Harila", "given": "Arja", "initials": "A", "orcid": "0000-0003-2767-5828", "researcher": {"href": "https://publications.scilifelab.se/researcher/440e4d697787402283eded5995b706b7.json"}}, {"family": "Rendo", "given": "Ver\u00f3nica", "initials": "V", "orcid": "0000-0002-2983-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f3fe17dd4464af585b16916a88c34b7.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0003-0071-6802", "researcher": {"href": "https://publications.scilifelab.se/researcher/f47bcb3a6ec94202afc945a9f02984da.json"}}, {"family": "Andersson", "given": "Claes", "initials": "C"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "NAR Genom Bioinform", "issn": "2631-9268", "issn-l": null, "volume": "6", "issue": "1", "pages": "lqae001"}, "abstract": "Functional precision medicine (FPM) aims to optimize patient-specific drug selection based on the unique characteristics of their cancer cells. Recent advancements in high throughput ex vivo drug profiling have accelerated interest in FPM. Here, we present a proof-of-concept study for an integrated experimental system that incorporates ex vivo treatment response with a single-cell gene expression output enabling barcoding of several drug conditions in one single-cell sequencing experiment. We demonstrate this through a proof-of-concept investigation focusing on the glucocorticoid-resistant acute lymphoblastic leukemia (ALL) E/R+ Reh cell line. Three different single-cell transcriptome sequencing (scRNA-seq) approaches were evaluated, each exhibiting high cell recovery and accurate tagging of distinct drug conditions. Notably, our comprehensive analysis revealed variations in library complexity, sensitivity (gene detection), and differential gene expression detection across the methods. Despite these differences, we identified a substantial transcriptional response to fludarabine, a highly relevant drug for treating high-risk ALL, which was consistently recapitulated by all three methods. These findings highlight the potential of our integrated approach for studying drug responses at the single-cell level and emphasize the importance of method selection in scRNA-seq studies. Finally, our data encompassing 27 327 cells are freely available to extend to future scRNA-seq methodological comparisons.", "doi": "10.1093/nargab/lqae001", "pmid": "38288374", "labels": {"NGI Short read": "Technology development", "NGI Single cell": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10823582"}, {"db": "pii", "key": "lqae001"}], "notes": [], "created": "2024-02-27T08:22:26.710Z", "modified": "2024-11-25T10:25:20.383Z"}, {"entity": "publication", "iuid": "7d88f50cb8d04a5fbc77dec9965b97fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d88f50cb8d04a5fbc77dec9965b97fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d88f50cb8d04a5fbc77dec9965b97fd"}}, "title": "Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs.", "authors": [{"family": "\u00c5s", "given": "Joel", "initials": "J", "orcid": "0000-0001-8687-0629", "researcher": {"href": "https://publications.scilifelab.se/researcher/21836f99416d438c90f2fabd9620c38f.json"}}, {"family": "Bertulyte", "given": "Ilma", "initials": "I"}, {"family": "Norgren", "given": "Nina", "initials": "N"}, {"family": "Johansson", "given": "Anna", "initials": "A"}, {"family": "Eriksson", "given": "Niclas", "initials": "N"}, {"family": "Green", "given": "Henrik", "initials": "H"}, {"family": "Wadelius", "given": "Mia", "initials": "M", "orcid": "0000-0002-6368-2622", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec07b9869a1f4b77b734c5dc567dc630.json"}}, {"family": "Hallberg", "given": "P\u00e4r", "initials": "P"}], "type": "journal article", "published": "2024-02-29", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "issn-l": "1932-6203", "volume": "19", "issue": "2", "pages": "e0299075"}, "abstract": "A genetic predisposition to central nervous system (CNS) toxicity induced by antimicrobial drugs (antibiotics, antivirals, antifungals, and antiparasitic drugs) has been suspected. Whole genome sequencing of 66 cases and 833 controls was performed to investigate whether antimicrobial drug-induced CNS toxicity was associated with genetic variation. The primary objective was to test whether antimicrobial-induced CNS toxicity was associated with seventeen efflux transporters at the blood-brain barrier. In this study, variants or structural elements in efflux transporters were not significantly associated with CNS toxicity. Secondary objectives were to test whether antimicrobial-induced CNS toxicity was associated with genes over the whole genome, with HLA, or with structural genetic variation. Uncommon variants in and close to three genes were significantly associated with CNS toxicity according to a sequence kernel association test combined with an optimal unified test (SKAT-O). These genes were LCP1 (q = 0.013), RETSAT (q = 0.013) and SFMBT2 (q = 0.035). Two variants were driving the LCP1 association: rs6561297 (p = 1.15x10-6, OR: 4.60 [95% CI: 2.51-8.46]) and the regulatory variant rs10492451 (p = 1.15x10-6, OR: 4.60 [95% CI: 2.51-8.46]). No common genetic variant, HLA-type or structural variation was associated with CNS toxicity. In conclusion, CNS toxicity due to antimicrobial drugs was associated with uncommon variants in LCP1, RETSAT and SFMBT2.", "doi": "10.1371/journal.pone.0299075", "pmid": "38422004", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "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": "pmc", "key": "PMC10903854"}, {"db": "pii", "key": "PONE-D-23-09336"}], "notes": [], "created": "2024-03-21T08:23:52.159Z", "modified": "2024-11-25T10:32:17.378Z"}, {"entity": "publication", "iuid": "c00414cd923a4f9e9a0751b4edc7a150", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c00414cd923a4f9e9a0751b4edc7a150.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c00414cd923a4f9e9a0751b4edc7a150"}}, "title": "Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.", "authors": [{"family": "Rengefors", "given": "Karin", "initials": "K"}, {"family": "Annenkova", "given": "Nataliia", "initials": "N"}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Svensson", "given": "Marie", "initials": "M"}, {"family": "Kremp", "given": "Anke", "initials": "A"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}], "type": "journal article", "published": "2024-02-29", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "14", "issue": "1", "pages": "4986", "issn-l": "2045-2322"}, "abstract": "Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.", "doi": "10.1038/s41598-024-55362-5", "pmid": "38424140", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10904836"}, {"db": "pii", "key": "10.1038/s41598-024-55362-5"}], "notes": [], "created": "2024-03-06T13:04:42.545Z", "modified": "2024-11-25T10:20:53.163Z"}, {"entity": "publication", "iuid": "a67f3e238b3e4111bd9611513342ec90", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a67f3e238b3e4111bd9611513342ec90.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a67f3e238b3e4111bd9611513342ec90"}}, "title": "Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea.", "authors": [{"family": "K\u00e4lin", "given": "Carol", "initials": "C"}, {"family": "Piombo", "given": "Edoardo", "initials": "E"}, {"family": "Bourras", "given": "Salim", "initials": "S"}, {"family": "Brantestam", "given": "Agnese Kolodinska", "initials": "AK"}, {"family": "Dubey", "given": "Mukesh", "initials": "M"}, {"family": "Elfstrand", "given": "Malin", "initials": "M"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2024-02-28", "journal": {"title": "BMC Plant Biol.", "issn": "1471-2229", "volume": "24", "issue": "1", "pages": "144", "issn-l": "1471-2229"}, "abstract": "Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches.\n\nIn this study, we inoculated roots of the pea (P. sativum L.) genotypes 'Linnea' (susceptible) and 'PI180693' (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype 'PI180693', Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor.\n\nThis study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.", "doi": "10.1186/s12870-024-04817-y", "pmid": "38413860", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10900555"}, {"db": "pii", "key": "10.1186/s12870-024-04817-y"}], "notes": [], "created": "2024-03-21T08:59:08.449Z", "modified": "2025-02-28T14:22:21.812Z"}, {"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": "7e532fb85545426880d8fb6fec942f51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e532fb85545426880d8fb6fec942f51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e532fb85545426880d8fb6fec942f51"}}, "title": "Epigenome-wide analysis of frailty: Results from two European twin cohorts.", "authors": [{"family": "Mak", "given": "Jonathan K L", "initials": "JKL", "orcid": "0000-0003-4454-8580", "researcher": {"href": "https://publications.scilifelab.se/researcher/4994e82ef4784f06aff8017a9cf9ad1c.json"}}, {"family": "Skovgaard", "given": "Asmus Cosmos", "initials": "AC"}, {"family": "Nygaard", "given": "Marianne", "initials": "M"}, {"family": "Kananen", "given": "Laura", "initials": "L", "orcid": "0000-0003-3742-8927", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95c9eeb27214482bbbca978d69d79c7.json"}}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Wang", "given": "Yunzhang", "initials": "Y"}, {"family": "Kuja-Halkola", "given": "Ralf", "initials": "R"}, {"family": "Karlsson", "given": "Ida K", "initials": "IK", "orcid": "0000-0003-3605-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2c87ada82ae43df9753a891305ddb40.json"}}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "H\u00e4gg", "given": "Sara", "initials": "S", "orcid": "0000-0002-2452-1500", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1d010dfe5d84a33b6a6c7ec815ca3dc.json"}}, {"family": "Soerensen", "given": "Mette", "initials": "M"}, {"family": "Jylh\u00e4v\u00e4", "given": "Juulia", "initials": "J"}], "type": "journal article", "published": "2024-02-27", "journal": {"title": "Aging Cell", "issn": "1474-9726", "pages": "e14135", "issn-l": "1474-9718"}, "abstract": "Epigenetics plays an important role in the aging process, but it is unclear whether epigenetic factors also influence frailty, an age-related state of physiological decline. In this study, we performed a meta-analysis of epigenome-wide association studies in four samples drawn from the Swedish Adoption/Twin Study of Aging (SATSA) and the Longitudinal Study of Aging Danish Twins (LSADT) to explore the association between DNA methylation and frailty. Frailty was defined using the frailty index (FI), and DNA methylation levels were measured in whole blood using Illumina's Infinium HumanMethylation450K and MethylationEPIC arrays. In the meta-analysis consisting of a total of 829 participants, we identified 589 CpG sites that were statistically significantly associated with either the continuous or categorical FI (false discovery rate <0.05). Many of these CpGs have previously been associated with age and age-related diseases. The identified sites were also largely directionally consistent in a longitudinal analysis using mixed-effects models in SATSA, where the participants were followed up to a maximum of 20 years. Moreover, we identified three differentially methylated regions within the MGRN1, MIR596, and TAPBP genes that have been linked to neuronal aging, tumor growth, and immune functions. Furthermore, our meta-analysis results replicated 34 of the 77 previously reported frailty-associated CpGs at p < 0.05. In conclusion, our findings demonstrate robust associations between frailty and DNA methylation levels in 589 novel CpGs, previously unidentified for frailty, and strengthen the role of neuronal/brain pathways in frailty.", "doi": "10.1111/acel.14135", "pmid": "38414347", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T08:58:19.904Z", "modified": "2024-03-21T08:58:20.068Z"}, {"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": "367948cbf0ae47cf812c5b5b3726fccf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/367948cbf0ae47cf812c5b5b3726fccf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/367948cbf0ae47cf812c5b5b3726fccf"}}, "title": "Long noncoding RNA plasmacytoma variant translocation 1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity.", "authors": [{"family": "Li", "given": "Chen", "initials": "C"}, {"family": "Sun", "given": "Chengxi", "initials": "C"}, {"family": "Mahapatra", "given": "Kunal Das", "initials": "KD"}, {"family": "Riihil\u00e4", "given": "Pilvi", "initials": "P"}, {"family": "Knuutila", "given": "Jaakko", "initials": "J"}, {"family": "Nissinen", "given": "Liisa", "initials": "L"}, {"family": "Lapins", "given": "Jan", "initials": "J"}, {"family": "K\u00e4h\u00e4ri", "given": "Veli-Matti", "initials": "VM"}, {"family": "Homey", "given": "Bernhard", "initials": "B"}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E"}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}], "type": "journal article", "published": "2024-02-16", "journal": {"title": "Br J Dermatol", "issn": "1365-2133", "volume": "190", "issue": "3", "pages": "415-426", "issn-l": null}, "abstract": "Cutaneous squamous cell carcinoma (cSCC) is one of the most common and fastest increasing forms of cancer worldwide with metastatic potential. Long noncoding RNAs (lncRNAs) are a group of RNA molecules with essential regulatory functions in both physiological and pathological processes.\n\nTo investigate the function and mode of action of lncRNA plasmacytoma variant translocation 1 (PVT1) in cSCC.\n\nQuantitative reverse transcriptase polymerase chain reaction and single-molecule in situ hybridization were used to quantify the expression level of PVT1 in normal skin, premalignant skin lesions, actinic keratosis (AK) and primary and metastatic cSCCs. The function of PVT1 in cSCC was investigated both in vivo (tumour xenografts) and in vitro (competitive cell growth assay, 5-ethynyl-2'-deoxyuridine incorporation assay, colony formation assay and tumour spheroid formation assay) upon CRISPR-Cas9-mediated knockout of the entire PVT1 locus, the knockout of exon 2 of PVT1, and locked nucleic acid (LNA) gapmer-mediated PVT1 knockdown. RNA sequencing analysis was conducted to identify genes and processes regulated by PVT1.\n\nWe identified PVT1 as a lncRNA upregulated in cSCC in situ and cSCC, associated with the malignant phenotype of cSCC. We showed that the expression of PVT1 in cSCC was regulated by MYC. Both CRISPR-Cas9 deletion of the entire PVT1 locus and LNA gapmer-mediated knockdown of PVT1 transcript impaired the malignant behaviour of cSCC cells, suggesting that PVT1 is an oncogenic transcript in cSCC. Furthermore, knockout of PVT1 exon 2 inhibited cSCC tumour growth both in vivo and in vitro, demonstrating that exon 2 is a critical element for the oncogenic role of PVT1. Mechanistically, we showed that PVT1 was localized in the cell nucleus and its deletion resulted in cellular senescence, increased cyclin-dependent kinase inhibitor 1 (p21/CDKN1A) expression and cell cycle arrest.\n\nOur study revealed a previously unrecognized role for exon 2 of PVT1 in its oncogenic role and that PVT1 suppresses cellular senescence in cSCC. PVT1 may be a potential biomarker and therapeutic target in cSCC.", "doi": "10.1093/bjd/ljad419", "pmid": "37930852", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7335666"}], "notes": [], "created": "2024-03-21T09:00:02.277Z", "modified": "2024-11-25T10:22:57.516Z"}, {"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": "c050833f0c82481bb5fca4a4262261f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c050833f0c82481bb5fca4a4262261f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c050833f0c82481bb5fca4a4262261f2"}}, "title": "Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.", "authors": [{"family": "Yildirim", "given": "Y", "initials": "Y"}, {"family": "Kristensson", "given": "D", "initials": "D"}, {"family": "Outomuro", "given": "D", "initials": "D"}, {"family": "Mikolajewski", "given": "D", "initials": "D"}, {"family": "R\u00f6din M\u00f6rch", "given": "P", "initials": "P"}, {"family": "Sniegula", "given": "S", "initials": "S"}, {"family": "Johansson", "given": "F", "initials": "F"}], "type": "journal article", "published": "2024-02-03", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "24", "issue": "1", "pages": "19", "issn-l": null}, "abstract": "Describing geographical variation in morphology of organisms in combination with data on genetic differentiation and biogeography can provide important information on how natural selection shapes such variation. Here we study genetic structure using ddRAD seq and wing shape variation using geometric morphometrics in 14 populations of the damselfly Lestes sponsa along its latitudinal range in Europe.\n\nThe genetic analysis showed a significant, yet relatively weak population structure with high genetic heterozygosity and low inbreeding coefficients, indicating that neutral processes contributed very little to the observed wing shape differences. The genetic analysis also showed that some regions of the genome (about 10%) are putatively shaped by selection. The phylogenetic analysis showed that the Spanish and French populations were the ancestral ones with northern Swedish and Finnish populations being the most derived ones. We found that wing shape differed significantly among populations and showed a significant quadratic (but weak) relationship with latitude. This latitudinal relationship was largely attributed to allometric effects of wing size, but non-allometric variation also explained a portion of this relationship. However, wing shape showed no phylogenetic signal suggesting that lineage-specific variation did not contribute to the variation along the latitudinal gradient. In contrast, wing size, which is correlated with body size in L. sponsa, had a strong negative correlation with latitude.\n\nOur results suggest a relatively weak population structure among the sampled populations across Europe, but a clear differentiation between south and north populations. The observed geographic phenotypic variation in wing shape may have been affected by different local selection pressures or environmental effects.", "doi": "10.1186/s12862-024-02207-4", "pmid": "38308224", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10838002"}, {"db": "pii", "key": "10.1186/s12862-024-02207-4"}], "notes": [], "created": "2024-03-21T09:24:09.188Z", "modified": "2024-11-25T10:29:31.490Z"}, {"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": "f9d5f8d15fc7400e9233f987f8a71a33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f9d5f8d15fc7400e9233f987f8a71a33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f9d5f8d15fc7400e9233f987f8a71a33"}}, "title": "Multimodal Single-Cell Sequencing of B Cells in Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Arvidsson", "given": "Gustav", "initials": "G", "orcid": "0000-0001-7396-1820", "researcher": {"href": "https://publications.scilifelab.se/researcher/29beb4f9dd8b460382eab4f916fc1072.json"}}, {"family": "Czarnewski", "given": "Paulo", "initials": "P", "orcid": "0000-0001-8150-4021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b84309de4e3946159c374ffa6d977560.json"}}, {"family": "Johansson", "given": "Alina", "initials": "A"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J", "orcid": "0000-0002-7230-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d4c2f630d484ee780c2c12aaabdb939.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Nordmark", "given": "Gunnel", "initials": "G", "orcid": "0000-0002-3829-7431", "researcher": {"href": "https://publications.scilifelab.se/researcher/188fda53498740dbb007441cc94bb1ad.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "issn-l": "2326-5191", "volume": "76", "issue": "2", "pages": "255-267"}, "abstract": "B cells are important in the pathogenesis of primary Sj\u00f6gren's syndrome (pSS). Patients positive for Sj\u00f6gren's syndrome antigen A/Sj\u00f6gren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression, and B cell receptor usage in pSS subgroups stratified for SSA/SSB antibodies.\r\n\r\nOver 230,000 B cells were isolated from peripheral blood of patients with pSS (n = 6 SSA-, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls and processed for single-cell RNA sequencing (scRNA-seq) and single-cell variable, diversity, and joining (VDJ) gene sequencing (scVDJ-seq).\r\n\r\nWe show that SSA/SSB+ patients present the highest and lowest proportion of na\u00efve and memory B cells, respectively, and the highest up-regulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared with other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification of patients with pSS and identified novel parameters that correlated to disease manifestations and antibody status.\r\n\r\nWe describe heterogeneity and molecular characteristics in B cells from patients with pSS, providing clues to intrinsic differences in B cells that affect the phenotype and outcome and allowing stratification of patients with pSS at improved resolution.", "doi": "10.1002/art.42683", "pmid": "37610265", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-09-20T16:42:27.105Z", "modified": "2024-11-05T18:21:35.829Z"}, {"entity": "publication", "iuid": "b6c8b4628a8b4d1e9ad4c1345f3d8d26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6c8b4628a8b4d1e9ad4c1345f3d8d26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6c8b4628a8b4d1e9ad4c1345f3d8d26"}}, "title": "Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.", "authors": [{"family": "Longo", "given": "Alessio", "initials": "A"}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Vanhala", "given": "Tytti", "initials": "T"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2024-02-00", "journal": {"title": "Anim Genet", "issn": "1365-2052", "volume": "55", "issue": "1", "pages": "87-98", "issn-l": "0268-9146"}, "abstract": "Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne ) and inbreeding (based on runs of homozygosity; FROH ) were similar amongst the three populations (Ne \u2248 50-80; median FROH \u2248 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.", "doi": "10.1111/age.13378", "pmid": "37994156", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCA_013265735.3"}], "notes": [], "created": "2024-03-21T08:48:47.551Z", "modified": "2024-03-21T08:48:47.647Z"}, {"entity": "publication", "iuid": "c6ee9d682b4440b98f597b4ff57d6037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6ee9d682b4440b98f597b4ff57d6037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6ee9d682b4440b98f597b4ff57d6037"}}, "title": "A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.", "authors": [{"family": "Lindel\u00f6f", "given": "Linnea", "initials": "L"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Enocsson", "given": "Helena", "initials": "H"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Diaz-Gallo", "given": "Lina-Marcela", "initials": "LM"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT consortium", "given": "", "initials": ""}, {"family": "ImmunoArray consortium", "given": "", "initials": ""}, {"family": "Nilsson Ekdahl", "given": "Kristina", "initials": "K"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Eriksson", "given": "Oskar", "initials": "O"}], "type": "multicenter study", "published": "2024-02-00", "journal": {"title": "J. Autoimmun.", "issn": "1095-9157", "issn-l": "0896-8411", "volume": "143", "issue": null, "pages": "103166"}, "abstract": "The complement system plays a central role in the pathogenesis of Systemic Lupus Erythematosus (SLE), but most studies have focused on the classical pathway. Ficolin-3 is the main initiator of the lectin pathway of complement in humans, but its role in systemic autoimmune disease has not been conclusively determined. Here, we combined biochemical and genetic approaches to assess the contribution of ficolin-3 to SLE risk and disease manifestations. Ficolin-3 activity was measured by a functional assay in serum or plasma samples from Swedish SLE patients (n = 786) and controls matched for age and sex (n = 566). Genetic variants in an extended 300 kb genomic region spanning the FCN3 locus were analyzed for their association with ficolin-3 activity and SLE manifestations in a Swedish multicenter cohort (n = 985). Patients with ficolin-3 activity in the highest tertile showed a strong enrichment in an SLE cluster defined by anti-Sm/DNA/nucleosome antibodies (OR 3.0, p < 0.001) and had increased rates of hematological disease (OR 1.4, p = 0.078) and lymphopenia (OR = 1.6, p = 0.039). Genetic variants associated with low ficolin-3 activity mapped to an extended haplotype in high linkage disequilibrium upstream of the FCN3 gene. Patients carrying the lead genetic variant associated with low ficolin-3 activity had a lower frequency of hematological disease (OR 0.67, p = 0.018) and lymphopenia (OR 0.63, p = 0.031) and fewer autoantibodies (p = 0.0019). Loss-of-function variants in the FCN3 gene were not associated with SLE, but four (0.5 %) SLE patients developed acquired ficolin-3 deficiency where ficolin-3 activity in serum was depleted following diagnosis of SLE. Taken together, our results provide genetic and biochemical evidence that implicate the lectin pathway in hematological SLE manifestations. We also identify lectin pathway activation through ficolin-3 as a factor that contributes to the autoantibody response in SLE.", "doi": "10.1016/j.jaut.2023.103166", "pmid": "38219652", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0896-8411(23)00175-0"}], "notes": [], "created": "2024-01-16T08:53:44.077Z", "modified": "2025-02-28T14:12:16.457Z"}, {"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": "bd2469b856a34c23bf93587d768559f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd2469b856a34c23bf93587d768559f2"}}, "title": "A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.", "authors": [{"family": "von Beek", "given": "Christopher", "initials": "C", "orcid": "0000-0001-6310-7583", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3ea7730832f4f45ae6583076d90418a.json"}}, {"family": "Fahlgren", "given": "Anna", "initials": "A"}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Di Martino", "given": "Maria Letizia", "initials": "ML", "orcid": "0000-0002-9491-4000", "researcher": {"href": "https://publications.scilifelab.se/researcher/708eae058cb3494f8407574a666a16f0.json"}}, {"family": "Lindahl", "given": "Otto", "initials": "O", "orcid": "0000-0001-7518-9483", "researcher": {"href": "https://publications.scilifelab.se/researcher/78053dd357c3435ba53aff83f06f28a4.json"}}, {"family": "Prensa", "given": "Grisna I", "initials": "GI", "orcid": "0009-0002-7101-7224", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d030d78925948d993999b66e1959acc.json"}}, {"family": "Mendez-Enriquez", "given": "Erika", "initials": "E", "orcid": "0000-0002-2114-2812", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae73474be904a638ec13a8f704a9154.json"}}, {"family": "Eriksson", "given": "Jens", "initials": "J", "orcid": "0000-0002-8945-2665", "researcher": {"href": "https://publications.scilifelab.se/researcher/b94e7f542841474d86d53aa48958f870.json"}}, {"family": "Hallgren", "given": "Jenny", "initials": "J", "orcid": "0000-0002-3685-5364", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe8b929dbe60446f96db17a5eb2ba6f3.json"}}, {"family": "F\u00e4llman", "given": "Maria", "initials": "M", "orcid": "0000-0001-6874-6384", "researcher": {"href": "https://publications.scilifelab.se/researcher/cadcd4e3e63742e7b9cbbb74907bf9fc.json"}}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}], "type": "journal article", "published": "2024-01-30", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "904", "issn-l": "2041-1723"}, "abstract": "Mast cells localize to mucosal tissues and contribute to innate immune defense against infection. How mast cells sense, differentiate between, and respond to bacterial pathogens remains a topic of ongoing debate. Using the prototype enteropathogen Salmonella Typhimurium (S.Tm) and other related enterobacteria, here we show that mast cells can regulate their cytokine secretion response to distinguish between extracellular and invasive bacterial infection. Tissue-invasive S.Tm and mast cells colocalize in the mouse gut during acute Salmonella infection. Toll-like Receptor 4 (TLR4) sensing of extracellular S.Tm, or pure lipopolysaccharide, causes a modest induction of cytokine transcripts and proteins, including IL-6, IL-13, and TNF. By contrast, type-III-secretion-system-1 (TTSS-1)-dependent S.Tm invasion of both mouse and human mast cells triggers rapid and potent inflammatory gene expression and >100-fold elevated cytokine secretion. The S.Tm TTSS-1 effectors SopB, SopE, and SopE2 here elicit a second activation signal, including Akt phosphorylation downstream of effector translocation, which combines with TLR activation to drive the full-blown mast cell response. Supernatants from S.Tm-infected mast cells boost macrophage survival and maturation from bone-marrow progenitors. Taken together, this study shows that mast cells can differentiate between extracellular and host-cell invasive enterobacteria via a two-step activation mechanism and tune their inflammatory output accordingly.", "doi": "10.1038/s41467-024-45057-w", "pmid": "38291037", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10828507"}, {"db": "pii", "key": "10.1038/s41467-024-45057-w"}], "notes": [], "created": "2024-03-21T12:10:55.423Z", "modified": "2024-03-21T12:10:55.804Z"}, {"entity": "publication", "iuid": "0533fbff25544d368a04f51d1e5e1a3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0533fbff25544d368a04f51d1e5e1a3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0533fbff25544d368a04f51d1e5e1a3b"}}, "title": "Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.", "authors": [{"family": "Harish", "given": "Ajith", "initials": "A"}, {"family": "Lopes Pinto", "given": "Fernando A", "initials": "FA"}, {"family": "Eriksson", "given": "Susanne", "initials": "S"}, {"family": "Johansson", "given": "Anna M", "initials": "AM"}], "type": "journal article", "published": "2024-01-22", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "89", "issn-l": "1471-2164"}, "abstract": "Several indigenous cattle breeds in Sweden are endangered. Conservation of their genetic diversity and genomic characterization is a priority.Whole-genome sequences (WGS) with a mean coverage of 25X, ranging from 14 to 41X were obtained for 30 individuals of the breeds Fj\u00e4llko, Fj\u00e4lln\u00e4ra, Bohuskulla, R\u00f6dkulla, Ringam\u00e5la, and V\u00e4neko. WGS-based genotyping revealed 22,548,028 variants in total, comprising 18,876,115 single nucleotide polymorphisms (SNPs) and 3,671,913 indels. Out of these, 1,154,779 SNPs and 304,467 indels were novel. Population stratification based on roughly 19 million SNPs showed two major groups of the breeds that correspond to northern and southern breeds. Overall, a higher genetic diversity was observed in the southern breeds compared to the northern breeds. While the population stratification was consistent with previous genome-wide SNP array-based analyses, the genealogy of the individuals inferred from WGS based estimates turned out to be more complex than expected from previous SNP-array based estimates. Polymorphisms and their predicted phenotypic consequences were associated with differences in the coat color phenotypes between the northern and southern breeds. Notably, these high-consequence polymorphisms were not represented in SNP arrays, which are used routinely for genotyping of cattle breeds.This study is the first WGS-based population genetic analysis of Swedish native cattle breeds. The genetic diversity of native breeds was found to be high. High-consequence polymorphisms were linked with desirable phenotypes using whole-genome genotyping, which highlights the pressing need for intensifying WGS-based characterization of the native breeds.", "doi": "10.1186/s12864-024-09959-9", "pmid": "38254050", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10802049"}, {"db": "pii", "key": "10.1186/s12864-024-09959-9"}], "notes": [], "created": "2024-03-21T08:57:34.995Z", "modified": "2024-03-21T08:57:34.998Z"}, {"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": "b4caed4485bd40efab57b71f77ec67ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4caed4485bd40efab57b71f77ec67ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4caed4485bd40efab57b71f77ec67ce"}}, "title": "Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.", "authors": [{"family": "Bergman", "given": "Ingrid", "initials": "I"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES"}, {"family": "Sassenhagen", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2024-01-18", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "volume": "87", "issue": "1", "pages": "33", "issn-l": "0095-3628"}, "abstract": "The freshwater raphidophyte Gonyostomum semen forms extensive summer blooms in northern European humic lakes. The development of these blooms might be facilitated by a lack of natural top-down control, as few zooplankton species are able to prey on these large algal cells (up to 100 \u03bcm) that expel trichocysts upon physical stress. In this study, we describe a small ciliate species (< 17 \u03bcm) that preys on G. semen by damaging the cell membrane until cytoplasm and organelles spill out. Sequencing of clonal cultures of the ciliate tentatively identified it as the prostomatid species Urotricha pseudofurcata. Grazing experiments illustrated that feeding by U. cf. pseudofurcata can significantly reduce cell concentrations of the microalga. However, differences in cell size and growth rate between two investigated ciliate strains resulted in noticeably different grazing pressure. Environmental sequencing data from five different lakes supported potential interactions between the two species. Urotricha cf. pseudofurcata might, thus, play an important role in aquatic ecosystems that are regularly dominated by G. semen, reducing the abundance of this bloom-forming microalga and enabling transfer of organic carbon to higher trophic levels.", "doi": "10.1007/s00248-024-02344-9", "pmid": "38236289", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796478"}, {"db": "pii", "key": "10.1007/s00248-024-02344-9"}], "notes": [], "created": "2024-03-21T09:24:50.987Z", "modified": "2024-03-21T09:24:50.990Z"}, {"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": "20c1a1e54fca4f0cb892dc1d755b69c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20c1a1e54fca4f0cb892dc1d755b69c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20c1a1e54fca4f0cb892dc1d755b69c0"}}, "title": "Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis).", "authors": [{"family": "Ozerov", "given": "M Y", "initials": "MY"}, {"family": "Noreikiene", "given": "K", "initials": "K"}, {"family": "Kahar", "given": "S", "initials": "S"}, {"family": "Flaj\u0161hans", "given": "M", "initials": "M"}, {"family": "Gross", "given": "R", "initials": "R"}, {"family": "Vasem\u00e4gi", "given": "A", "initials": "A"}], "type": "journal article", "published": "2024-01-11", "journal": {"title": "Comp Biochem Physiol B Biochem Mol Biol", "issn": "1879-1107", "volume": "271", "pages": "110941", "issn-l": null}, "abstract": "Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multi-tissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.", "doi": "10.1016/j.cbpb.2024.110941", "pmid": "38218377", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1096-4959(24)00008-3"}], "notes": [], "created": "2024-03-21T08:56:46.467Z", "modified": "2025-02-28T14:11:45.742Z"}, {"entity": "publication", "iuid": "f0568a2c147043eeb312c4016dbb907f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0568a2c147043eeb312c4016dbb907f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0568a2c147043eeb312c4016dbb907f"}}, "title": "Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents.", "authors": [{"family": "Gollnisch", "given": "Raphael", "initials": "R"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "ISME J", "issn": "1751-7370", "volume": "18", "issue": "1", "issn-l": "1751-7362"}, "abstract": "The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the USA. Our aim was to investigate if populations of Gonyostomum semen in Europe and in the USA are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on single-amplified genomes combined with Restriction-site Associated DNA sequencing that allows de novo genotyping of natural single-cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the USA and identified two distinct population clusters, one in Europe and another in the USA. Low genetic diversity in European populations supports the hypothesized recent expansion of Gonyostomum semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables that may have led to ecological divergence of population clusters. Overall, our results show that single-amplified genomes combined with Restriction-site Associated DNA sequencing can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.", "doi": "10.1093/ismejo/wrae045", "pmid": "38489771", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11065318"}, {"db": "pii", "key": "7630124"}], "notes": [], "created": "2024-05-16T06:27:02.910Z", "modified": "2025-02-28T14:18:49.908Z"}, {"entity": "publication", "iuid": "98e4505a97e8498295f664d0b66ace12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/98e4505a97e8498295f664d0b66ace12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/98e4505a97e8498295f664d0b66ace12"}}, "title": "Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris.", "authors": [{"family": "Duan", "given": "Tianlin", "initials": "T", "orcid": "0000-0002-8719-7998", "researcher": {"href": "https://publications.scilifelab.se/researcher/78c1a5d458814388bbcbbe6a020944d6.json"}}, {"family": "Sicard", "given": "Adrien", "initials": "A"}, {"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S", "orcid": "0000-0001-7260-4573", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ce5a8d7ac9a490eb2e261aeb75088d4.json"}}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Allopolyploidization is a frequent evolutionary transition in plants that combines whole-genome duplication (WGD) and interspecific hybridization. The genome of an allopolyploid species results from initial interactions between parental genomes and long-term evolution. Distinguishing the contributions of these two phases is essential to understanding the evolutionary trajectory of allopolyploid species. Here, we compared phenotypic and transcriptomic changes in natural and resynthesized Capsella allotetraploids with their diploid parental species. We focused on phenotypic traits associated with the selfing syndrome and on transcription-level phenomena such as expression-level dominance (ELD), transgressive expression (TRE), and homoeolog expression bias (HEB). We found that selfing syndrome, high pollen, and seed quality in natural allotetraploids likely resulted from long-term evolution. Similarly, TRE and most down-regulated ELD were only found in natural allopolyploids. Natural allotetraploids also had more ELD toward the self-fertilizing parental species than resynthesized allotetraploids, mirroring the establishment of the selfing syndrome. However, short-term changes mattered, and 40% of the cases of ELD in natural allotetraploids were already observed in resynthesized allotetraploids. Resynthesized allotetraploids showed striking variation of HEB among chromosomes and individuals. Homoeologous synapsis was its primary source and may still be a source of genetic variation in natural allotetraploids. In conclusion, both short- and long-term mechanisms contributed to transcriptomic and phenotypic changes in natural allotetraploids. However, the initial gene expression changes were largely reshaped during long-term evolution leading to further morphological changes.", "doi": "10.7554/eLife.88398", "pmid": "38189348", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10945474"}, {"db": "pii", "key": "88398"}], "notes": [], "created": "2024-03-21T13:55:14.769Z", "modified": "2024-11-25T10:34:07.268Z"}, {"entity": "publication", "iuid": "56fbf8aaced9497f957befcc3c5c0dbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56fbf8aaced9497f957befcc3c5c0dbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56fbf8aaced9497f957befcc3c5c0dbb"}}, "title": "A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.", "authors": [{"family": "Biderre-Petit", "given": "Corinne", "initials": "C", "orcid": "0000-0001-7962-4171", "researcher": {"href": "https://publications.scilifelab.se/researcher/8199e3021db54bb9b2f9124a682ac305.json"}}, {"family": "Courtine", "given": "Damien", "initials": "D"}, {"family": "Hennequin", "given": "Claire", "initials": "C"}, {"family": "Galand", "given": "Pierre E", "initials": "PE", "orcid": "0000-0002-2238-3247", "researcher": {"href": "https://publications.scilifelab.se/researcher/a36433c063bf4305afd6ac1ba7a67ddf.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Debroas", "given": "Didier", "initials": "D", "orcid": "0000-0002-9915-1268", "researcher": {"href": "https://publications.scilifelab.se/researcher/6146106a7ee449e5bda7d6e8773b60dc.json"}}, {"family": "Monjot", "given": "Arthur", "initials": "A", "orcid": "0000-0002-6978-4785", "researcher": {"href": "https://publications.scilifelab.se/researcher/46d5728dbea84c50bf7f2b183558f7c2.json"}}, {"family": "Lep\u00e8re", "given": "C\u00e9cile", "initials": "C", "orcid": "0000-0003-4767-0477", "researcher": {"href": "https://publications.scilifelab.se/researcher/796cc43ff3074c069d822502ad0e3449.json"}}, {"family": "Divne", "given": "Anna-Maria", "initials": "A"}, {"family": "Hochart", "given": "Corentin", "initials": "C"}], "type": "journal article", "published": "2024-01-08", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": null, "issue": null, "pages": "e13923"}, "abstract": "The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.", "doi": "10.1111/1755-0998.13923", "pmid": "38189173", "labels": {"Microbial Single Cell Genomics": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-15T10:09:02.759Z", "modified": "2024-02-27T08:39:51.267Z"}, {"entity": "publication", "iuid": "edb9aa23ac704f2384a042691edc79e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edb9aa23ac704f2384a042691edc79e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edb9aa23ac704f2384a042691edc79e2"}}, "title": "Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite.", "authors": [{"family": "C\u012brulis", "given": "Aivars", "initials": "A", "orcid": "0000-0003-3472-865X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed7cd12abf3e450288217a8acaa2190d.json"}}, {"family": "Nord\u00e9n", "given": "Anna K", "initials": "AK"}, {"family": "Churcher", "given": "Allison M", "initials": "AM"}, {"family": "Ramm", "given": "Steven A", "initials": "SA"}, {"family": "Zadesenets", "given": "Kira S", "initials": "KS"}, {"family": "Abbott", "given": "Jessica K", "initials": "JK", "orcid": "0000-0002-8743-2089", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be37bf315f34e18b7ad8714da1381b8.json"}}], "type": "journal article", "published": "2024-01-05", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "1", "pages": null}, "abstract": "The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.", "doi": "10.1093/gbe/evad235", "pmid": "38155579", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10786194"}, {"db": "pii", "key": "7503504"}], "notes": [], "created": "2024-01-09T14:09:35.198Z", "modified": "2025-02-28T14:17:57.633Z"}, {"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": "5c597fc7742544a6b34a0e5fd1b7a1bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5c597fc7742544a6b34a0e5fd1b7a1bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5c597fc7742544a6b34a0e5fd1b7a1bb"}}, "title": "Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens.", "authors": [{"family": "Guo", "given": "Ying", "initials": "Y"}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ"}, {"family": "R\u00f6nneburg", "given": "Tilman", "initials": "T"}, {"family": "Wang", "given": "Shouzhi", "initials": "S"}, {"family": "Li", "given": "Hui", "initials": "H"}, {"family": "Hu", "given": "Xiaoxiang", "initials": "X"}, {"family": "Carlborg", "given": "\u00d6rjan", "initials": "\u00d6"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Poult. Sci.", "issn": "1525-3171", "volume": "103", "issue": "1", "pages": "103232", "issn-l": "0032-5791"}, "abstract": "We compared the genomes of multiple domestic chicken breeds with red and white earlobes to identify the differentiated regions between groups of breeds differing in earlobe color. This was done using a selective sweep mapping approach based on whole-genome sequence data. The most significant selective sweep was identified on chromosome 11, where the white earlobe chicken breeds originated from Mediterranean share a common haplotype, and where multiple candidate genes are located. The most plausible functional candidate gene is the Melanocortin 1 Receptor (MC1R), a receptor known to regulate pigmentation in the skin and hair, and it is also the gene with the strongest positional support from the haplotype-based analyses. It, however, still needs to be explored experimentally to identify effects also on chicken earlobe color variation. Our study is the first exploration of the genetic basis of white earlobe color in Mediterranean chickens using a selective sweep mapping method based on whole-genome sequencing data and shows its value for identifying likely functional genes mediating the pigmentation in earlobe. It also indicates a potential novel role of MC1R in birds and exemplifies how selection on fancy traits has influenced the genome during formation of the modern chicken breeds.", "doi": "10.1016/j.psj.2023.103232", "pmid": "37980749", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10692716"}, {"db": "pii", "key": "S0032-5791(23)00751-4"}], "notes": [], "created": "2024-01-08T15:29:48.324Z", "modified": "2024-01-08T15:29:48.327Z"}, {"entity": "publication", "iuid": "bfae70dd68a54db286b9e8e040803c9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfae70dd68a54db286b9e8e040803c9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfae70dd68a54db286b9e8e040803c9f"}}, "title": "The genetic legacy of the expansion of Bantu-speaking peoples in Africa.", "authors": [{"family": "Fortes-Lima", "given": "Cesar A", "initials": "CA", "orcid": "0000-0002-9310-5009", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a1afb9addfa42b4aa92a74ed8a8586b.json"}}, {"family": "Burgarella", "given": "Concetta", "initials": "C"}, {"family": "Hammar\u00e9n", "given": "Rickard", "initials": "R", "orcid": "0000-0001-9017-591X", "researcher": {"href": "https://publications.scilifelab.se/researcher/01a7b62a04c14b99bd73fb436006e4ff.json"}}, {"family": "Eriksson", "given": "Anders", "initials": "A", "orcid": "0000-0003-3436-3726", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d31ca9cd2d4c658ff92d9726311d75.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Jolly", "given": "Cecile", "initials": "C"}, {"family": "Semo", "given": "Armando", "initials": "A"}, {"family": "Gunnink", "given": "Hilde", "initials": "H", "orcid": "0000-0002-5508-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/153efdc0d8f54dc1bd754526479a3b42.json"}}, {"family": "Pacchiarotti", "given": "Sara", "initials": "S", "orcid": "0000-0003-1360-5060", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8565dac645f45aaaf34ea46fac71703.json"}}, {"family": "Mundeke", "given": "Leon", "initials": "L"}, {"family": "Matonda", "given": "Igor", "initials": "I"}, {"family": "Muluwa", "given": "Joseph Koni", "initials": "JK"}, {"family": "Coutros", "given": "Peter", "initials": "P", "orcid": "0000-0002-4861-6432", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c95e69649fb40d3944d65a07c7e76b8.json"}}, {"family": "Nyambe", "given": "Terry S", "initials": "TS"}, {"family": "Cikomola", "given": "Justin Cirhuza", "initials": "JC", "orcid": "0000-0002-0856-5992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4058aac2a3bf4fe4a6d8724d002ea864.json"}}, {"family": "Coetzee", "given": "Vinet", "initials": "V"}, {"family": "de Castro", "given": "Minique", "initials": "M"}, {"family": "Ebbesen", "given": "Peter", "initials": "P"}, {"family": "Delanghe", "given": "Joris", "initials": "J", "orcid": "0000-0002-5702-6792", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc00e2044f7246578cbea5abdf98e844.json"}}, {"family": "Stoneking", "given": "Mark", "initials": "M"}, {"family": "Barham", "given": "Lawrence", "initials": "L", "orcid": "0000-0002-5474-4668", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f2502e25e9047bc811c878c90289cfa.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Meyer", "given": "Anja", "initials": "A", "orcid": "0000-0002-5275-9276", "researcher": {"href": "https://publications.scilifelab.se/researcher/67901afbd54943c3997b3c6348bfb94f.json"}}, {"family": "Steyn", "given": "Maryna", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Rocha", "given": "Jorge", "initials": "J", "orcid": "0000-0001-5460-7615", "researcher": {"href": "https://publications.scilifelab.se/researcher/37e0a929cf884352bbdc844b4db86f28.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Pakendorf", "given": "Brigitte", "initials": "B"}, {"family": "Bostoen", "given": "Koen", "initials": "K", "orcid": "0000-0003-2284-6165", "researcher": {"href": "https://publications.scilifelab.se/researcher/026b51a02da64bc99d42f6df582b29d4.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "625", "issue": "7995", "pages": "540-547", "issn-l": "0028-0836"}, "abstract": "The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.", "doi": "10.1038/s41586-023-06770-6", "pmid": "38030719", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10794141"}, {"db": "pii", "key": "10.1038/s41586-023-06770-6"}], "notes": [], "created": "2023-12-01T06:47:49.351Z", "modified": "2024-11-25T10:19:18.159Z"}, {"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": "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": "0e680eec7e28428ba9cc34cfcdb773fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e680eec7e28428ba9cc34cfcdb773fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e680eec7e28428ba9cc34cfcdb773fe"}}, "title": "Population genomic data reveal low genetic diversity, divergence and local adaptation among threatened Reeves's Pheasant (Syrmaticus reevesii)", "authors": [{"family": "Lu", "given": "Qi", "initials": "Q"}, {"family": "Wang", "given": "Pengcheng", "initials": "P"}, {"family": "Chang", "given": "Jiang", "initials": "J"}, {"family": "Chen", "given": "De", "initials": "D"}, {"family": "Gao", "given": "Shenghan", "initials": "S"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}, {"family": "Zhang", "given": "Zhengwang", "initials": "Z"}], "type": "journal-article", "published": "2024-00-00", "journal": {"title": "Avian Research", "issn": "2053-7166", "volume": "15", "pages": "100156", "issn-l": null}, "abstract": null, "doi": "10.1016/j.avrs.2023.100156", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2024-03-21T08:49:30.981Z", "modified": "2025-12-04T17:15:18.325Z"}, {"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": "5646472bef1e4cf5a38babba13f39b12", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5646472bef1e4cf5a38babba13f39b12.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5646472bef1e4cf5a38babba13f39b12"}}, "title": "Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells.", "authors": [{"family": "Abadikhah", "given": "Marie", "initials": "M"}, {"family": "Liu", "given": "Ming", "initials": "M"}, {"family": "Persson", "given": "Frank", "initials": "F"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}, {"family": "Farewell", "given": "Anne", "initials": "A"}, {"family": "Sun", "given": "Jie", "initials": "J"}, {"family": "Modin", "given": "Oskar", "initials": "O"}], "type": "journal article", "published": "2023-12-15", "journal": {"title": "Biofilm", "issn": "2590-2075", "volume": "6", "pages": "100161", "issn-l": null}, "abstract": "In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54-80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10-16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61-98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0-20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64-89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.", "doi": "10.1016/j.bioflm.2023.100161", "pmid": "37859795", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582064"}, {"db": "pii", "key": "S2590-2075(23)00058-8"}], "notes": [], "created": "2023-11-29T11:35:13.039Z", "modified": "2023-11-29T11:35:13.056Z"}, {"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": "fa0c81dcc024441fa1eeb827056ba874", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa0c81dcc024441fa1eeb827056ba874.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa0c81dcc024441fa1eeb827056ba874"}}, "title": "Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse.", "authors": [{"family": "Kurt", "given": "Zeyneb", "initials": "Z", "orcid": "0000-0003-3186-8091", "researcher": {"href": "https://publications.scilifelab.se/researcher/64250f1d007945c3897e7698e2dabf55.json"}}, {"family": "Cheng", "given": "Jenny", "initials": "J", "orcid": "0009-0009-2248-1697", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2b5c909f04a4bce9d13a29d39f0e00b.json"}}, {"family": "Barrere-Cain", "given": "Rio", "initials": "R"}, {"family": "McQuillen", "given": "Caden N", "initials": "CN", "orcid": "0000-0002-7762-9283", "researcher": {"href": "https://publications.scilifelab.se/researcher/107d075ac0ff498cbc0d1571db912569.json"}}, {"family": "Saleem", "given": "Zara", "initials": "Z"}, {"family": "Hsu", "given": "Neil", "initials": "N"}, {"family": "Jiang", "given": "Nuoya", "initials": "N"}, {"family": "Pan", "given": "Calvin", "initials": "C"}, {"family": "Franz\u00e9n", "given": "Oscar", "initials": "O", "orcid": "0000-0002-7573-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/da9f587e682f433dbcdbe932861d1a69.json"}}, {"family": "Koplev", "given": "Simon", "initials": "S"}, {"family": "Wang", "given": "Susanna", "initials": "S", "orcid": "0009-0006-0254-8418", "researcher": {"href": "https://publications.scilifelab.se/researcher/d94dc3b61cff49288601993fed78788c.json"}}, {"family": "Bj\u00f6rkegren", "given": "Johan", "initials": "J"}, {"family": "Lusis", "given": "Aldons J", "initials": "AJ", "orcid": "0000-0001-9013-0228", "researcher": {"href": "https://publications.scilifelab.se/researcher/534cbc36b84f44ddbdbb7e5cc78c11a9.json"}}, {"family": "Blencowe", "given": "Montgomery", "initials": "M", "orcid": "0000-0001-7147-1895", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6456f51239c473685cf9af4ad7e7e0e.json"}}, {"family": "Yang", "given": "Xia", "initials": "X", "orcid": "0000-0002-3971-038X", "researcher": {"href": "https://publications.scilifelab.se/researcher/71b78d5687ba491d8c1dddd171483557.json"}}], "type": "journal article", "published": "2023-12-07", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "12", "issn-l": "2050-084X"}, "abstract": "Mouse models have been used extensively to study human coronary artery disease (CAD) or atherosclerosis and to test therapeutic targets. However, whether mouse and human share similar genetic factors and pathogenic mechanisms of atherosclerosis has not been thoroughly investigated in a data-driven manner. We conducted a cross-species comparison study to better understand atherosclerosis pathogenesis between species by leveraging multiomics data. Specifically, we compared genetically driven and thus CAD-causal gene networks and pathways, by using human GWAS of CAD from the CARDIoGRAMplusC4D consortium and mouse GWAS of atherosclerosis from the Hybrid Mouse Diversity Panel (HMDP) followed by integration with functional multiomics human (STARNET and GTEx) and mouse (HMDP) databases. We found that mouse and human shared >75% of CAD causal pathways. Based on network topology, we then predicted key regulatory genes for both the shared pathways and species-specific pathways, which were further validated through the use of single cell data and the latest CAD GWAS. In sum, our results should serve as a much-needed guidance for which human CAD-causal pathways can or cannot be further evaluated for novel CAD therapies using mouse models.", "doi": "10.7554/eLife.88266", "pmid": "38060277", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10703441"}, {"db": "pii", "key": "88266"}], "notes": [], "created": "2024-01-08T15:29:00.638Z", "modified": "2024-01-08T15:29:01.015Z"}, {"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": "7d6870c445a44b8e9a55a8424dfa6383", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d6870c445a44b8e9a55a8424dfa6383.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d6870c445a44b8e9a55a8424dfa6383"}}, "title": "Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.", "authors": [{"family": "Jensen", "given": "Axel", "initials": "A", "orcid": "0000-0003-1766-560X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f139b7f3dac49e28ef6430637d88592.json"}}, {"family": "Swift", "given": "Frances", "initials": "F"}, {"family": "de Vries", "given": "Dorien", "initials": "D"}, {"family": "Beck", "given": "Robin M D", "initials": "RMD"}, {"family": "Kuderna", "given": "Lukas F K", "initials": "LFK"}, {"family": "Knauf", "given": "Sascha", "initials": "S"}, {"family": "Chuma", "given": "Idrissa S", "initials": "IS"}, {"family": "Keyyu", "given": "Julius D", "initials": "JD"}, {"family": "Kitchener", "given": "Andrew C", "initials": "AC", "orcid": "0000-0003-2594-0827", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e8441bdcd504f7ebcc29c55337dd5ac.json"}}, {"family": "Farh", "given": "Kyle", "initials": "K"}, {"family": "Rogers", "given": "Jeffrey", "initials": "J", "orcid": "0000-0002-7374-6490", "researcher": {"href": "https://publications.scilifelab.se/researcher/18b3aaf283e443feb46f08e2aba6dc3d.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T"}, {"family": "Detwiler", "given": "Kate M", "initials": "KM"}, {"family": "Roos", "given": "Christian", "initials": "C"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2023-12-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "40", "issue": "12", "issn-l": "0737-4038"}, "abstract": "Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.", "doi": "10.1093/molbev/msad247", "pmid": "37987553", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10691879"}, {"db": "pii", "key": "7439455"}], "notes": [], "created": "2024-01-08T15:46:27.376Z", "modified": "2024-01-16T13:48:31.531Z"}, {"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": "24281e6606fc498595f006d4846e5c40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24281e6606fc498595f006d4846e5c40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24281e6606fc498595f006d4846e5c40"}}, "title": "DNA elements tether canonical Polycomb Repressive Complex 1 to human genes.", "authors": [{"family": "Barrasa", "given": "Juan I", "initials": "JI"}, {"family": "Kahn", "given": "Tatyana G", "initials": "TG"}, {"family": "Lundkvist", "given": "Moa J", "initials": "MJ"}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB", "orcid": "0000-0003-4790-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2751a236629d4b8bb9fff42cad6ff614.json"}}], "type": "journal article", "published": "2023-11-27", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "51", "issue": "21", "pages": "11613-11633", "issn-l": "0305-1048"}, "abstract": "Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to repress key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report the identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. We use the term tether to describe a process leading to a prominent presence of canonical PRC1 at certain genomic sites, although the complex is unlikely to interact with DNA directly. Detailed analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 or PRC2 to ones capable of tethering both complexes. The emerging picture is similar to the paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.", "doi": "10.1093/nar/gkad889", "pmid": "37855680", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "7321990"}, {"db": "pmc", "key": "PMC10681801"}], "notes": [], "created": "2023-11-29T11:38:28.542Z", "modified": "2023-11-29T11:38:28.552Z"}, {"entity": "publication", "iuid": "644ff655a61e46c08a5438a23c82830c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/644ff655a61e46c08a5438a23c82830c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/644ff655a61e46c08a5438a23c82830c"}}, "title": "RecView: an interactive R application for locating recombination positions using pedigree data.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2023-11-25", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "712", "issn-l": "1471-2164"}, "abstract": "Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes.\n\nWe present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions.\n\nRecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub ( https://github.com/HKyleZhang/RecView.git ).", "doi": "10.1186/s12864-023-09807-2", "pmid": "38007417", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10676570"}, {"db": "pii", "key": "10.1186/s12864-023-09807-2"}], "notes": [], "created": "2024-01-08T16:11:18.459Z", "modified": "2024-01-16T13:48:31.644Z"}, {"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": "7e7ba23c03714d3d9b58baa6d2f778a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e7ba23c03714d3d9b58baa6d2f778a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e7ba23c03714d3d9b58baa6d2f778a3"}}, "title": "Novel PNKP mutations associated with reduced DNA single-strand break repair and severe microcephaly, seizures, and developmental delay.", "authors": [{"family": "Thuresson", "given": "Ann-Charlotte", "initials": "A"}, {"family": "Brazina", "given": "Jan", "initials": "J"}, {"family": "Akram", "given": "Talia", "initials": "T"}, {"family": "Albrecht", "given": "Julia", "initials": "J"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Soussi Zander", "given": "Cecilia", "initials": "C"}, {"family": "Caldecott", "given": "Keith W", "initials": "KW"}], "type": "journal article", "published": "2023-11-02", "journal": {"title": "Mol Genet Genomic Med", "issn": "2324-9269", "issn-l": "2324-9269", "volume": null, "issue": null, "pages": "e2295"}, "abstract": "Microcephaly with early-onset seizures (MCSZ) is a neurodevelopmental disorder caused by pathogenic variants in the DNA strand break repair protein, polynucleotide kinase 3'-phosphatase (PNKP).\r\n\r\nWe have used whole genome sequencing and Sanger sequencing to identify disease-causing variants, followed by a minigene assay, Western blotting, alkaline comet assay, \u03b3H2AX, and ADP-ribose immunofluorescence.\r\n\r\nHere, we describe a patient with compound heterozygous variants in PNKP, including a missense variant in the DNA phosphatase domain (T323M) and a novel splice acceptor site variant within the DNA kinase domain that we show leads to exon skipping. We show that primary fibroblasts derived from the patient exhibit greatly reduced levels of PNKP protein and reduced rates of DNA single-strand break repair, confirming that the mutated PNKP alleles are dysfunctional.\r\n\r\nThe data presented show that the detected compound heterozygous variants result in reduced levels of PNKP protein, which affect the repair of both oxidative and TOP1-induced single-strand breaks, and most likely causes MCSZ in this patient.", "doi": "10.1002/mgg3.2295", "pmid": "37916443", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T11:00:34.255Z", "modified": "2024-01-16T13:48:31.746Z"}, {"entity": "publication", "iuid": "f361c17689bc48929bd23e7d629f9f1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b"}}, "title": "Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Tarka", "given": "Maja", "initials": "M", "orcid": "0000-0001-9651-1101", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0abfbfc5bb4d5fb77f356c6ad80a34.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2023-11-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 \u00d7 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 \u00d7 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.", "doi": "10.1093/gbe/evad180", "pmid": "37793164", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10627410"}, {"db": "pii", "key": "7289221"}], "notes": [], "created": "2023-11-29T10:54:38.925Z", "modified": "2024-01-16T13:48:31.754Z"}, {"entity": "publication", "iuid": "551fd99639b84ce0a81b1e975a93fbcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/551fd99639b84ce0a81b1e975a93fbcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/551fd99639b84ce0a81b1e975a93fbcd"}}, "title": "Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence.", "authors": [{"family": "Lumpi", "given": "Theresa", "initials": "T", "orcid": "0000-0002-1202-7222", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdcba53ace234cb9b8ad49d220abf665.json"}}, {"family": "Guo", "given": "Xin", "initials": "X"}, {"family": "Lindstr\u00f6m", "given": "Eva S", "initials": "ES", "orcid": "0000-0001-8920-3071", "researcher": {"href": "https://publications.scilifelab.se/researcher/9290d334ce5a4488b8afd2af511e02ad.json"}}], "type": "journal article", "published": "2023-11-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "25", "issue": "11", "pages": "2289-2302", "issn-l": "1462-2912"}, "abstract": "When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.", "doi": "10.1111/1462-2920.16450", "pmid": "37381117", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T12:43:22.827Z", "modified": "2024-01-16T13:48:31.783Z"}, {"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": "3be027fad7744b0f91376a35ec831490", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3be027fad7744b0f91376a35ec831490.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3be027fad7744b0f91376a35ec831490"}}, "title": "Complete Mitochondrial DNA Genome Variation in the Swedish Population.", "authors": [{"family": "Sturk-Andreaggi", "given": "Kimberly", "initials": "K", "orcid": "0000-0001-6857-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1cbf7b4fd94b17b1c37712634b7638.json"}}, {"family": "Bodner", "given": "Martin", "initials": "M", "orcid": "0000-0002-3870-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/455fefcf430d4b7e8433b3c7b3856b4b.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": "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"}, {"family": "Allen", "given": "Marie", "initials": "M"}], "type": "journal article", "published": "2023-10-25", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "14", "issue": "11", "issn-l": "2073-4425"}, "abstract": "The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.", "doi": "10.3390/genes14111989", "pmid": "38002932", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10671102"}, {"db": "pii", "key": "genes14111989"}], "notes": [], "created": "2023-11-30T13:00:25.373Z", "modified": "2023-11-30T13:00:25.400Z"}, {"entity": "publication", "iuid": "dfc74d55aa694120a0e496375231c4dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfc74d55aa694120a0e496375231c4dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfc74d55aa694120a0e496375231c4dc"}}, "title": "Polymorphic parasitic larvae cooperate to build swimming colonies luring hosts.", "authors": [{"family": "Krupenko", "given": "Darya", "initials": "D"}, {"family": "Miroliubov", "given": "Aleksei", "initials": "A"}, {"family": "Kryukov", "given": "Emil", "initials": "E"}, {"family": "Faure", "given": "Louis", "initials": "L"}, {"family": "Minemizu", "given": "Ryo", "initials": "R"}, {"family": "Haag", "given": "Lars", "initials": "L"}, {"family": "Lundgren", "given": "Magnus", "initials": "M"}, {"family": "Kameneva", "given": "Polina", "initials": "P"}, {"family": "Kastriti", "given": "Maria Eleni", "initials": "ME"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}], "type": "journal article", "published": "2023-10-23", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "33", "issue": "20", "pages": "4524-4531.e4", "issn-l": "0960-9822"}, "abstract": "Parasites have evolved a variety of astonishing strategies to survive within their hosts, yet the most challenging event in their personal chronicles is the passage from one host to another. It becomes even more complex when a parasite needs to pass through the external environment. Therefore, the free-living stages of parasites present a wide range of adaptations for transmission. Parasitic flatworms from the group Digenea (flukes) have free-living larvae, cercariae, which are remarkably diverse in structure and behavior.1,2 One of the cercariae transmission strategies is to attain a prey-like appearance for the host.3 This can be done through the formation of a swimming aggregate of several cercariae adjoined together by their tails.4 Through the use of live observations and light, electron, and confocal microscopy, we described such a supposedly prey-mimetic colony comprising cercariae of two distinct morphotypes. They are functionally specialized: larger morphotype (sailors) enable motility, and smaller morphotype (passengers) presumably facilitate infection. The analysis of local read alignments between the two samples reveals that both cercaria types have identical 18S, 28S, and 5.8S rRNA genes. Further phylogenetic analysis of these ribosomal sequences indicates that our specimen belongs to the digenean family Acanthocolpidae, likely genus Pleorchis. This discovery provides a unique example and a novel insight into how morphologically and functionally heterogeneous individuals of the same species cooperate to build colonial organisms for the purpose of infection. This strategy bears resemblance to the cooperating castes of the same species found among insects.5.", "doi": "10.1016/j.cub.2023.08.090", "pmid": "37741283", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(23)01170-3"}], "notes": [], "created": "2023-11-29T13:25:24.376Z", "modified": "2025-02-27T04:14:54.724Z"}, {"entity": "publication", "iuid": "335442be797344c78004c386eda66ecf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/335442be797344c78004c386eda66ecf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/335442be797344c78004c386eda66ecf"}}, "title": "Screening for atypical porcine pestivirus in Swedish boar semen used for artificial insemination and a characterisation of the seminal RNA microbiome including the virome.", "authors": [{"family": "Stenberg", "given": "Hedvig", "initials": "H"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}], "type": "journal article", "published": "2023-10-20", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "volume": "19", "issue": "1", "pages": "219", "issn-l": null}, "abstract": "This study aimed to characterise the RNA microbiome, including the virome of extended semen from Swedish breeding boars, with particular focus on Atypical porcine pestivirus (APPV). This neurotropic virus, associated with congenital tremor type A-II in piglets, was recently demonstrated to induce the disease through insemination with semen from infected boars.\n\nFrom 124 Artificial Insemination (AI) doses from Swedish breeding boars, APPV was detected in one dose in addition to a sparse seminal RNA virome, characterised by retroviruses, phages, and some fecal-associated contaminants. The detected seminal microbiome was large and characterized by Gram-negative bacteria from the phylum Proteobacteria, mainly consisting of apathogenic or opportunistic bacteria. The proportion of bacteria with a pathogenic potential was low, and no antimicrobial resistance genes (ARGs) were detected in the datasets.\n\nOverall, the results indicate a good health status among Swedish breeding boars. The detection of APPV in semen raises the question of whether routine screening for APPV in breeding boars should be instigated.", "doi": "10.1186/s12917-023-03762-6", "pmid": "37864222", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10588136"}, {"db": "pii", "key": "10.1186/s12917-023-03762-6"}], "notes": [], "created": "2023-11-29T11:41:20.114Z", "modified": "2024-01-16T13:48:31.917Z"}, {"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": "467d9682bec746ed878a1bacf430dbca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/467d9682bec746ed878a1bacf430dbca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/467d9682bec746ed878a1bacf430dbca"}}, "title": "Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.", "authors": [{"family": "Sar\u00e9n", "given": "Tina", "initials": "T", "orcid": "0000-0001-5227-6779", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8f06b113565445f8dc2882a926229b6.json"}}, {"family": "Ramachandran", "given": "Mohanraj", "initials": "M", "orcid": "0000-0003-2685-0575", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3fefc78a0b040faa998efb8fde7b920.json"}}, {"family": "Gammelg\u00e5rd", "given": "Gustav", "initials": "G", "orcid": "0009-0008-5522-0103", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f8652afc79e4fe39e82bb49a5dc5307.json"}}, {"family": "L\u00f6vgren", "given": "Tanja", "initials": "T", "orcid": "0000-0003-2170-0682", "researcher": {"href": "https://publications.scilifelab.se/researcher/a578be87e95941fe8d59d344d03d1dd2.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications.scilifelab.se/researcher/00052b54a3d24fd4a6e648f987d15e5f.json"}}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K", "orcid": "0000-0003-2224-7090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb8c1fc5f704cbfb87471226485ae1f.json"}}, {"family": "Wikstr\u00f6m", "given": "Kristina", "initials": "K", "orcid": "0009-0000-1027-2534", "researcher": {"href": "https://publications.scilifelab.se/researcher/0922ad45252045e9b2ac4d8ad264a718.json"}}, {"family": "Hashemi", "given": "Jamileh", "initials": "J", "orcid": "0000-0002-4997-3765", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1dd38f2d9644c1c8a9bf870fc69ef2a.json"}}, {"family": "Freyhult", "given": "Eva", "initials": "E", "orcid": "0000-0003-0226-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/be110f11a53d4dcfa3bfd1657167895e.json"}}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H", "orcid": "0000-0002-8701-969X", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e4a209929642ceaadf3e0aed6b8c69.json"}}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Hagberg", "given": "Hans", "initials": "H", "orcid": "0000-0001-7855-2452", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec21157056f48e49cb2f7c528d16b1d.json"}}, {"family": "Loskog", "given": "Angelica", "initials": "A", "orcid": "0000-0001-8583-6138", "researcher": {"href": "https://publications.scilifelab.se/researcher/5730068a851041ecb0bce96c2954bb28.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G", "orcid": "0000-0002-0594-724X", "researcher": {"href": "https://publications.scilifelab.se/researcher/11313af3f4a241ecb93af23ab2652195.json"}}, {"family": "Essand", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9725-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5afc47ab0814c09909af3c66217a3a6.json"}}], "type": "journal article", "published": "2023-10-13", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "29", "issue": "20", "pages": "4139-4152"}, "abstract": "Although CD19 chimeric antigen receptor T cells (CAR-T) therapy has shown remarkable success in B-cell malignancies, a substantial fraction of patients do not obtain a long-term clinical response. This could be influenced by the quality of the individual CAR-T infusion product. To shed some light on this, clinical outcome was correlated to characteristics of CAR-T infusion products.\n\nIn this phase II study, patients with B-cell lymphoma (n = 23) or leukemia (n = 1) received one or two infusions of third-generation CD19-directed CAR-Ts (2 \u00d7 108/m2). The clinical trial was registered at clinicaltrials.gov: NCT03068416. We investigated the transcriptional profile of individual CD19 CAR-T infusion products using targeted single-cell RNA sequencing and multicolor flow cytometry.\n\nTwo CAR-T infusions were not better than one in the settings used in this study. As for the CAR-T infusion products, we found that effector-like CD8+CAR-Ts with a high polyfunctionality, high cytotoxic and cytokine production profile, and low dysfunctional signature were associated with clinical response. An extended ex vivo expansion time during CAR-T manufacturing negatively influenced the proportion of effector CD8+CAR-Ts in the infusion product.\n\nWe identified cell-intrinsic characteristics of effector CD8+CAR-Ts correlating with response that could be used as an indicator for clinical outcome. The results in the study also serve as a guide to CAR-T manufacturing practices.", "doi": "10.1158/1078-0432.CCR-23-0178", "pmid": "37540566", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Affinity Proteomics Uppsala": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10570681"}, {"db": "pii", "key": "728314"}, {"db": "ClinicalTrials.gov", "key": "NCT03068416"}], "notes": [], "created": "2023-09-20T16:40:48.854Z", "modified": "2024-11-12T12:30:30.156Z"}, {"entity": "publication", "iuid": "dc9a30bd8f0e49a59ae2fc54afee5c1c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc9a30bd8f0e49a59ae2fc54afee5c1c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc9a30bd8f0e49a59ae2fc54afee5c1c"}}, "title": "Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M"}, {"family": "\u00d6vern\u00e4s", "given": "Elin", "initials": "E"}, {"family": "Lagensj\u00f6", "given": "Johanna", "initials": "J"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Petri", "given": "Anna", "initials": "A"}, {"family": "Wiman", "given": "Ann-Christin", "initials": "A"}, {"family": "Ramsell", "given": "Jon", "initials": "J"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Gezelius", "given": "Henrik", "initials": "H"}, {"family": "Martin", "given": "Tom", "initials": "T"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Ekberg", "given": "Sara", "initials": "S"}, {"family": "Erlandsson", "given": "Rikard", "initials": "R"}, {"family": "Larsson", "given": "Pontus", "initials": "P"}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Hellstedt Kerje", "given": "Susanne", "initials": "S"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Ameur", "given": "Adam", "initials": "A"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}], "type": "journal article", "published": "2023-10-10", "journal": {"title": "BMC Res Notes", "issn": "1756-0500", "issn-l": "1756-0500", "volume": "16", "issue": "1", "pages": "265"}, "abstract": "The aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into the complex aberrant karyotype of REH, and be used as reference datasets for sequencing data quality assessment or for methods development.\r\n\r\nThis paper describes 33 datasets corresponding to 867 gigabases of raw sequencing data generated from the REH cell line. These datasets include five different approaches for whole genome sequencing (WGS) on four sequencing platforms, two RNA sequencing (RNA-seq) techniques on two different sequencing platforms, DNA methylation sequencing, and single-cell ATAC-sequencing.", "doi": "10.1186/s13104-023-06537-2", "pmid": "37817248", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10566058"}, {"db": "pii", "key": "10.1186/s13104-023-06537-2"}], "notes": [], "created": "2023-10-12T11:13:24.427Z", "modified": "2024-01-16T13:48:31.989Z"}, {"entity": "publication", "iuid": "57d336fde81e4a409b232134a6c24a50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57d336fde81e4a409b232134a6c24a50"}}, "title": "Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Bi", "given": "Huijuan", "initials": "H"}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S"}, {"family": "Lei", "given": "Weipan", "initials": "W"}, {"family": "Chen", "given": "Juexin", "initials": "J"}, {"family": "Wei", "given": "Chentao", "initials": "C"}, {"family": "Liu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4580-5518", "researcher": {"href": "https://publications.scilifelab.se/researcher/abd2de623f33467b89b1cf800db4b3f5.json"}}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Widemo", "given": "Fredrik", "initials": "F"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-10-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "12", "pages": "msad224"}, "abstract": "A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves two rare inversion haplotypes (Satellite and Faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (Independent) haplotype indicates that the inversion could be as old as 4 million years. Here we have constructed a highly contiguous genome assembly of the inversion region for both the Independent and Satellite haplotypes. Based on the new data we estimate that the recombination event(s) creating the Satellite haplotype occurred only about 70,000 years ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the Satellite and Faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N gene CENPN is disrupted by the inversion, and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.", "doi": "10.1093/molbev/msad224", "pmid": "37804117", "labels": {"NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7296052"}], "notes": [], "created": "2023-10-10T08:45:20.886Z", "modified": "2024-01-16T13:48:31.996Z"}, {"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": "97328d83a5ff458481fbad51e7615b21", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97328d83a5ff458481fbad51e7615b21"}}, "title": "Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.", "authors": [{"family": "Merino", "given": "Irene", "initials": "I"}, {"family": "Guasca", "given": "Alexandra Olarte", "initials": "AO"}, {"family": "Krmela", "given": "Ales", "initials": "A"}, {"family": "Arif", "given": "Usman", "initials": "U"}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"family": "Westerberg", "given": "Erik", "initials": "E"}, {"family": "Jalmi", "given": "Siddhi Kashinanth", "initials": "SK"}, {"family": "Hajslova", "given": "Jana", "initials": "J"}, {"family": "Schulzova", "given": "Vera", "initials": "V"}, {"family": "Sitbon", "given": "Folke", "initials": "F"}], "type": "journal article", "published": "2023-10-04", "journal": {"title": "Front Plant Sci", "issn": "1664-462X", "issn-l": "1664-462X", "volume": "14", "issue": null, "pages": "1210850"}, "abstract": "High levels of toxic steroidal glycoalkaloids (SGAs) in potato tubers constitute a recognized food quality problem. Tuber SGA levels vary between potato cultivars and can increase after post-harvest stresses such as wounding and light exposure. A few cultivars, e.g., 'Magnum Bonum' and 'Lenape,' have been withdrawn from commercial sales due to excessive SGA levels during some cultivation years. However, these sudden SGA increases are diffucult to predict, and their causes are not understood. To identify external and genetic factors that underlie sudden SGA increases in certain potato cultivars, we have here in a 2-year study investigated 'Magnum Bonum' and five additional table potato cultivars for their SGA levels after wounding and light exposure.\r\n\r\nResults showed that 'Magnum Bonum' has an unusual strong SGA response to light exposure, but not to wounding, whereas 'Bintje' displayed an opposite regulation. Levels of calystegine alkaloids were not significantly altered by treatments, implicating independent metabolic regulation of SGA and calystegine levels also under conditions of high SGA accumulation. Metabolomic and transcriptomic analyses identified a small number of key genes whose expression correlated with SGA differences between cultivars. Overexpression of two key genes in transgenic low-SGA potato cultivars increased their leaf SGA levels significantly.\r\n\r\nThe results show that a strong response to light can underlie the SGA peaks that occasionally occur in certain potato cultivars and indicate that a between-cultivar variation in the expression of single SGA key genes can account for cultivar SGA differerences. We propose that current attempts to mitigate the SGA hazard will benefit from an increased consideration of cultivar-dependent SGA responses to post-harvest conditions, particularly light exposure. The identified key SGA genes can now be used as a molecular tool in this work.", "doi": "10.3389/fpls.2023.1210850", "pmid": "37860257", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10582707"}], "notes": [], "created": "2023-11-16T12:04:12.160Z", "modified": "2024-01-16T13:48:32.011Z"}, {"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": "9aef338ade194b078421af40a611fa5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9aef338ade194b078421af40a611fa5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9aef338ade194b078421af40a611fa5a"}}, "title": "B cell polygenic risk scores associate with anti-dsDNA antibodies and nephritis in systemic lupus erythematosus.", "authors": [{"family": "Hedenstedt", "given": "Anna", "initials": "A", "orcid": "0009-0007-1596-1233", "researcher": {"href": "https://publications.scilifelab.se/researcher/83ae75c2cfd64c9488ea2a07119d0f4d.json"}}, {"family": "Reid", "given": "Sarah", "initials": "S"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML", "orcid": "0000-0002-8454-1351", "researcher": {"href": "https://publications.scilifelab.se/researcher/d162e060954d420e825884f254886dcd.json"}}, {"family": "Skoglund", "given": "Elisabeth", "initials": "E"}, {"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Frodlund", "given": "Martina", "initials": "M"}, {"family": "Lerang", "given": "Karoline", "initials": "K"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Rudin", "given": "Anna", "initials": "A"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}], "type": "journal article", "published": "2023-10-00", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "10", "issue": "2", "issn-l": "2053-8790"}, "abstract": "B cell function and autoantibodies are important in SLE pathogenesis. In this work, we aimed to investigate the impact of cumulative SLE B cell genetics on SLE subphenotype and autoantibody profile.\n\nFemale patients with SLE (n=1248) and healthy controls (n=400) were genotyped using Illumina's Global Screening Array. Two polygenic risk scores (PRSs), one representing B cell genes and the other B cell activation genes, were calculated for each individual using risk loci for SLE in genes assigned to B cell-related pathways according to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology and Reactome Databases.\n\nDouble-stranded DNA (dsDNA) antibodies were more prevalent among patients with a high compared with a low SLE B cell PRS (OR 1.47 (1.07 to 2.01), p=0.018), and effect sizes were augmented in patients with human leucocyte antigen (HLA) risk haplotypes HLA-DRB1*03:01 and HLA-DRB1*15:01 (DRB1*03/15 -/- (OR 0.99 (0.56 to 1.77), p=0.98; DRB1*03/15 +/- or -/+ (OR 1.64 (1.06 to 2.54), p=0.028; and DRB1*03/15 +/+ (OR 4.47 (1.21 to 16.47), p=0.024). Further, a high compared with a low B cell PRS was associated with low complement levels in DRB1*03/15 +/+ patients (OR 3.92 (1.22 to 12.64), p=0.022). The prevalence of lupus nephritis (LN) was higher in patients with a B cell activation PRS above the third quartile compared with patients below (OR 1.32 (1.00 to 1.74), p=0.048).\n\nHigh genetic burden related to B cell function is associated with dsDNA antibody development and LN. Assessing B cell PRSs may be important in order to determine immunological pathways influencing SLE and to predict clinical phenotype.", "doi": "10.1136/lupus-2023-000926", "pmid": "37844960", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10582984"}, {"db": "pii", "key": "10/2/e000926"}], "notes": [], "created": "2023-11-29T10:59:36.253Z", "modified": "2023-11-29T10:59:36.317Z"}, {"entity": "publication", "iuid": "0e6c5f5e44e3406b9d3f38f57c040da5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e6c5f5e44e3406b9d3f38f57c040da5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e6c5f5e44e3406b9d3f38f57c040da5"}}, "title": "Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.", "authors": [{"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Sendell-Price", "given": "Ashley T", "initials": "AT"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Visscher", "given": "Peter M", "initials": "PM", "orcid": "0000-0002-2143-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcdb41d4720b436494304f74e33206ae.json"}}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR", "orcid": "0000-0002-7347-5758", "researcher": {"href": "https://publications.scilifelab.se/researcher/18a184c706054257a130b2ae0694d858.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": "2023-09-29", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "381", "issue": "6665", "pages": "eadf6218"}, "abstract": "A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Gal\u00e1pagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.", "doi": "10.1126/science.adf6218", "pmid": "37769091", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-10-12T11:14:44.927Z", "modified": "2024-01-16T13:48:32.043Z"}, {"entity": "publication", "iuid": "cfad3d491ac3446ca70f18e88f73c834", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cfad3d491ac3446ca70f18e88f73c834.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cfad3d491ac3446ca70f18e88f73c834"}}, "title": "Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.", "authors": [{"family": "Riihim\u00e4ki", "given": "Miia", "initials": "M"}, {"family": "Fegraeus", "given": "Kim", "initials": "K"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Waern", "given": "Ida", "initials": "I"}, {"family": "Wernersson", "given": "Sara", "initials": "S"}, {"family": "Akula", "given": "Srinivas", "initials": "S"}, {"family": "Hellman", "given": "Lars", "initials": "L"}, {"family": "Raine", "given": "Amanda", "initials": "A"}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "16261"}, "abstract": "Equine asthma (EA) is a heterogenous, complex disease, with a significant negative impact on horse welfare and performance. EA and human asthma share fundamental similarities, making EA a useful model for studying the disease. One relevant sample type for investigating chronic lung inflammation is bronchoalveolar lavage fluid (BALF), which provides a snapshot of the immune cells present in the alveolar space. To investigate the immune cell landscape of the respiratory tract in horses with mild-to-moderate equine asthma (mEA) and healthy controls, single-cell RNA sequencing was conducted on equine BALF cells. We characterized the major immune cell populations present in equine BALF, as well as subtypes thereof. Interestingly, the most significantly upregulated gene discovered in cases of mEA was FKBP5, a chaperone protein involved in regulating the activity of the glucocorticoid receptor.", "doi": "10.1038/s41598-023-43368-4", "pmid": "37758813", "labels": {"NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Single cell": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10533524"}, {"db": "pii", "key": "10.1038/s41598-023-43368-4"}], "notes": [], "created": "2023-11-27T21:49:44.494Z", "modified": "2024-02-27T08:16:23.788Z"}, {"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": "2e31abdf99b245178c96a47d5696b8da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2e31abdf99b245178c96a47d5696b8da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2e31abdf99b245178c96a47d5696b8da"}}, "title": "Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus).", "authors": [{"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Naboulsi", "given": "Rakan", "initials": "R"}, {"family": "de Koning", "given": "Dirk-Jan", "initials": "DJ"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C"}], "type": "journal article", "published": "2023-09-04", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "24", "issue": "1", "pages": "519", "issn-l": "1471-2164"}, "abstract": "Substantial variation in male fertility is regularly observed in farmed Arctic charr. However, detailed investigations of its fluctuation during a reproductive season and across years are lacking. Furthermore, information about the effect of underlying genetic factors influencing sperm quality is scarce. The current study focused on seasonal and age-related factors that may affect sperm quality characteristics in males reared in natural and delayed photoperiods. Animals were sampled three times for two consecutive years, and sperm quality parameters were recorded using a computer-assisted sperm analysis (CASA) system. Thereafter, high-throughput sequencing technologies were applied, aiming to identify genomic regions related to the variation of sperm quality throughout the reproductive season.\n\nAn across-season variation in the recorded sperm quality parameters was evident. Overall, 29% and 42% of males from the natural and delayed spawning groups had a highly variable total progressive motility. Males at four years of age showed significantly higher sperm motility and velocities during the early October and November recordings compared to the following year when the same animals were five years of age. On the other hand, the opposite was observed regarding sperm concentration during the last sampling. A genome-wide FST scan detected SNP differentiation among males with high and low variability in total progressive motility (PM) on eight chromosomes (FST > 0.17), Genome wide windows with the highest FST contained SNPs in proximity (within 250 kb up- and downstream distance) to 16 genes with sperm quality biological functions in mammalian species.\n\nOur findings provide a detailed view of seasonal, age-related, and genetic effects on sperm quality and can be used to guide decisions on broodstock selection and hatchery management.", "doi": "10.1186/s12864-023-09614-9", "pmid": "37667174", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10478403"}, {"db": "pii", "key": "10.1186/s12864-023-09614-9"}], "notes": [], "created": "2023-11-29T10:58:03.579Z", "modified": "2023-11-29T10:58:03.583Z"}, {"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": "20bb1b4554cb4d499841f007d0b0230a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20bb1b4554cb4d499841f007d0b0230a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20bb1b4554cb4d499841f007d0b0230a"}}, "title": "Stratified genetic analysis reveals sex differences in MPO-ANCA-associated vasculitis.", "authors": [{"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Stegmayr", "given": "Bernd", "initials": "B"}, {"family": "Baslund", "given": "Bo", "initials": "B"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A", "orcid": "0000-0002-9752-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6ee3e8a4124c5f8d6506ab762949ae.json"}}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Sv\u00e4rd", "given": "Anna", "initials": "A"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Herlitz", "given": "Hans", "initials": "H"}, {"family": "S\u00f6derbergh", "given": "Annika", "initials": "A"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}], "type": "journal article", "published": "2023-09-01", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "issn-l": "1462-0324", "volume": "62", "issue": "9", "pages": "3213-3218"}, "abstract": "To identify and genetically characterize subgroups of patients with ANCA-associated vasculitides (AAV) based on sex and ANCA subtype.\n\nA previously established SNP dataset derived from DNA sequencing of 1853 genes and genotyping of 1088 Scandinavian cases with AAV and 1589 controls was stratified for sex and ANCA subtype and analysed for association with five top AAV SNPs. rs9274619, a lead variant at the HLA-DQB1/HLA-DQA2 locus previously associated with AAV positive for myeloperoxidase (MPO)-ANCA, was analysed for association with the cumulative disease involvement of ten different organ systems.\n\nrs9274619 showed a significantly stronger association to MPO-ANCA-positive females than males [P = 2.0 \u00d7 10-4, OR = 2.3 (95% CI 1.5, 3.5)], whereas proteinase 3 (PR3)-ANCA-associated variants rs1042335, rs9277341 (HLA-DPB1/A1) and rs28929474 (SERPINA1) were equally associated with females and males with PR3-ANCA. In MPO-ANCA-positive cases, carriers of the rs9274619 risk allele were more prone to disease engagement of eyes [P = 0.021, OR = 11 (95% CI 2.2, 205)] but less prone to pulmonary involvement [P = 0.026, OR = 0.52 (95% CI 0.30, 0.92)]. Moreover, AAV with both MPO-ANCA and PR3-ANCA was associated with the PR3-ANCA lead SNP rs1042335 [P = 0.0015, OR = 0.091 (95% CI 0.0022, 0.55)] but not with rs9274619.\n\nFemales and males with MPO-ANCA-positive AAV differ in genetic predisposition to disease, suggesting at least partially distinct disease mechanisms between the sexes. Double ANCA-positive AAV cases are genetically similar to PR3-ANCA-positive cases, providing clues to the clinical follow-up and treatment of these patients.", "doi": "10.1093/rheumatology/kead152", "pmid": "37004177", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10473270"}, {"db": "pii", "key": "7099616"}], "notes": [], "created": "2023-04-04T12:12:11.801Z", "modified": "2024-01-16T13:48:32.331Z"}, {"entity": "publication", "iuid": "574c8505fa834097a975bfc1cdc70d36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/574c8505fa834097a975bfc1cdc70d36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/574c8505fa834097a975bfc1cdc70d36"}}, "title": "Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus.", "authors": [{"family": "Puthanveed", "given": "Vinitha", "initials": "V"}, {"family": "Singh", "given": "Khushwant", "initials": "K"}, {"family": "Poimenopoulou", "given": "Efstratia", "initials": "E"}, {"family": "Pettersson", "given": "Josefin", "initials": "J"}, {"family": "Siddique", "given": "Abu Bakar", "initials": "AB"}, {"family": "Kvarnheden", "given": "Anders", "initials": "A", "orcid": "0000-0001-9394-7700", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf67998333e74016847b7a6d3f121e7b.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Phytopathology", "issn": "0031-949X", "issn-l": null, "volume": "113", "issue": "9", "pages": "1788-1798"}, "abstract": "Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA, and TuYV was detected in all fields except one. In the counties of Sk\u00e5ne, Kalmar, and \u00d6sterg\u00f6tland, the average incidence of TuYV-infected plants was 75%, and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed coinfection with TuYV-associated RNA. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV, together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes. [Formula: see text] Copyright \u00a9 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.", "doi": "10.1094/PHYTO-11-22-0446-V", "pmid": "36802872", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-27T21:54:07.736Z", "modified": "2024-01-16T13:48:32.357Z"}, {"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": "155b51259682437faf22ad2c6fa5b409", "links": {"self": {"href": "https://publications.scilifelab.se/publication/155b51259682437faf22ad2c6fa5b409.json"}, "display": {"href": "https://publications.scilifelab.se/publication/155b51259682437faf22ad2c6fa5b409"}}, "title": "Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows.", "authors": [{"family": "Catal\u00e1n", "given": "Ana", "initials": "A", "orcid": "0000-0002-4543-748X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5edac0f763941e29cbe9595b998023b.json"}}, {"family": "Merondun", "given": "Justin", "initials": "J"}, {"family": "Knief", "given": "Ulrich", "initials": "U", "orcid": "0000-0001-6959-3033", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d8858c7c7b44a008a172bc637957ce1.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "19", "issue": "9", "pages": "e1010901", "issn-l": "1553-7390"}, "abstract": "The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5<Zf:ZZm<1). The underlying mechanism remains largely elusive. Here, we quantified gene expression for a total of 15 male and female Eurasian crows (Corvus (corone) spp.) raised under common garden conditions. In addition, we characterized aspects of the regulatory epigenetic landscape quantifying chromatin accessibility (ATAC-seq) and 5mC methylation profiles. Partial dosage balance and compensation was due to female upregulation of Z-linked genes which covaried significantly with increased chromatin accessibility of the female Z chromosome. 5mC methylation was tissue and sex chromosome-specific, but unrelated to dosage. With the exception of the pseudo-autosomal region (PAR), female upregulation of gene expression was evenly spread across the Z chromosome without evidence for regional centers of epigenetic regulation, as has, for example, been suggested for the male hypermethylated region (MHM) in chicken. Our results suggest that partial dosage balance and compensation in female heterogametic systems are tightly linked to chromosome-wide, epigenetic control of the female Z chromosome mediated by differential chromatin accessibility.", "doi": "10.1371/journal.pgen.1010901", "pmid": "37747941", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10575545"}, {"db": "pii", "key": "PGENETICS-D-23-00282"}], "notes": [], "created": "2023-11-29T11:12:52.573Z", "modified": "2023-11-29T11:12:52.615Z"}, {"entity": "publication", "iuid": "9fb879c926904883b9330093264e5427", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fb879c926904883b9330093264e5427.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fb879c926904883b9330093264e5427"}}, "title": "Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour.", "authors": [{"family": "Zhang", "given": "Hanzhao", "initials": "H"}, {"family": "Konjusha", "given": "Dardan", "initials": "D"}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "Tararuk", "given": "Tatsiana", "initials": "T"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}], "type": "journal article", "published": "2023-08-22", "journal": {"title": "Cell Oncol (Dordr)", "issn": "2211-3436", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Retinoblastoma, a childhood cancer, is most frequently caused by bi-allelic inactivation of RB1 gene. However, other oncogenic mutations such as MYCN amplification can induce retinoblastoma with proficient RB1. Previously, we established RB1-proficient MYCN-overexpressing retinoblastoma models both in human organoids and chicken. Here, we investigate the regulatory events in MYCN-induced retinoblastoma carcinogenesis based on the model in chicken.\r\n\r\nMYCN transformed retinal cells in culture were obtained from in vivo MYCN electroporated chicken embryo retina. The expression profiles were analysed by RNA sequencing. Chemical treatments, qRT-PCR, flow cytometry, immunohisto- and immunocytochemistry and western blot were applied to study the properties and function of these cells.\r\n\r\nThe expression profile of MYCN-transformed retinal cells in culture showed cone photoreceptor progenitor signature and robustly increased levels of E2Fs. This expression profile was consistently observed in long-term culture. Chemical treatments confirmed RB1 proficiency in these cells. The cells were insensitive to p53 activation but inhibition of E2f efficiently induced cell cycle arrest followed by apoptosis.\r\n\r\nIn conclusion, with proficient RB1, MYCN-induced high level of E2F expression dysregulates the cell cycle and contributes to retinoblastoma carcinogenesis. The increased level of E2f renders the cells to adopt a similar mechanistic phenotype to a RB1-deficient tumour.", "doi": "10.1007/s13402-023-00863-0", "pmid": "37606819", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1007/s13402-023-00863-0"}], "notes": [], "created": "2023-11-02T09:10:58.573Z", "modified": "2024-01-16T13:48:32.442Z"}, {"entity": "publication", "iuid": "b0fc64bb3f354c23a4cefe81c8290ef8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b0fc64bb3f354c23a4cefe81c8290ef8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b0fc64bb3f354c23a4cefe81c8290ef8"}}, "title": "Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes.", "authors": [{"family": "M\u00e1rton", "given": "Zsuzsanna", "initials": "Z"}, {"family": "Csit\u00e1ri", "given": "Bianka", "initials": "B"}, {"family": "Felf\u00f6ldi", "given": "Tam\u00e1s", "initials": "T", "orcid": "0000-0003-2009-2478", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a452e1d353649bc860f59485fc8bf03.json"}}, {"family": "Hidas", "given": "Andr\u00e1s", "initials": "A"}, {"family": "Jord\u00e1n", "given": "Ferenc", "initials": "F"}, {"family": "Szab\u00f3", "given": "Attila", "initials": "A"}, {"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": "2023-08-22", "journal": {"title": "FEMS Microbiol. Ecol.", "issn": "1574-6941", "volume": "99", "issue": "9", "issn-l": "0168-6496"}, "abstract": "Seasonal environmental variation is a leading driver of microbial planktonic community assembly and interactions. However, departures from usual seasonal trends are often reported. To understand the role of local stressors in modifying seasonal succession, we sampled fortnightly, throughout three seasons, five nearby shallow soda lakes exposed to identical seasonal and meteorological changes. We characterised their microeukaryotic and bacterial communities by amplicon sequencing of the 16S and 18S rRNA gene, respectively. Biological interactions were inferred by analyses of synchronous and time-shifted interaction networks, and the keystone taxa of the communities were topologically identified. The lakes showed similar succession patterns during the study period with spring being characterised by the relevance of trophic interactions and a certain level of community stability followed by a more dynamic and variable summer-autumn period. Adaptation to general seasonal changes happened through shared core microbiome of the lakes. Stochastic events such as desiccation disrupted common network attributes and introduced shifts from the prevalent seasonal trajectory. Our results demonstrated that, despite being extreme and highly variable habitats, shallow soda lakes exhibit certain similarities in the seasonality of their planktonic communities, yet local stressors such as droughts instigate deviations from prevalent trends to a greater extent for microeukaryotic than for bacterial communities.", "doi": "10.1093/femsec/fiad095", "pmid": "37586889", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10449373"}, {"db": "pii", "key": "7243381"}], "notes": [], "created": "2023-11-29T11:26:09.024Z", "modified": "2024-01-16T13:48:32.450Z"}, {"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": "9343655379b04dd9a0b4d89466148dab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9343655379b04dd9a0b4d89466148dab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9343655379b04dd9a0b4d89466148dab"}}, "title": "Bacterial bioindicators enable biological status classification along the continental Danube river.", "authors": [{"family": "Fontaine", "given": "Laurent", "initials": "L"}, {"family": "Pin", "given": "Lorenzo", "initials": "L"}, {"family": "Savio", "given": "Domenico", "initials": "D"}, {"family": "Friberg", "given": "Nikolai", "initials": "N"}, {"family": "Kirschner", "given": "Alexander K T", "initials": "AKT"}, {"family": "Farnleitner", "given": "Andreas H", "initials": "AH"}, {"family": "Eiler", "given": "Alexander", "initials": "A", "orcid": "0000-0001-9916-9567", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7286785c9334dcba90273b69f81c018.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "862", "issn-l": "2399-3642"}, "abstract": "Despite the importance of bacteria in aquatic ecosystems and their predictable diversity patterns across space and time, biomonitoring tools for status assessment relying on these organisms are widely lacking. This is partly due to insufficient data and models to identify reliable microbial predictors. Here, we show metabarcoding in combination with multivariate statistics and machine learning allows to identify bacterial bioindicators for existing biological status classification systems. Bacterial beta-diversity dynamics follow environmental gradients and the observed associations highlight potential bioindicators for ecological outcomes. Spatio-temporal links spanning the microbial communities along the river allow accurate prediction of downstream biological status from upstream information. Network analysis on amplicon sequence veariants identify as good indicators genera Fluviicola, Acinetobacter, Flavobacterium, and Rhodoluna, and reveal informational redundancy among taxa, which coincides with taxonomic relatedness. The redundancy among bacterial bioindicators reveals mutually exclusive taxa, which allow accurate biological status modeling using as few as 2-3 amplicon sequence variants. As such our models show that using a few bacterial amplicon sequence variants from globally distributed genera allows for biological status assessment along river systems.", "doi": "10.1038/s42003-023-05237-8", "pmid": "37596339", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-023-05237-8"}, {"db": "pmc", "key": "PMC10439154"}], "notes": [], "created": "2023-08-21T05:58:55.824Z", "modified": "2023-08-21T05:58:55.835Z"}, {"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": "ec41cb3ea29c430eb8044c7b6d1c640b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec41cb3ea29c430eb8044c7b6d1c640b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec41cb3ea29c430eb8044c7b6d1c640b"}}, "title": "Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal.", "authors": [{"family": "Bensch", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-8449-9843", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a204f1b0fe34b8999893abe65fb3e8c.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Tolf", "given": "Conny", "initials": "C"}, {"family": "Waldenstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1152-4235", "researcher": {"href": "https://publications.scilifelab.se/researcher/53013aa313214e26abdb18ea0199371f.json"}}, {"family": "Z\u00f6ttl", "given": "Markus", "initials": "M", "orcid": "0000-0002-5582-2306", "researcher": {"href": "https://publications.scilifelab.se/researcher/e262a41c07044bd88a4bd6f1dcc2f1eb.json"}}], "type": "journal article", "published": "2023-08-16", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "In social species, group members commonly show substantial similarity in gut microbiome composition. Such similarities have been hypothesized to arise either by shared environmental effects or by host relatedness. However, disentangling these factors is difficult, because group members are often related, and social groups typically share similar environmental conditions. In this study, we conducted a cross-foster experiment under controlled laboratory conditions in group-living Damaraland mole-rats (Fukomys damarensis) and used 16S amplicon sequencing to disentangle the effects of the environment and relatedness on gut microbiome similarity and diversity. Our results show that a shared environment is the main factor explaining gut microbiome similarity, overshadowing any effect of host relatedness. Together with studies in wild animal populations, our results suggest that among conspecifics environmental factors are more powerful drivers of gut microbiome composition similarity than host genetics.", "doi": "10.1111/jeb.14208", "pmid": "37584218", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T11:41:57.913Z", "modified": "2023-11-29T11:41:58.018Z"}, {"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": "3964f1e7f99c42f09a08ee5fd125ad18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3964f1e7f99c42f09a08ee5fd125ad18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3964f1e7f99c42f09a08ee5fd125ad18"}}, "title": "Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia.", "authors": [{"family": "Rezayee", "given": "Fatemah", "initials": "F"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I"}, {"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Syv\u00e4nen", "given": "Ann Christine", "initials": "AC"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}, {"family": "Olsson-Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Pietras", "given": "Christina Orsmark", "initials": "CO"}, {"family": "Staffas", "given": "Anna", "initials": "A"}, {"family": "Palmqvist", "given": "Lars", "initials": "L"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2023-08-14", "journal": {"title": "Front Oncol", "issn": "2234-943X", "issn-l": "2234-943X", "volume": "13", "issue": null, "pages": "1217712"}, "abstract": "The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods.\n\nFor this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL.\n\nBoth the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions.\n\nThe filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.", "doi": "10.3389/fonc.2023.1217712", "pmid": "37664045", "labels": {"Clinical Genomics Stockholm": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10470829"}], "notes": [], "created": "2023-11-22T21:44:19.108Z", "modified": "2024-11-20T20:05:01.286Z"}, {"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": "3bc1aebcc63f41edbfce850538cda6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4"}}, "title": "Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Ala-Hulkko", "given": "Terhi", "initials": "T", "orcid": "0000-0002-0884-2152", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f4036f2bc54136a489b22aaba390d7.json"}}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Constantinescu", "given": "Mihai", "initials": "M"}, {"family": "Rotea", "given": "Mihai", "initials": "M"}, {"family": "Palinca\u0219", "given": "Nona", "initials": "N", "orcid": "0000-0001-5308-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4275405ad5045da8909e05ac7fb9dd9.json"}}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Czerniak", "given": "Lech", "initials": "L", "orcid": "0000-0002-0352-5385", "researcher": {"href": "https://publications.scilifelab.se/researcher/73f2691cdc7f424784c4a7d1dbb2957e.json"}}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "\u0141apo", "given": "Jerzy", "initials": "J"}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "Soficaru", "given": "Andrei", "initials": "A"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Netea", "given": "Mihai G", "initials": "MG", "orcid": "0000-0003-2421-6052", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b25efbd9ee43e7a873baaaec4cf34c.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0009-0007-4490-2494", "researcher": {"href": "https://publications.scilifelab.se/researcher/178194b694e04e8d9520328ddda9bd11.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.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": "2023-08-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "793", "issn-l": "2399-3642"}, "abstract": "The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.", "doi": "10.1038/s42003-023-05131-3", "pmid": "37558731", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10412644"}, {"db": "pii", "key": "10.1038/s42003-023-05131-3"}], "notes": [], "created": "2023-08-14T06:19:02.423Z", "modified": "2024-01-16T13:48:32.510Z"}, {"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": "070b694696014ed78f1f2be943ae1025", "links": {"self": {"href": "https://publications.scilifelab.se/publication/070b694696014ed78f1f2be943ae1025.json"}, "display": {"href": "https://publications.scilifelab.se/publication/070b694696014ed78f1f2be943ae1025"}}, "title": "Relation between HLA and copy number variation of steroid 21-hydroxylase in a Swedish cohort of patients with autoimmune Addison's disease.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C", "orcid": "0000-0001-5872-4253", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a05532d3aad4e2dbe00a4724e8dddd8.json"}}, {"family": "Eriksson", "given": "Daniel", "initials": "D"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Aranda-Guill\u00e9n", "given": "Maribel", "initials": "M"}, {"family": "Landegren", "given": "Nils", "initials": "N"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Consortium", "given": "DISSECT", "initials": "D"}, {"family": ",,", "given": "", "initials": ""}, {"family": "Consortium", "given": "ImmunoArray", "initials": "I"}, {"family": ",,", "given": "", "initials": ""}, {"family": "Group", "given": "Swedish Addison Registry Study", "initials": "SARS"}, {"family": ",,", "given": "", "initials": ""}, {"family": "Bensing", "given": "Sophie", "initials": "S", "orcid": "0000-0002-9193-2860", "researcher": {"href": "https://publications.scilifelab.se/researcher/acae2ad8ca844588b2b850c863034b7b.json"}}, {"family": "Pielberg", "given": "Gerli Rosengren", "initials": "GR"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O", "orcid": "0000-0001-6091-9914", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c547dc809a14cdaa47b623cf638162b.json"}}], "type": "journal article", "published": "2023-08-02", "journal": {"title": "Eur. J. Endocrinol.", "issn": "1479-683X", "issn-l": "0804-4643", "volume": "189", "issue": "2", "pages": "235-241"}, "abstract": "Autoantibodies against the adrenal enzyme 21-hydroxylase is a hallmark manifestation in autoimmune Addison's disease (AAD). Steroid 21-hydroxylase is encoded by CYP21A2, which is located in the human leucocyte antigen (HLA) region together with the highly similar pseudogene CYP21A1P. A high level of copy number variation is seen for the 2 genes, and therefore, we asked whether genetic variation of the CYP21 genes is associated with AAD.\r\n\r\nCase-control study on patients with AAD and healthy controls.\r\n\r\nUsing next-generation DNA sequencing, we estimated the copy number of CYP21A2 and CYP21A1P, together with HLA alleles, in 479 Swedish patients with AAD and autoantibodies against 21-hydroxylase and in 1393 healthy controls.\r\n\r\nWith 95% of individuals carrying 2 functional 21-hydroxylase genes, no difference in CYP21A2 copy number was found when comparing patients and controls. In contrast, we discovered a lower copy number of the pseudogene CYP21A1P among AAD patients (P = 5 \u00d7 10-44), together with associations of additional nucleotide variants, in the CYP21 region. However, the strongest association was found for HLA-DQB1*02:01 (P = 9 \u00d7 10-63), which, in combination with the DRB1*04:04-DQB1*03:02 haplotype, imposed the greatest risk of AAD.\r\n\r\nWe identified strong associations between copy number variants in the CYP21 region and risk of AAD, although these associations most likely are due to linkage disequilibrium with disease-associated HLA class II alleles.", "doi": "10.1093/ejendo/lvad102", "pmid": "37553728", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7239340"}], "notes": [], "created": "2023-11-27T21:51:56.107Z", "modified": "2024-01-16T13:48:32.542Z"}, {"entity": "publication", "iuid": "6fac894c455046668ab3f18eed8a7f8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fac894c455046668ab3f18eed8a7f8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fac894c455046668ab3f18eed8a7f8d"}}, "title": "Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia.", "authors": [{"family": "Eriksson", "given": "Anna", "initials": "A", "orcid": "0000-0002-8853-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cfc6bb334e455d9f64172ff43e3428.json"}}, {"family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f3bfe35ddf41e5beb4312d3408a7ea.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A", "orcid": "0000-0001-8749-7299", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a3ea9e722b4c72a7f00a61b5c9fe0a.json"}}, {"family": "Rippin", "given": "Martin", "initials": "M", "orcid": "0000-0003-4362-0122", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b30009265224c56b99e1afd024b5240.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "research support, non-u.s. gov't", "published": "2023-08-01", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "29", "issue": "15", "pages": "2826-2834"}, "abstract": "In acute myeloid leukemia (AML), somatic mutations (commonly missense, nonsense, and frameshift indels) in RUNX1 are associated with a dismal clinical outcome. Inherited RUNX1 mutations cause familial platelet disorder. As approximately 5%-10% of germline RUNX1 mutations are large exonic deletions, we hypothesized that such exonic RUNX1 aberrations may also be acquired during the development of AML.\n\nSixty patients with well-characterized AML were analyzed with multiplex ligation-dependent probe amplification (n = 60), microarray (n = 11), and/or whole-genome sequencing (n = 8).\n\nIn total, 25 (42% of the cohort) RUNX1-aberrant patients (defined by the presence of classical mutations and/or exonic deletions) were identified. Sixteen patients (27%) carried only exonic deletions, 5 (8%) carried classical mutations, and 4 (7%) carried both exonic deletions and mutations. No significant difference was observed between patients with classical RUNX1 mutations and RUNX1 exonic deletions in median overall survival (OS, 53.1 vs. 38.8 months, respectively, P = 0.63). When applying the European Leukemia Net (ELN) classification including the RUNX1-aberrant group, 20% of the patients initially stratified as intermediate-risk (5% of the whole cohort) were reassigned to the high-risk group, which improved the performance of ELN classification regarding OS between intermediate- and high-risk groups (18.9 vs. 9.6 months, P = 0.09).\n\nSomatic RUNX1 exonic deletions constitute a novel recurrent aberration in AML. Our findings have important clinical implications regarding AML classification, risk stratification, and treatment decision. Moreover, they argue in favor of further investigating such genomic aberrations not only in RUNX1 but also in other genes implicated in cancer biology and management. See related commentary by Chakraborty and Stengel, p. 2742.", "doi": "10.1158/1078-0432.CCR-23-0122", "pmid": "37022349", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "725154"}], "notes": [], "created": "2023-11-29T08:28:02.202Z", "modified": "2024-01-16T13:48:32.633Z"}, {"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": "eb2054fcd72f4e85a7d459c134350840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb2054fcd72f4e85a7d459c134350840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb2054fcd72f4e85a7d459c134350840"}}, "title": "Clones on the run: The genomics of a recently expanded partially clonal species.", "authors": [{"family": "Pereyra", "given": "Ricardo T", "initials": "RT"}, {"family": "Rafajlovi\u0107", "given": "Marina", "initials": "M"}, {"family": "De Wit", "given": "Pierre", "initials": "P", "orcid": "0000-0003-4709-3438", "researcher": {"href": "https://publications.scilifelab.se/researcher/95b69d4724ce4b69819c0a1578cd56eb.json"}}, {"family": "Pinder", "given": "Matthew", "initials": "M"}, {"family": "Kinnby", "given": "Alexandra", "initials": "A"}, {"family": "T\u00f6pel", "given": "Mats", "initials": "M"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K", "orcid": "0000-0003-0176-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/a376951d80cd405183f4ff8606df8bbc.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "32", "issue": "15", "pages": "4209-4223", "issn-l": "0962-1083"}, "abstract": "Why species that in their core areas mainly reproduce sexually become enriched with clones in marginal populations (\"geographic parthenogenesis\") remains unclear. Earlier hypotheses have emphasized that selection might promote clonality because it protects locally adapted genotypes. On the other hand, it also hampers recombination and adaptation to changing conditions. The aim of the present study was to investigate the early stages of range expansion in a partially clonal species and what drives an increase in cloning during such expansion. We used genome-wide sequencing to investigate the origin and evolution of large clones formed in a macroalgal species (Fucus vesiculosus) during a recent expansion into the postglacial Baltic Sea. We found low but persistent clonality in core populations, while at range margins, large dominant clonal lineages had evolved repeatedly from different sexual populations. A range expansion model showed that even when asexual recruitment is less favourable than sexual recruitment in core populations, repeated bottlenecks at the expansion front can establish a genetically eroded clonal wave that spreads ahead of a sexual wave into the new area. Genetic variation decreases by drift following repeated bottlenecks at the expansion front. This results in the emerging clones having low expected heterozygosity, which corroborated our empirical observations. We conclude that Baker's Law (clones being favoured by uniparental reproductive assurance in new areas) can play an important role during range expansion in partially clonal species, resulting in a complex spatiotemporal mosaic of clonal and sexual lineages that might persist during thousands of generations.", "doi": "10.1111/mec.16996", "pmid": "37199478", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-29T09:04:27.425Z", "modified": "2023-11-29T09:04:27.440Z"}, {"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": "b5090ee7f17e4311876f2e97125ba47d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5090ee7f17e4311876f2e97125ba47d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5090ee7f17e4311876f2e97125ba47d"}}, "title": "Cutaneous squamous cell carcinoma-derived extracellular vesicles exert an oncogenic role by activating cancer-associated fibroblasts.", "authors": [{"family": "Li", "given": "Chen", "initials": "C", "orcid": "0000-0002-7199-4298", "researcher": {"href": "https://publications.scilifelab.se/researcher/acadd10dfac94eda9e9c951a8c04d6cb.json"}}, {"family": "Sun", "given": "Chengxi", "initials": "C", "orcid": "0000-0002-1050-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b42a5450dfd4211981fee0603acf321.json"}}, {"family": "Lohcharoenkal", "given": "Warangkana", "initials": "W"}, {"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Zheng", "given": "Wenyi", "initials": "W"}, {"family": "G\u00f6rgens", "given": "Andr\u00e9", "initials": "A", "orcid": "0000-0001-9198-0857", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea5f85e2c23a4515a39a2fa23d665a99.json"}}, {"family": "Gustafsson", "given": "Manuela O", "initials": "MO"}, {"family": "El Andaloussi", "given": "Samir", "initials": "S"}, {"family": "Sonkoly", "given": "Enik\u00f6", "initials": "E"}, {"family": "Pivarcsi", "given": "Andor", "initials": "A", "orcid": "0000-0003-2196-1102", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ca870317234573a3da5dffb24bb268.json"}}], "type": "journal article", "published": "2023-07-26", "journal": {"title": "Cell Death Discov", "issn": "2058-7716", "volume": "9", "issue": "1", "pages": "260", "issn-l": "2058-7716"}, "abstract": "Cutaneous squamous cell carcinoma (cSCC) is a fast-increasing cancer with metastatic potential. Extracellular vesicles (EVs) are small membrane-bound vesicles that play important roles in intercellular communication, particularly in the tumor microenvironment (TME). Here we report that cSCC cells secrete an increased number of EVs relative to normal human epidermal keratinocytes (NHEKs) and that interfering with the capacity of cSCC to secrete EVs inhibits tumor growth in vivo in a xenograft model of human cSCC. Transcriptome analysis of tumor xenografts by RNA-sequencing enabling the simultaneous quantification of both the human and the mouse transcripts revealed that impaired EV-production of cSCC cells prominently altered the phenotype of stromal cells, in particular genes related to extracellular matrix (ECM)-formation and epithelial-mesenchymal transition (EMT). In line with these results, co-culturing of human dermal fibroblasts (HDFs) with cSCC cells, but not with normal keratinocytes in vitro resulted in acquisition of cancer-associated fibroblast (CAF) phenotype. Interestingly, EVs derived from metastatic cSCC cells, but not primary cSCCs or NHEKs, were efficient in converting HDFs to CAFs. Multiplex bead-based flow cytometry assay and mass-spectrometry (MS)-based proteomic analyses revealed the heterogenous cargo of cSCC-derived EVs and that especially EVs derived from metastatic cSCCs carry proteins associated with EV-biogenesis, EMT, and cell migration. Mechanistically, EVs from metastatic cSCC cells result in the activation of TGF\u03b2 signaling in HDFs. Altogether, our study suggests that cSCC-derived EVs mediate cancer-stroma communication, in particular the conversion of fibroblasts to CAFs, which eventually contribute to cSCC progression.", "doi": "10.1038/s41420-023-01555-2", "pmid": "37495566", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10372068"}, {"db": "pii", "key": "10.1038/s41420-023-01555-2"}], "notes": [], "created": "2023-11-29T11:23:30.604Z", "modified": "2024-01-16T13:48:32.858Z"}, {"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": "3a1a5b9ee3754ffbb4b6a74c5b1396cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3a1a5b9ee3754ffbb4b6a74c5b1396cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3a1a5b9ee3754ffbb4b6a74c5b1396cd"}}, "title": "Forest Fire Influence on Tomicus piniperda-Associated Fungal Communities and Phloem Nutrient Availability of Colonized Pinus sylvestris.", "authors": [{"family": "Kluting", "given": "Kerri", "initials": "K"}, {"family": "Strid", "given": "Ylva", "initials": "Y"}, {"family": "Six", "given": "Diana", "initials": "D"}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2023-07-00", "journal": {"title": "Microb. Ecol.", "issn": "1432-184X", "issn-l": "0095-3628", "volume": "86", "issue": "1", "pages": "224-239"}, "abstract": "Forest fire is known to positively affect bark beetle populations by providing fire-damaged trees with impaired defenses for infestation. Tomicus piniperda, the common pine shoot beetle, breeds and lays eggs under the bark of stressed pine trees and is considered a serious forest pest within its native range. Wood-colonizing fungi have been hypothesized to improve substrate quality and detoxify tree defensive chemistry to indirectly facilitate tree colonization by beetles. While some bark beetle species form symbiotic associations with fungi and actively vector their partners when colonizing new trees, T. piniperda does not have mycangia or body hairs for specific vectoring of fungi. To explore the T. piniperda-associated fungal community for signs of specific association, we used ITS metabarcoding to separately characterize fungal communities associated with surface and gut of male and female beetles. We also characterized the temporal changes in fungal community and nutrient status of pine phloem with and without beetle galleries. Sampling was performed 2 years after a natural forest fire and included both burnt and unburnt sites. In our study system, we find that forest fire significantly impacts the fungal community composition associated with T. piniperda and that fire may also indirectly change nutrient availability in phloem to beetle galleries. We conclude that T. piniperda can vector fungi to newly colonized trees but the absence of positive effects on substrate quality and minimal effects of sex indicate that vectoring of associated fungal communities is not a strategy associated with the T. piniperda life cycle.", "doi": "10.1007/s00248-022-02066-w", "pmid": "35831642", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10293462"}, {"db": "pii", "key": "10.1007/s00248-022-02066-w"}], "notes": [], "created": "2023-09-04T12:09:36.897Z", "modified": "2024-01-16T13:48:33.043Z"}, {"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": "48bf04137ea64df1b6b70285f4f67cd2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48bf04137ea64df1b6b70285f4f67cd2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48bf04137ea64df1b6b70285f4f67cd2"}}, "title": "Mutations in the CYP27B1 gene cause vitamin D dependent rickets in pugs.", "authors": [{"family": "Rohdin", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-7698-550X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c17d3c315f7149bb93ac86f48a18ab99.json"}}, {"family": "Wang", "given": "Chao", "initials": "C"}, {"family": "Brander", "given": "Gustaf", "initials": "G"}, {"family": "Rondahl", "given": "Veronica", "initials": "V"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Friling", "given": "Lisa", "initials": "L"}, {"family": "Fischetti", "given": "Anthony", "initials": "A"}, {"family": "Meadows", "given": "Jennifer", "initials": "J"}, {"family": "H\u00e4ggstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0000-0003-3402-023X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e1779188e20402294f12861a8232e71.json"}}, {"family": "J\u00e4derlund", "given": "Karin Hultin", "initials": "KH"}, {"family": "Ljungvall", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6617-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b19ecb541c4d13a685b574390e8104.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "case reports", "published": "2023-06-09", "journal": {"title": "J. Vet. Intern. Med.", "issn": "1939-1676", "volume": "37", "issue": "4", "pages": "1507-1513", "issn-l": "0891-6640"}, "abstract": "Rickets is a disorder of bone development and can be the result of either dietary or genetic causes. Here, related pugs from 2 litters were included. Three pugs had clinical signs including, lameness, bone deformities, and dyspnea. One other pug was found dead. Radiographs of 2 affected pugs, 5 and 6 months old, showed generalized widening, and irregular margination of the physes of both the appendicular and the axial skeleton with generalized decrease in bone opacity and bulbous swelling of the costochondral junctions. Two pugs had low serum calcium and 1,25 (OH)2 D3 concentrations. Test results further indicated secondary hyperparathyroidism with adequate concentrations of 25-hydroxyvitamin D. Necropsy revealed tongue-like projections of cartilage extending into the metaphysis consistent with rickets, loss of metaphyseal mineralization and lung pathology. Vitamin D-dependent rickets was diagnosed. A truncating mutation in the 1\u03b1-hydroxylase gene (CYP27B1) was identified by genome sequence analysis of the pugs with VDDR type 1A. Vitamin D-dependent rickets type 1A can occur in young pugs, and if left untreated is a life-threatening condition. Early medical intervention can reverse clinical signs and should be instituted as soon as possible.", "doi": "10.1111/jvim.16791", "pmid": "37293695", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10365047"}], "notes": [], "created": "2023-11-29T10:49:54.098Z", "modified": "2024-01-16T13:48:33.185Z"}, {"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": "4ab0b7f2d3b44dedbf4230ac6274f925", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ab0b7f2d3b44dedbf4230ac6274f925.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ab0b7f2d3b44dedbf4230ac6274f925"}}, "title": "Ablation of ZC3H11A causes early embryonic lethality and dysregulation of metabolic processes.", "authors": [{"family": "Younis", "given": "Shady", "initials": "S"}, {"family": "Jouneau", "given": "Alice", "initials": "A"}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M"}, {"family": "Oudin", "given": "Jean-Francois", "initials": "JF"}, {"family": "Adenot", "given": "Pierre", "initials": "P"}, {"family": "Omar", "given": "Jihad", "initials": "J"}, {"family": "Brochard", "given": "Vincent", "initials": "V"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}], "type": "journal article", "published": "2023-06-06", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "23", "pages": "e2216799120", "issn-l": "0027-8424"}, "abstract": "ZC3H11A (zinc finger CCCH domain-containing protein 11A) is a stress-induced mRNA-binding protein required for efficient growth of nuclear-replicating viruses. The cellular functions of ZC3H11A during embryonic development are unknown. Here, we report the generation and phenotypic characterization of Zc3h11a knockout (KO) mice. Heterozygous null Zc3h11a mice were born at the expected frequency without distinguishable phenotypic differences compared with wild-type mice. In contrast, homozygous null Zc3h11a mice were missing, indicating that Zc3h11a is crucial for embryonic viability and survival. Zc3h11a -/- embryos were detected at the expected Mendelian ratios up to late preimplantation stage (E4.5). However, phenotypic characterization at E6.5 revealed degeneration of Zc3h11a -/- embryos, indicating developmental defects around the time of implantation. Transcriptomic analyses documented a dysregulation of glycolysis and fatty acid metabolic pathways in Zc3h11a-/- embryos at E4.5. Proteomic analysis indicated a tight interaction between ZC3H11A and mRNA-export proteins in embryonic stem cells. CLIP-seq analysis demonstrated that ZC3H11A binds a subset of mRNA transcripts that are critical for metabolic regulation of embryonic cells. Furthermore, embryonic stem cells with an induced deletion of Zc3h11a display an impaired differentiation toward epiblast-like cells and impaired mitochondrial membrane potential. Altogether, the results show that ZC3H11A is participating in export and posttranscriptional regulation of selected mRNA transcripts required to maintain metabolic processes in embryonic cells. While ZC3H11A is essential for the viability of the early mouse embryo, inactivation of Zc3h11a expression in adult tissues using a conditional KO did not lead to obvious phenotypic defects.", "doi": "10.1073/pnas.2216799120", "pmid": "37252988", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10266022"}], "notes": [], "created": "2023-11-29T11:18:46.020Z", "modified": "2023-11-29T11:18:46.029Z"}, {"entity": "publication", "iuid": "b72895f9bcf545a6a05e8b4ba0657679", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b72895f9bcf545a6a05e8b4ba0657679.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b72895f9bcf545a6a05e8b4ba0657679"}}, "title": "Phenotypic and transcriptomic acclimation of the green microalga Raphidocelis subcapitata to high environmental levels of the herbicide diflufenican.", "authors": [{"family": "G\u00f3mez-Mart\u00ednez", "given": "Daniela", "initials": "D"}, {"family": "Bengtson", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Anders K", "initials": "AK"}, {"family": "Clarke", "given": "Adrian K", "initials": "AK"}, {"family": "Nilsson", "given": "Rolf Henrik", "initials": "RH"}, {"family": "Kristiansson", "given": "Erik", "initials": "E"}, {"family": "Corcoll", "given": "Nat\u00e0lia", "initials": "N"}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "volume": "875", "pages": "162604", "issn-l": "0048-9697"}, "abstract": "Herbicide pollution poses a worldwide threat to plants and freshwater ecosystems. However, the understanding of how organisms develop tolerance to these chemicals and the associated trade-off expenses are largely unknown. This study aims to investigate the physiological and transcriptional mechanisms underlying the acclimation of the green microalgal model species Raphidocelis subcapitata (Selenastraceae) towards the herbicide diflufenican, and the fitness costs associated with tolerance development. Algae were exposed for 12 weeks (corresponding to 100 generations) to diflufenican at the two environmental concentrations 10 and 310 ng/L. The monitoring of growth, pigment composition, and photosynthetic performance throughout the experiment revealed an initial dose-dependent stress phase (week 1) with an EC50 of 397 ng/L, followed by a time-dependent recovery phase during weeks 2 to 4. After week 4, R. subcapitata was acclimated to diflufenican exposure with a similar growth rate, content of carotenoids, and photosynthetic performance as the unexposed control algae. This acclimation state of the algae was explored in terms of tolerance acquisition, changes in the fatty acids composition, diflufenican removal rate, cell size, and changes in mRNA gene expression profile, revealing potential fitness costs associated with acclimation, such as up-regulation of genes related to cell division, structure, morphology, and reduction of cell size. Overall, this study demonstrates that R. subcapitata can quickly acclimate to environmental but toxic levels of diflufenican; however, the acclimation is associated with trade-off expenses that result in smaller cell size.", "doi": "10.1016/j.scitotenv.2023.162604", "pmid": "36878298", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0048-9697(23)01220-2"}], "notes": [], "created": "2023-11-29T13:30:43.924Z", "modified": "2023-11-29T13:30:43.928Z"}, {"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": "8d34b82577f64f6b877c9b79fd1ede24", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d34b82577f64f6b877c9b79fd1ede24.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d34b82577f64f6b877c9b79fd1ede24"}}, "title": "The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus).", "authors": [{"family": "Fuentes-Pardo", "given": "Angela P", "initials": "AP", "orcid": "0000-0002-5734-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/f08a3b9b781b4ef9971a667a40b62d93.json"}}, {"family": "Farrell", "given": "Edward D", "initials": "ED", "orcid": "0000-0002-0070-9154", "researcher": {"href": "https://publications.scilifelab.se/researcher/941224a45e9242398fbcd4dacbe812c1.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", "orcid": "0000-0002-4164-4246", "researcher": {"href": "https://publications.scilifelab.se/researcher/b51f6d45361e4aa187fc74870a38ac3f.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": "2023-06-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "6", "pages": "1201-1219", "issn-l": "1752-4571"}, "abstract": "Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.", "doi": "10.1111/eva.13559", "pmid": "37360028", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10286234"}, {"db": "pii", "key": "EVA13559"}], "notes": [], "created": "2023-08-14T06:20:40.908Z", "modified": "2024-01-16T13:48:33.272Z"}, {"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": "2aed043e07494edeb8d66c6047ca7cfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2aed043e07494edeb8d66c6047ca7cfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2aed043e07494edeb8d66c6047ca7cfd"}}, "title": "Northwest African Neolithic initiated by migrants from Iberia and Levant.", "authors": [{"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG", "orcid": "0000-0002-6119-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/eea5b7ccd8f84d44b2e0be03f5c4e762.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Mart\u00ednez-S\u00e1nchez", "given": "Rafael M", "initials": "RM"}, {"family": "Vera-Rodr\u00edguez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Iriarte", "given": "Eneko", "initials": "E", "orcid": "0000-0001-8365-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/112f0c5761e84deea89b2b7cb68521ce.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Bokbot", "given": "Youssef", "initials": "Y"}, {"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"}}], "type": "comparative study", "published": "2023-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "618", "issue": "7965", "pages": "550-556"}, "abstract": "In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.", "doi": "10.1038/s41586-023-06166-6", "pmid": "37286608", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10266975"}, {"db": "pii", "key": "10.1038/s41586-023-06166-6"}], "notes": [], "created": "2023-11-29T10:51:14.891Z", "modified": "2024-01-16T13:48:33.294Z"}, {"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": "b1ca32c9035c4f99ba117f53cb7df654", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1ca32c9035c4f99ba117f53cb7df654.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1ca32c9035c4f99ba117f53cb7df654"}}, "title": "SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.", "authors": [{"family": "Gollnisch", "given": "Raphael", "initials": "R", "orcid": "0000-0001-6177-8877", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f78f6e8cacf4eba9104fbfd2ab26f66.json"}}, {"family": "Wallenius", "given": "Joel", "initials": "J"}, {"family": "Gribble", "given": "Kristin E", "initials": "KE"}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Rengefors", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2023-05-02", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "40", "issue": "5", "pages": null}, "abstract": "Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.", "doi": "10.1093/molbev/msad095", "pmid": "37079883", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10202595"}, {"db": "pii", "key": "7133828"}], "notes": [], "created": "2023-05-24T12:59:17.974Z", "modified": "2024-01-16T13:48:33.441Z"}, {"entity": "publication", "iuid": "2110e1a811fc4f6db742533b43bdd50a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2110e1a811fc4f6db742533b43bdd50a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2110e1a811fc4f6db742533b43bdd50a"}}, "title": "Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.", "authors": [{"family": "Mosquera", "given": "Katherine D", "initials": "KD"}, {"family": "Nilsson", "given": "Louise K J", "initials": "LKJ"}, {"family": "de Oliveira", "given": "Marta Rodrigues", "initials": "MR"}, {"family": "Rocha", "given": "Elerson Matos", "initials": "EM"}, {"family": "Marinotti", "given": "Osvaldo", "initials": "O"}, {"family": "H\u00e5kansson", "given": "Sebastian", "initials": "S"}, {"family": "Tadei", "given": "Wanderli P", "initials": "WP"}, {"family": "de Souza", "given": "Antonia Queiroz Lima", "initials": "AQL"}, {"family": "Terenius", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2023-05-01", "journal": {"title": "Parasit Vectors", "issn": "1756-3305", "volume": "16", "issue": "1", "pages": "156", "issn-l": "1756-3305"}, "abstract": "The neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.\n\nLarvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.\n\nWe found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.\n\nOur findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito-microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.", "doi": "10.1186/s13071-023-05749-6", "pmid": "37127597", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10150499"}, {"db": "pii", "key": "10.1186/s13071-023-05749-6"}], "notes": [], "created": "2023-05-05T06:04:21.836Z", "modified": "2024-01-16T13:48:33.490Z"}, {"entity": "publication", "iuid": "63814c2828f14ee58cef696374d723d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63814c2828f14ee58cef696374d723d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63814c2828f14ee58cef696374d723d9"}}, "title": "Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.", "authors": [{"family": "Gr\u00fcttner", "given": "Jana", "initials": "J", "orcid": "0000-0002-2507-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/28fb027f36d94b85afb5e1325fd0ed7b.json"}}, {"family": "van Rijn", "given": "Jorik M", "initials": "JM", "orcid": "0000-0003-2865-4455", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f2defce179d4632a4e7d60666417ab2.json"}}, {"family": "Geiser", "given": "Petra", "initials": "P", "orcid": "0000-0003-2785-4201", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae0bf10f41dc4698b19288809bae2dd6.json"}}, {"family": "Florbrant", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1630-4442", "researcher": {"href": "https://publications.scilifelab.se/researcher/360f8004f9394dabb68f1f9e0725e42c.json"}}, {"family": "Webb", "given": "Dominic-Luc", "initials": "DL", "orcid": "0000-0002-6979-9194", "researcher": {"href": "https://publications.scilifelab.se/researcher/868fca24b48f440eb2417acdb04e73d3.json"}}, {"family": "Hellstr\u00f6m", "given": "Per M", "initials": "PM", "orcid": "0000-0001-8428-0772", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85863b505f34d7e95a23ac127b9d6dc.json"}}, {"family": "Sundbom", "given": "Magnus", "initials": "M", "orcid": "0000-0002-6243-2859", "researcher": {"href": "https://publications.scilifelab.se/researcher/a54316faa45947bd92615d27a38c2b87.json"}}, {"family": "Sellin", "given": "Mikael E", "initials": "ME", "orcid": "0000-0002-8355-0803", "researcher": {"href": "https://publications.scilifelab.se/researcher/f797357bcd3d4447bff96c20873dd500.json"}}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG", "orcid": "0000-0002-7392-1746", "researcher": {"href": "https://publications.scilifelab.se/researcher/b01942d70ef84a1db3aaccab65af9c57.json"}}], "type": "journal article", "published": "2023-05-00", "journal": {"title": "PLoS Pathog.", "issn": "1553-7374", "volume": "19", "issue": "5", "pages": "e1011372", "issn-l": "1553-7366"}, "abstract": "Giardia intestinalis is a non-invasive, protozoan parasite infecting the upper small intestine of most mammals. Symptomatic infections cause the diarrhoeal disease giardiasis in humans and animals, but at least half of the infections are asymptomatic. However, the molecular underpinnings of these different outcomes of the infection are still poorly defined. Here, we studied the early transcriptional response to G. intestinalis trophozoites, the disease-causing life-cycle stage, in human enteroid-derived, 2-dimensional intestinal epithelial cell (IEC) monolayers. Trophozoites preconditioned in media that maximise parasite fitness triggered only neglectable inflammatory transcription in the IECs during the first hours of co-incubation. By sharp contrast, \"non-fit\" or lysed trophozoites induced a vigorous IEC transcriptional response, including high up-regulation of many inflammatory cytokines and chemokines. Furthermore, \"fit\" trophozoites could even suppress the stimulatory effect of lysed trophozoites in mixed infections, suggesting active G. intestinalis suppression of the IEC response. By dual-species RNA-sequencing, we defined the IEC and G. intestinalis gene expression programs associated with these differential outcomes of the infection. Taken together, our results inform on how G. intestinalis infection can lead to such highly variable effects on the host, and pinpoints trophozoite fitness as a key determinant of the IEC response to this common parasite.", "doi": "10.1371/journal.ppat.1011372", "pmid": "37141303", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10187934"}, {"db": "pii", "key": "PPATHOGENS-D-22-02213"}], "notes": [], "created": "2023-05-22T07:22:26.525Z", "modified": "2023-05-22T07:22:26.821Z"}, {"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": "975c24b0b06442ffa2f3706d774f15a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/975c24b0b06442ffa2f3706d774f15a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/975c24b0b06442ffa2f3706d774f15a8"}}, "title": "\u200bComparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.", "authors": [{"family": "Moon", "given": "Katherine L", "initials": "KL", "orcid": "0000-0002-0795-3096", "researcher": {"href": "https://publications.scilifelab.se/researcher/4761aeff839047fb977b0a347da4b2cb.json"}}, {"family": "Huson", "given": "Heather J", "initials": "HJ", "orcid": "0000-0001-8299-0447", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d550f894cde4251b5b8e7b41022db7c.json"}}, {"family": "Morrill", "given": "Kathleen", "initials": "K", "orcid": "0000-0002-9139-453X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16283fa15c524fe69225a6b86822f0e3.json"}}, {"family": "Wang", "given": "Ming-Shan", "initials": "M"}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Srikanth", "given": "Krishnamoorthy", "initials": "K", "orcid": "0000-0002-5205-193X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba9ba40f2c594bc18d5ab34ba55d6e6f.json"}}, {"family": "Zoonomia Consortium", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Svenson", "given": "Gavin J", "initials": "GJ", "orcid": "0000-0003-0207-6458", "researcher": {"href": "https://publications.scilifelab.se/researcher/703555ba027b4719a036ef315366377a.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn5887"}, "abstract": "We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian husky breed. Balto's genotype predicts a combination of coat features atypical for modern sled dog breeds, and a slightly smaller stature. He had enhanced starch digestion compared with Greenland sled dogs and a compendium of derived homozygous coding variants at constrained positions in genes connected to bone and skin development. We propose that Balto's population of origin, which was less inbred and genetically healthier than that of modern breeds, was adapted to the extreme environment of 1920s Alaska.", "doi": "10.1126/science.abn5887", "pmid": "37104591", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1893725"}, {"db": "pmc", "key": "PMC10184777"}], "notes": [], "created": "2023-12-01T09:07:28.377Z", "modified": "2024-01-16T13:48:33.546Z"}, {"entity": "publication", "iuid": "8ee42fe5c10a4a589cf92177bcc10041", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ee42fe5c10a4a589cf92177bcc10041.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ee42fe5c10a4a589cf92177bcc10041"}}, "title": "Three-dimensional genome rewiring in loci with human accelerated regions.", "authors": [{"family": "Keough", "given": "Kathleen C", "initials": "KC", "orcid": "0000-0002-7481-0511", "researcher": {"href": "https://publications.scilifelab.se/researcher/60254d61d3d64a8e80eee17c1e3d24db.json"}}, {"family": "Whalen", "given": "Sean", "initials": "S", "orcid": "0000-0002-6648-3610", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a791e66720648dd817179e8626dfe69.json"}}, {"family": "Inoue", "given": "Fumitaka", "initials": "F", "orcid": "0000-0003-0657-434X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d37d0d68e4b0a96010704bb7d2136.json"}}, {"family": "Przytycki", "given": "Pawel F", "initials": "PF", "orcid": "0000-0002-3360-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdeddfa32b3e41318e8cd6fea8b619f1.json"}}, {"family": "Fair", "given": "Tyler", "initials": "T"}, {"family": "Deng", "given": "Chengyu", "initials": "C", "orcid": "0000-0003-3595-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/25f79619fa6f46ce9bb13a6abcad6165.json"}}, {"family": "Steyert", "given": "Marilyn", "initials": "M", "orcid": "0000-0003-4095-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/9940f9ae5fcd43ed8582432bfe8588d5.json"}}, {"family": "Ryu", "given": "Hane", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor", "initials": "E", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Nowakowski", "given": "Tomasz", "initials": "T", "orcid": "0000-0003-2345-4964", "researcher": {"href": "https://publications.scilifelab.se/researcher/9afca838449f4601844b1462c2ceb953.json"}}, {"family": "Ahituv", "given": "Nadav", "initials": "N", "orcid": "0000-0002-7434-8144", "researcher": {"href": "https://publications.scilifelab.se/researcher/24ed3745c2ab498c98cd24d6766c9019.json"}}, {"family": "Pollen", "given": "Alex", "initials": "A", "orcid": "0000-0003-3263-8634", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a70ab2e0b994621b4993fe25baed4fe.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabm1696"}, "abstract": "Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs.", "doi": "10.1126/science.abm1696", "pmid": "37104607", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-01T08:54:13.311Z", "modified": "2024-01-16T13:48:33.575Z"}, {"entity": "publication", "iuid": "0c70433579774cc297a55baabec049ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c70433579774cc297a55baabec049ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c70433579774cc297a55baabec049ea"}}, "title": "The functional and evolutionary impacts of human-specific deletions in conserved elements.", "authors": [{"family": "Xue", "given": "James R", "initials": "JR", "orcid": "0000-0002-3332-5747", "researcher": {"href": "https://publications.scilifelab.se/researcher/c910e64598674d5da576b3b5057afb43.json"}}, {"family": "Mackay-Smith", "given": "Ava", "initials": "A", "orcid": "0000-0003-0404-0563", "researcher": {"href": "https://publications.scilifelab.se/researcher/a60ce7b39d8c4b25bfddc8b8cd460970.json"}}, {"family": "Mouri", "given": "Kousuke", "initials": "K", "orcid": "0000-0003-1712-6833", "researcher": {"href": "https://publications.scilifelab.se/researcher/66c28c463e194c4395f03776335db2f1.json"}}, {"family": "Garcia", "given": "Meilin Fernandez", "initials": "MF", "orcid": "0000-0002-8745-9775", "researcher": {"href": "https://publications.scilifelab.se/researcher/c28f08d4f61f4c07ae57f56d220ab158.json"}}, {"family": "Dong", "given": "Michael X", "initials": "MX", "orcid": "0000-0003-4084-3099", "researcher": {"href": "https://publications.scilifelab.se/researcher/d44d219b319346c481c82d69d5055cd8.json"}}, {"family": "Akers", "given": "Jared F", "initials": "JF", "orcid": "0000-0002-9270-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/11555b05f1914cd8b1a63a07335d9f70.json"}}, {"family": "Noble", "given": "Mark", "initials": "M", "orcid": "0000-0002-9618-120X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d35842f19164723979bd2e19ae4c470.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Noonan", "given": "James P", "initials": "JP", "orcid": "0000-0001-9632-5835", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e35cb8e4ed64e5a8c5583b81c29bb65.json"}}, {"family": "Capellini", "given": "Terence D", "initials": "TD", "orcid": "0000-0003-3842-8478", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ca4d388b3314861afe8593858bac9ab.json"}}, {"family": "Brennand", "given": "Kristen J", "initials": "KJ", "orcid": "0000-0003-0993-5956", "researcher": {"href": "https://publications.scilifelab.se/researcher/79ac89080d28492ab5fb4012939b0994.json"}}, {"family": "Tewhey", "given": "Ryan", "initials": "R", "orcid": "0000-0002-4607-8001", "researcher": {"href": "https://publications.scilifelab.se/researcher/08c06e4a031147ec8e0a4692b86a8198.json"}}, {"family": "Sabeti", "given": "Pardis C", "initials": "PC", "orcid": "0000-0002-9843-1890", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a05c59f83114ac68c7bd1a0930fa0c9.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2253"}, "abstract": "Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.", "doi": "10.1126/science.abn2253", "pmid": "37104592", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897409"}, {"db": "pmc", "key": "PMC10202372"}], "notes": [], "created": "2023-12-01T09:07:31.011Z", "modified": "2024-01-16T13:48:33.587Z"}, {"entity": "publication", "iuid": "44039aa0a48d4c0caad589efc02597cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44039aa0a48d4c0caad589efc02597cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44039aa0a48d4c0caad589efc02597cf"}}, "title": "The contribution of historical processes to contemporary extinction risk in placental mammals.", "authors": [{"family": "Wilder", "given": "Aryn P", "initials": "AP", "orcid": "0000-0003-4970-6891", "researcher": {"href": "https://publications.scilifelab.se/researcher/582a7c9cf0214c8b9063df22f49910d5.json"}}, {"family": "Supple", "given": "Megan A", "initials": "MA", "orcid": "0000-0002-0204-7852", "researcher": {"href": "https://publications.scilifelab.se/researcher/68aab878c786406da6d8810c1ca6eb04.json"}}, {"family": "Subramanian", "given": "Ayshwarya", "initials": "A", "orcid": "0000-0002-4134-7612", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbf15f9b2bd447f49e0bbc5c8d4d3b21.json"}}, {"family": "Mudide", "given": "Anish", "initials": "A", "orcid": "0000-0002-6174-2345", "researcher": {"href": "https://publications.scilifelab.se/researcher/99494338a7704bad94a32a59b2357181.json"}}, {"family": "Swofford", "given": "Ross", "initials": "R", "orcid": "0000-0003-3676-8479", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bf782e1d8b646daa53455586d8bf706.json"}}, {"family": "Serres-Armero", "given": "Aitor", "initials": "A"}, {"family": "Steiner", "given": "Cynthia", "initials": "C", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Koepfli", "given": "Klaus-Peter", "initials": "K"}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4ea50a4fe3147f3b979ccaa8a2a0de4.json"}}, {"family": "Munoz Fuentes", "given": "Violeta", "initials": "V", "orcid": "0000-0003-3574-546X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f2bdc1125af4e71b43d057c36e76967.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f76d7e48d843d39046582156da3615.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Shapiro", "given": "Beth", "initials": "B", "orcid": "0000-0002-2733-7776", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e998b6760594d43b00e50c4f6a27d05.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn5856"}, "abstract": "Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective population size (Ne) affects heterozygosity and deleterious genetic load and how these factors may contribute to extinction risk. We find that species with smaller historical Ne carry a proportionally larger burden of deleterious alleles owing to long-term accumulation and fixation of genetic load and have a higher risk of extinction. This suggests that historical demography can inform contemporary resilience. Models that included genomic data were predictive of species' conservation status, suggesting that, in the absence of adequate census or ecological data, genomic information may provide an initial risk assessment.", "doi": "10.1126/science.abn5856", "pmid": "37104572", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1893031"}, {"db": "pmc", "key": "PMC10184782"}], "notes": [], "created": "2023-12-01T08:54:18.907Z", "modified": "2024-01-16T13:48:33.595Z"}, {"entity": "publication", "iuid": "bfb6fdc7339947a692119410b04c42a1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bfb6fdc7339947a692119410b04c42a1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bfb6fdc7339947a692119410b04c42a1"}}, "title": "Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.", "authors": [{"family": "Kaplow", "given": "Irene M", "initials": "IM", "orcid": "0000-0002-8924-8269", "researcher": {"href": "https://publications.scilifelab.se/researcher/9bbc94842b1f4195b678beee7cc8cf6e.json"}}, {"family": "Lawler", "given": "Alyssa J", "initials": "AJ", "orcid": "0000-0002-2151-5164", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac870df8d074925b9956e82fba828eb.json"}}, {"family": "Sch\u00e4ffer", "given": "Daniel E", "initials": "DE", "orcid": "0000-0003-3608-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be4ccbb9fd247eaa3320c4f1a8d64dc.json"}}, {"family": "Srinivasan", "given": "Chaitanya", "initials": "C", "orcid": "0000-0002-1487-541X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1f3803c67844809b8d460e321034287.json"}}, {"family": "Sestili", "given": "Heather H", "initials": "HH", "orcid": "0000-0002-3944-3429", "researcher": {"href": "https://publications.scilifelab.se/researcher/247a3b572c934443a8b06bf1eeab2e06.json"}}, {"family": "Wirthlin", "given": "Morgan E", "initials": "ME", "orcid": "0000-0001-7967-7070", "researcher": {"href": "https://publications.scilifelab.se/researcher/d37d43eda07f49fa8f44adf0d1f41b5a.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Prasad", "given": "Kavya", "initials": "K", "orcid": "0000-0003-3419-5670", "researcher": {"href": "https://publications.scilifelab.se/researcher/68bbc313fcd344e2adb1ab5d8d7f8581.json"}}, {"family": "Brown", "given": "Ashley R", "initials": "AR", "orcid": "0000-0002-3091-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/31ed0f654aa3485e8b2a02f902981f32.json"}}, {"family": "Zhang", "given": "Xiaomeng", "initials": "X", "orcid": "0000-0002-8536-6460", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f4e1e573fa54ccc88171795e61d2a7a.json"}}, {"family": "Foley", "given": "Kathleen", "initials": "K", "orcid": "0000-0003-0923-1326", "researcher": {"href": "https://publications.scilifelab.se/researcher/03f76d7e48d843d39046582156da3615.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dedda53aab044eabd09ae377084ff9d.json"}}, {"family": "Zoonomia Consortium**", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Meyer", "given": "Wynn K", "initials": "WK", "orcid": "0000-0001-7978-3877", "researcher": {"href": "https://publications.scilifelab.se/researcher/d168f23b63994217b3b082c3cd70561b.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabm7993"}, "abstract": "Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.", "doi": "10.1126/science.abm7993", "pmid": "37104615", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897368"}, {"db": "pmc", "key": "PMC10322212"}], "notes": [], "created": "2023-12-01T09:07:36.543Z", "modified": "2024-01-16T13:48:33.603Z"}, {"entity": "publication", "iuid": "c579ad21c5b84f01bac1beeb5e447116", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c579ad21c5b84f01bac1beeb5e447116.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c579ad21c5b84f01bac1beeb5e447116"}}, "title": "Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.", "authors": [{"family": "Andrews", "given": "Gregory", "initials": "G", "orcid": "0000-0002-9880-3965", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f84c888473d45ea8d8e97945d508705.json"}}, {"family": "Fan", "given": "Kaili", "initials": "K", "orcid": "0000-0002-8723-7902", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f65b033be1343e48895a7c99903717c.json"}}, {"family": "Pratt", "given": "Henry E", "initials": "HE", "orcid": "0000-0001-9413-834X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c565845faf8049c6b076a0470fe95b1a.json"}}, {"family": "Phalke", "given": "Nishigandha", "initials": "N"}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Moore", "given": "Jill E", "initials": "JE", "orcid": "0000-0002-3023-0806", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa6791c7bf0450298988030f7c64667.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn7930"}, "abstract": "Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription factor binding sites (TFBSs). We identified 439,461 cCREs and 2,024,062 TFBSs under evolutionary constraint. Genes near constrained elements perform fundamental cellular processes, whereas genes near primate-specific elements are involved in environmental interaction, including odor perception and immune response. About 20% of TFBSs are transposable element-derived and exhibit intricate patterns of gains and losses during primate evolution whereas sequence variants associated with complex traits are enriched in constrained TFBSs. Our annotations illuminate the regulatory functions of the human genome.", "doi": "10.1126/science.abn7930", "pmid": "37104580", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": null}, "xrefs": [], "notes": [], "created": "2023-12-01T08:31:26.561Z", "modified": "2024-01-16T13:48:33.610Z"}, {"entity": "publication", "iuid": "6cea0eb350cd40bba54717d8b627da6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cea0eb350cd40bba54717d8b627da6b"}}, "title": "Leveraging base-pair mammalian constraint to understand genetic variation and human disease.", "authors": [{"family": "Sullivan", "given": "Patrick F", "initials": "PF", "orcid": "0000-0002-6619-873X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d95de0b5ab14586980a6a13c8299346.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Gazal", "given": "Steven", "initials": "S", "orcid": "0000-0003-4510-5730", "researcher": {"href": "https://publications.scilifelab.se/researcher/fecc8307017145088589536e3c312515.json"}}, {"family": "Phan", "given": "BaDoi N", "initials": "BN", "orcid": "0000-0001-6331-5980", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9e37df4e5c54204a19ea394e1f7651e.json"}}, {"family": "Li", "given": "Xue", "initials": "X", "orcid": "0000-0002-9126-2692", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfa777bbc9d34c0e9f4920decc7cdcb3.json"}}, {"family": "Genereux", "given": "Diane P", "initials": "DP", "orcid": "0000-0001-5770-0989", "researcher": 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"0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Roy", "given": "Ananya", "initials": "A"}, {"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e069a0271e4a1fbc31fd3cb440366f.json"}}, {"family": "Marinescu", "given": "Voichita D", "initials": "VD", "orcid": "0000-0002-4803-4707", "researcher": {"href": "https://publications.scilifelab.se/researcher/087384bb1f8743158b76352c8847d48d.json"}}, {"family": "Wang", "given": "Chao", "initials": "C", "orcid": "0000-0003-3936-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/202a8fd115e14824809a362a7cfc5a41.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": 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"NR", "orcid": "0000-0001-7421-3357", "researcher": {"href": "https://publications.scilifelab.se/researcher/15a175036d9f44f9b4090d7d431f78d7.json"}}, {"family": "Li", "given": "Yun", "initials": "Y", "orcid": "0000-0002-9275-4189", "researcher": {"href": "https://publications.scilifelab.se/researcher/c294ce82ce8946428048b9b4e3e9cad8.json"}}, {"family": "Johnson", "given": "Jessica", "initials": "J", "orcid": "0000-0002-4519-3120", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2cc5da674c44d4cb58c1f98d145043a.json"}}, {"family": "Chen", "given": "Jiawen", "initials": "J", "orcid": "0000-0002-6193-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/39de15a492f34e4b8e237e748c38524b.json"}}, {"family": "Zoonomia Consortium\u00a7", "given": "", "initials": ""}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Reilly", "given": "Steven K", "initials": "SK", "orcid": "0000-0003-3140-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c12bcf707394bb5b9c34075aba19f13.json"}}, {"family": "Hughes", "given": "Graham M", "initials": "GM", "orcid": "0000-0003-3088-345X", "researcher": {"href": "https://publications.scilifelab.se/researcher/800da869332a45b9b4c7bd8fd5522666.json"}}, {"family": "Weng", "given": "Zhiping", "initials": "Z", "orcid": "0000-0002-3032-7966", "researcher": {"href": "https://publications.scilifelab.se/researcher/25ad44250cba4b0cba5250b07f764ba3.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Forsberg-Nilsson", "given": "Karin", "initials": "K", "orcid": "0000-0003-0692-6245", "researcher": {"href": "https://publications.scilifelab.se/researcher/5da04859250141a0a7271a69c7da9176.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn2937"}, "abstract": "Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.", "doi": "10.1126/science.abn2937", "pmid": "37104612", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897004"}, {"db": "pmc", "key": "PMC10259825"}], "notes": [], "created": "2023-12-01T08:54:10.456Z", "modified": "2024-01-16T13:48:33.619Z"}, {"entity": "publication", "iuid": "048080e8a4d44a78bbecf7078f9d6901", "links": {"self": {"href": "https://publications.scilifelab.se/publication/048080e8a4d44a78bbecf7078f9d6901.json"}, "display": {"href": "https://publications.scilifelab.se/publication/048080e8a4d44a78bbecf7078f9d6901"}}, "title": "Integrating gene annotation with orthology inference at scale.", "authors": [{"family": "Kirilenko", "given": "Bogdan M", "initials": "BM", "orcid": "0000-0002-9394-4275", "researcher": {"href": "https://publications.scilifelab.se/researcher/104f94382f604235ac8edd862204924e.json"}}, {"family": "Munegowda", "given": "Chetan", "initials": "C", "orcid": "0000-0002-3790-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ffdf84352a347a790277d9a7debbe28.json"}}, {"family": "Osipova", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-6769-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/f048ee0785094c2fa3e5b79eba6d1900.json"}}, {"family": "Jebb", "given": "David", "initials": "D"}, {"family": "Sharma", "given": "Virag", "initials": "V", "orcid": "0000-0003-4086-4105", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bfd936285cc49c6b40d3c3d0ee4ed26.json"}}, {"family": "Blumer", "given": "Moritz", "initials": "M", "orcid": "0000-0002-5775-1767", "researcher": {"href": "https://publications.scilifelab.se/researcher/58505e8b013b4428bb69b52b1d2f5cf1.json"}}, {"family": "Morales", "given": "Ariadna E", "initials": "AE", "orcid": "0000-0002-0637-7349", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d82eb099b284f068e85ba556ef1cbf5.json"}}, {"family": "Ahmed", "given": "Alexis-Walid", "initials": "A"}, {"family": "Kontopoulos", "given": "Dimitrios-Georgios", "initials": "D"}, {"family": "Hilgers", "given": "Leon", "initials": "L", "orcid": "0000-0002-3539-2513", "researcher": {"href": "https://publications.scilifelab.se/researcher/819689e4085e481b931f20d96a395a27.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Hiller", "given": "Michael", "initials": "M", "orcid": "0000-0003-3024-1449", "researcher": {"href": "https://publications.scilifelab.se/researcher/c304600adfb24d45a7bd0c94f55d1f5b.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3107"}, "abstract": "Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.", "doi": "10.1126/science.abn3107", "pmid": "37104600", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1898035"}, {"db": "pmc", "key": "PMC10193443"}], "notes": [], "created": "2023-12-01T09:07:33.771Z", "modified": "2024-01-16T13:48:33.629Z"}, {"entity": "publication", "iuid": "1b55f000e45e48569ce691e5f288112a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b55f000e45e48569ce691e5f288112a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b55f000e45e48569ce691e5f288112a"}}, "title": "Insights into mammalian TE diversity through the curation of 248 genome assemblies.", "authors": [{"family": "Osmanski", "given": "Austin B", "initials": "AB", "orcid": "0000-0002-1485-6446", "researcher": {"href": "https://publications.scilifelab.se/researcher/861bdbbf0e72446795a267d6d0a4cb81.json"}}, {"family": "Paulat", "given": "Nicole S", "initials": "NS", "orcid": "0000-0002-6881-2588", "researcher": {"href": "https://publications.scilifelab.se/researcher/58778de33da041ceba1481ae528dbb0c.json"}}, {"family": "Korstian", "given": "Jenny", "initials": "J", "orcid": "0000-0003-3872-8948", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3541cf73dab433cace7f4e670155278.json"}}, {"family": "Grimshaw", "given": "Jenna R", "initials": "JR", "orcid": "0000-0001-7673-5167", "researcher": {"href": "https://publications.scilifelab.se/researcher/1658aea21a524780b67bfdca293ab1d0.json"}}, {"family": "Halsey", "given": "Michaela", "initials": "M"}, {"family": "Sullivan", "given": "Kevin A M", "initials": "KAM", "orcid": "0000-0001-8499-0491", "researcher": {"href": "https://publications.scilifelab.se/researcher/13f0fe7f177c4422bd5ab25dd2a070c6.json"}}, {"family": "Moreno-Santill\u00e1n", "given": "Diana D", "initials": "DD", "orcid": "0000-0003-2153-0732", "researcher": {"href": "https://publications.scilifelab.se/researcher/460f9988264e4be58157b65c376561b0.json"}}, {"family": "Crookshanks", "given": "Claudia", "initials": "C"}, {"family": "Roberts", "given": "Jacquelyn", "initials": "J"}, {"family": "Garcia", "given": "Carlos", "initials": "C", "orcid": "0000-0001-9194-4514", "researcher": {"href": "https://publications.scilifelab.se/researcher/f836e2eaf97a4f09837704347f112324.json"}}, {"family": "Johnson", "given": "Matthew G", "initials": "MG", "orcid": "0000-0002-1958-6334", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e75a950635a403eb0e34a15cdf0fef2.json"}}, {"family": "Densmore", "given": "Llewellyn D", "initials": "LD", "orcid": "0000-0002-6681-5507", "researcher": {"href": "https://publications.scilifelab.se/researcher/941b0334a8374ec79bfaf95881b370ff.json"}}, {"family": "Stevens", "given": "Richard D", "initials": "RD"}, {"family": "Zoonomia Consortium\u2020", "given": "", "initials": ""}, {"family": "Rosen", "given": "Jeb", "initials": "J", "orcid": "0000-0002-8832-1276", "researcher": {"href": "https://publications.scilifelab.se/researcher/39406330ee844bdbb9476ee472ff44a8.json"}}, {"family": "Storer", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-9619-5265", "researcher": {"href": "https://publications.scilifelab.se/researcher/17dbab57213847a8b685d1fd7d0885d8.json"}}, {"family": "Hubley", "given": "Robert", "initials": "R", "orcid": "0000-0001-9261-3821", "researcher": {"href": "https://publications.scilifelab.se/researcher/76c6f83d0eb34efc9e50811d6af5a0b1.json"}}, {"family": "Smit", "given": "Arian F A", "initials": "AFA", "orcid": "0000-0003-2088-3165", "researcher": {"href": "https://publications.scilifelab.se/researcher/34068300dba84e9f80ffde962a8ca49b.json"}}, {"family": "D\u00e1valos", "given": "Liliana M", "initials": "LM", "orcid": "0000-0002-4327-7697", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c73133e743c4560a2660c7ab5b036cd.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn1430"}, "abstract": "We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.", "doi": "10.1126/science.abn1430", "pmid": "37104570", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-12-01T08:54:16.075Z", "modified": "2024-01-16T13:48:33.640Z"}, {"entity": "publication", "iuid": "d7e4da3ff4c54966b53e2e1210128441", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7e4da3ff4c54966b53e2e1210128441"}}, "title": "Evolutionary constraint and innovation across hundreds of placental mammals.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ", "orcid": "0000-0002-6355-7581", "researcher": {"href": 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"researcher": {"href": "https://publications.scilifelab.se/researcher/bedfc4bc5b6e421da56cfe2bebfa21f3.json"}}, {"family": "Navarro", "given": "Arcadi", "initials": "A", "orcid": "0000-0003-2162-8246", "researcher": {"href": "https://publications.scilifelab.se/researcher/c541642111d94cb8a682b1ff8bea41ac.json"}}, {"family": "Paten", "given": "Benedict", "initials": "B", "orcid": "0000-0001-8863-3539", "researcher": {"href": "https://publications.scilifelab.se/researcher/956ebe9c0b6e43d7ac2a568519f43431.json"}}, {"family": "Pollard", "given": "Katherine S", "initials": "KS", "orcid": "0000-0002-9870-6196", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb2a865a28524f55bb5d9df3db79563f.json"}}, {"family": "Ray", "given": "David A", "initials": "DA", "orcid": "0000-0002-3340-3987", "researcher": {"href": "https://publications.scilifelab.se/researcher/1637808586b2454190e734d575cf0140.json"}}, {"family": "Ruf", "given": "Irina", "initials": "I", "orcid": "0000-0002-9728-1210", "researcher": {"href": "https://publications.scilifelab.se/researcher/838b4e91f9484f26a6dcc1404051a38a.json"}}, {"family": "Ryder", "given": "Oliver A", "initials": "OA", "orcid": "0000-0003-2427-763X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a55f8ea442f4168a8426ae4a2c43a46.json"}}, {"family": "Pfenning", "given": "Andreas R", "initials": "AR", "orcid": "0000-0002-3447-9801", "researcher": {"href": "https://publications.scilifelab.se/researcher/579e32fe57da4d738b7fbf0a57fb6faf.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabn3943"}, "abstract": "Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.", "doi": "10.1126/science.abn3943", "pmid": "37104599", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1896905"}, {"db": "pmc", "key": "PMC10250106"}], "notes": [], "created": "2023-12-01T08:40:50.036Z", "modified": "2024-01-16T13:48:33.655Z"}, {"entity": "publication", "iuid": "5da7c081abc141ff8b4814107fd6c56d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5da7c081abc141ff8b4814107fd6c56d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5da7c081abc141ff8b4814107fd6c56d"}}, "title": "A genomic timescale for placental mammal evolution.", "authors": [{"family": "Foley", "given": "Nicole M", "initials": "NM", "orcid": "0000-0002-8169-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a0b5fa8c458409794479e010bdf8425.json"}}, {"family": "Mason", "given": "Victor C", "initials": "VC"}, {"family": "Harris", "given": "Andrew J", "initials": "AJ", "orcid": "0000-0001-6373-7446", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c2b9909ba9147b39741671de325f90f.json"}}, {"family": "Bredemeyer", "given": "Kevin R", "initials": "KR", "orcid": "0000-0002-1374-6050", "researcher": {"href": "https://publications.scilifelab.se/researcher/54402aedeec3424588e9bdffabd77c0f.json"}}, {"family": "Damas", "given": "Joana", "initials": "J", "orcid": "0000-0003-4857-2510", "researcher": {"href": "https://publications.scilifelab.se/researcher/86c0daf03cc84d55a831bfe99448a389.json"}}, {"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2f6f17d3e4b4b7e8f47349bda4c1bb0.json"}}, {"family": "Eizirik", "given": "Eduardo", "initials": "E", "orcid": "0000-0002-9658-0999", "researcher": {"href": "https://publications.scilifelab.se/researcher/102a98d00d9b4643aafb72e08a273ac9.json"}}, {"family": "Gatesy", "given": "John", "initials": "J", "orcid": "0000-0003-3061-7741", "researcher": {"href": "https://publications.scilifelab.se/researcher/be557f53354548e584381076522b78ba.json"}}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK", "orcid": "0000-0002-4343-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bd97378a1cc403db0923895adde15e3.json"}}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Zoonomia Consortium\u2021", "given": "", "initials": ""}, {"family": "Springer", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-7335-6946", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb2b4f352f9b4e8b9f20da68caa94912.json"}}, {"family": "Murphy", "given": "William J", "initials": "WJ", "orcid": "0000-0003-3699-0723", "researcher": {"href": "https://publications.scilifelab.se/researcher/bedfc4bc5b6e421da56cfe2bebfa21f3.json"}}], "type": "journal article", "published": "2023-04-28", "journal": {"title": "Science", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "380", "issue": "6643", "pages": "eabl8189"}, "abstract": "The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.", "doi": "10.1126/science.abl8189", "pmid": "37104581", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "mid", "key": "NIHMS1897334"}, {"db": "pmc", "key": "PMC10233747"}], "notes": [], "created": "2023-12-01T08:38:42.154Z", "modified": "2024-01-16T13:48:33.669Z"}, {"entity": "publication", "iuid": "03f6f1b4cfe24ceea3859aa58e725308", "links": {"self": {"href": "https://publications.scilifelab.se/publication/03f6f1b4cfe24ceea3859aa58e725308.json"}, "display": {"href": "https://publications.scilifelab.se/publication/03f6f1b4cfe24ceea3859aa58e725308"}}, "title": "Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.", "authors": [{"family": "Rosenbaum", "given": "Adam", "initials": "A"}, {"family": "Dahlin", "given": "Anna M", "initials": "AM"}, {"family": "Andersson", "given": "Ulrika", "initials": "U"}, {"family": "Bj\u00f6rkblom", "given": "Benny", "initials": "B"}, {"family": "Wu", "given": "Wendy Yi-Ying", "initials": "WY"}, {"family": "Hedman", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wibom", "given": "Carl", "initials": "C"}, {"family": "Melin", "given": "Beatrice", "initials": "B"}], "type": "journal article", "published": "2023-04-25", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "13", "issue": "1", "pages": "6777"}, "abstract": "Genome-wide association studies (GWAS) have contributed to our understanding of glioma susceptibility. To date, 25 risk loci for development of any of the glioma subtypes are known. However, GWAS studies reveal little about the molecular processes that lead to increased risk, especially for non-coding single nucleotide polymorphisms (SNP). A particular SNP in intron 2 of LRIG1, rs11706832, has been shown to increase the susceptibility for IDH1 mutated low-grade gliomas (LGG). Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is important in cancer development as it negatively regulates the epidermal growth factor receptor (EGFR); however, the mechanism responsible for this particular risk SNP and its potential effect on LRIG1 are not known. Using CRISPR-CAS9, we edited rs11706832 in HEK293T cells. Four HEK293T clones with the risk allele were compared to four clones with the non-risk allele for LRIG1 and SLC25A26 gene expression using RT-qPCR, for global gene expression using RNA-seq, and for metabolites using gas chromatography-mass spectrometry (GC-MS). The experiment did not reveal any significant effect of the SNP on the expression levels or splicing patterns of LRIG1 or SLC25A26. The global gene expression analysis revealed that the risk allele C was associated with upregulation of several mitochondrial genes. Gene enrichment analysis of 74 differentially expressed genes in the genome revealed a significant enrichment of type I interferon response genes, where many genes were downregulated for the risk allele C. Gene expression data of IDH1 mutated LGGs from the cancer genome atlas (TCGA) revealed a similar under expression of type I interferon genes associated with the risk allele. This study found the expression levels and splicing patterns of LRIG1 and SLC25A26 were not affected by the SNP in HEK293T cells. However, the risk allele was associated with a downregulation of genes involved in the innate immune response both in the HEK293T cells and in the LGG data from TCGA.", "doi": "10.1038/s41598-023-33923-4", "pmid": "37185361", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10130147"}, {"db": "pii", "key": "10.1038/s41598-023-33923-4"}], "notes": [], "created": "2023-08-30T07:04:23.132Z", "modified": "2025-10-17T13:03:14.040Z"}, {"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": "091bc2001e6e49a1a25c43f310e57220", "links": {"self": {"href": "https://publications.scilifelab.se/publication/091bc2001e6e49a1a25c43f310e57220.json"}, "display": {"href": "https://publications.scilifelab.se/publication/091bc2001e6e49a1a25c43f310e57220"}}, "title": "Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.", "authors": [{"family": "Pappas", "given": "Fotis", "initials": "F"}, {"family": "Kurta", "given": "Khrystyna", "initials": "K"}, {"family": "Vanhala", "given": "Tytti", "initials": "T"}, {"family": "Jeuthe", "given": "Henrik", "initials": "H"}, {"family": "Hagen", "given": "\u00d8rjan", "initials": "\u00d8"}, {"family": "Beir\u00e3o", "given": "Jos\u00e9", "initials": "J"}, {"family": "Palaiokostas", "given": "Christos", "initials": "C", "orcid": "0000-0002-4480-4612", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1d6c65f53a8434cb1d5dd4c7bf5d444.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "16", "issue": "4", "pages": "797-813", "issn-l": "1752-4571"}, "abstract": "Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.", "doi": "10.1111/eva.13537", "pmid": "37124091", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10130564"}, {"db": "pii", "key": "EVA13537"}], "notes": [], "created": "2023-11-29T11:32:33.735Z", "modified": "2023-11-29T11:32:33.768Z"}, {"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": "1b64b2e873f440098c5413b843a1c9cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64b2e873f440098c5413b843a1c9cf"}}, "title": "From high masked to high realized genetic load in inbred Scandinavian wolves.", "authors": [{"family": "Smeds", "given": "Linn\u00e9a", "initials": "L", "orcid": "0000-0002-8415-9259", "researcher": {"href": "https://publications.scilifelab.se/researcher/b46a4a275c954de8bb969ef4cda9e33b.json"}}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2023-04-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "32", "issue": "7", "pages": "1567-1580"}, "abstract": "When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.", "doi": "10.1111/mec.16802", "pmid": "36458895", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.7m0cfxpzj"}], "notes": [], "created": "2023-11-29T09:02:42.251Z", "modified": "2024-01-16T13:48:33.734Z"}, {"entity": "publication", "iuid": "15a5346b36f14d278fc4cf5675a02135", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15a5346b36f14d278fc4cf5675a02135.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15a5346b36f14d278fc4cf5675a02135"}}, "title": "SLC38A10 Deficiency in Mice Affects Plasma Levels of Threonine and Histidine in Males but Not in Females: A Preliminary Characterization Study of SLC38A10-/- Mice.", "authors": [{"family": "Lindberg", "given": "Frida A", "initials": "FA", "orcid": "0000-0003-4665-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/a44e6d2a6d0d4187be202fc76db7905e.json"}}, {"family": "Nordenankar", "given": "Karin", "initials": "K"}, {"family": "Forsberg", "given": "Erica C", "initials": "EC"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}], "type": "journal article", "published": "2023-03-30", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "14", "issue": "4", "issn-l": "2073-4425"}, "abstract": "Solute carriers belong to the biggest group of transporters in the human genome, but more knowledge is needed to fully understand their function and possible role as therapeutic targets. SLC38A10, a poorly characterized solute carrier, is preliminary characterized here. By using a knockout mouse model, we studied the biological effects of SLC38A10 deficiency in vivo. We performed a transcriptomic analysis of the whole brain and found seven differentially expressed genes in SLC38A10-deficient mice (Gm48159, Nr4a1, Tuba1c, Lrrc56, mt-Tp, Hbb-bt and Snord116/9). By measuring amino acids in plasma, we found lower levels of threonine and histidine in knockout males, whereas no amino acid levels were affected in females, suggesting that SLC38A10-/- might affect sexes differently. Using RT-qPCR, we investigated the effect of SLC38A10 deficiency on mRNA expression of other SLC38 members, Mtor and Rps6kb1 in the brain, liver, lung, muscle, and kidney, but no differences were found. Relative telomere length measurement was also taken, as a marker for cellular age, but no differences were found between the genotypes. We conclude that SLC38A10 might be important for keeping amino acid homeostasis in plasma, at least in males, but no major effects were seen on transcriptomic expression or telomere length in the whole brain.", "doi": "10.3390/genes14040835", "pmid": "37107593", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10138244"}, {"db": "pii", "key": "genes14040835"}], "notes": [], "created": "2023-05-22T20:21:42.460Z", "modified": "2025-10-17T13:03:14.094Z"}, {"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": "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": "3ec4d200a0024c8da044c7667d25768e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3ec4d200a0024c8da044c7667d25768e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3ec4d200a0024c8da044c7667d25768e"}}, "title": "Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes.", "authors": [{"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC"}, {"family": "Chmielarz", "given": "Miko\u0142aj", "initials": "M"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Brandt", "given": "Christian", "initials": "C"}, {"family": "Viehweger", "given": "Adrian", "initials": "A"}, {"family": "H\u00f6lzer", "given": "Martin", "initials": "M"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2023-03-10", "journal": {"title": "Biotechnol Biofuels Bioprod", "issn": "2731-3654", "volume": "16", "issue": "1", "pages": "42", "issn-l": null}, "abstract": "Lipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at different timepoints of cultivation, and a differential gene expression analysis was performed between cells grown at a similar physiological situation.\n\nWe observed enhanced transcription of genes involved in oxidative phosphorylation and enzymes localized in mitochondria in CGHH compared to CG. Genes involved in protein turnover, including those encoding ribosomal proteins, translation elongation factors, and genes involved in building the proteasome also showed an enhanced transcription in CGHH compared to CG. At 10 h cultivation, another group of activated genes in CGHH was involved in \u03b2-oxidation, handling oxidative stress and degradation of xylose and aromatic compounds. Potential bypasses of the standard GUT1 and GUT2-glycerol assimilation pathway were also expressed and upregulated in CGHH 10 h. When the additional carbon sources from HH were completely consumed, at CGHH 36 h, their transcription decreased and NAD+-dependent glycerol-3-phosphate dehydrogenase was upregulated compared to CG 60 h, generating NADH instead of NADPH with glycerol catabolism. TPI1 was upregulated in CGHH compared to cells grown on CG in all physiological situations, potentially channeling the DHAP formed through glycerol catabolism into glycolysis. The highest number of upregulated genes encoding glycolytic enzymes was found after 36 h in CGHH, when all additional carbon sources were already consumed.\n\nWe suspect that the physiological reason for the accelerated glycerol assimilation and faster lipid production, was primarily the activation of enzymes that provide energy.", "doi": "10.1186/s13068-023-02294-3", "pmid": "36899390", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9999650"}, {"db": "pii", "key": "10.1186/s13068-023-02294-3"}], "notes": [], "created": "2023-11-30T12:59:39.548Z", "modified": "2023-11-30T12:59:39.563Z"}, {"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": "07fe9e3eec8b4340aa05343a657ea24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d"}}, "title": "Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.", "authors": [{"family": "Rifkin", "given": "Riaan F", "initials": "RF", "orcid": "0000-0003-1791-3706", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b6691b2d64749e197ef0ddd36fd5af1.json"}}, {"family": "Vikram", "given": "Surendra", "initials": "S", "orcid": "0000-0002-4721-2890", "researcher": {"href": "https://publications.scilifelab.se/researcher/9171a14995cc47de9fb4d70bf4fe9aa9.json"}}, {"family": "Alcorta", "given": "Jaime", "initials": "J"}, {"family": "Ramond", "given": "Jean-Baptiste", "initials": "JB", "orcid": "0000-0003-4790-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f9b3ec176bd489daeeb78e1ef0a1acf.json"}}, {"family": "Cowan", "given": "Don A", "initials": "DA", "orcid": "0000-0001-8059-861X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc756e07160f4c888fbdc7612936db03.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "240", "issn-l": "2399-3642"}, "abstract": "The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.", "doi": "10.1038/s42003-023-04582-y", "pmid": "36869137", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9984395"}, {"db": "pii", "key": "10.1038/s42003-023-04582-y"}], "notes": [], "created": "2023-11-29T11:28:26.513Z", "modified": "2023-11-29T11:28:26.659Z"}, {"entity": "publication", "iuid": "0834b002d95d4369a2817a82baf8a196", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0834b002d95d4369a2817a82baf8a196.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0834b002d95d4369a2817a82baf8a196"}}, "title": "ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.", "authors": [{"family": "Mainwaring", "given": "Oliver J", "initials": "OJ", "orcid": "0000-0002-7973-9849", "researcher": {"href": "https://publications.scilifelab.se/researcher/494a0479041f41149902feb34f668043.json"}}, {"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "Zhao", "given": "Miao", "initials": "M", "orcid": "0000-0002-4895-1177", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c4e2515b414dee94aaeca71569699b.json"}}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Borgenvik", "given": "Anna", "initials": "A"}, {"family": "Breinschmid", "given": "Laura", "initials": "L"}, {"family": "Verbaan", "given": "Annemieke D", "initials": "AD"}, {"family": "Richardson", "given": "Stacey", "initials": "S"}, {"family": "Thompson", "given": "Dean", "initials": "D"}, {"family": "Clifford", "given": "Steven C", "initials": "SC"}, {"family": "Hill", "given": "Rebecca M", "initials": "RM"}, {"family": "Annusver", "given": "Karl", "initials": "K", "orcid": "0000-0002-9515-7216", "researcher": {"href": "https://publications.scilifelab.se/researcher/941902f72c214c868d0136cf433442a7.json"}}, {"family": "Sundstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Holmberg", "given": "Karl O", "initials": "KO"}, {"family": "Kasper", "given": "Maria", "initials": "M", "orcid": "0000-0002-6117-2717", "researcher": {"href": "https://publications.scilifelab.se/researcher/b036a8a125ca4f0896f2e832e1248dc0.json"}}, {"family": "Hutter", "given": "Sonja", "initials": "S"}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "1221", "issn-l": "2041-1723"}, "abstract": "Medulloblastoma, the most common malignant pediatric brain tumor, often harbors MYC amplifications. Compared to high-grade gliomas, MYC-amplified medulloblastomas often show increased photoreceptor activity and arise in the presence of a functional ARF/p53 suppressor pathway. Here, we generate an immunocompetent transgenic mouse model with regulatable MYC that develop clonal tumors that molecularly resemble photoreceptor-positive Group 3 medulloblastoma. Compared to MYCN-expressing brain tumors driven from the same promoter, pronounced ARF silencing is present in our MYC-expressing model and in human medulloblastoma. While partial Arf suppression causes increased malignancy in MYCN-expressing tumors, complete Arf depletion promotes photoreceptor-negative high-grade glioma formation. Computational models and clinical data further identify drugs targeting MYC-driven tumors with a suppressed but functional ARF pathway. We show that the HSP90 inhibitor, Onalespib, significantly targets MYC-driven but not MYCN-driven tumors in an ARF-dependent manner. The treatment increases cell death in synergy with cisplatin and demonstrates potential for targeting MYC-driven medulloblastoma.", "doi": "10.1038/s41467-023-36847-9", "pmid": "36869047", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9984535"}, {"db": "pii", "key": "10.1038/s41467-023-36847-9"}], "notes": [], "created": "2023-05-22T20:23:04.680Z", "modified": "2024-01-16T13:48:33.867Z"}, {"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": "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": "fb41fa7668a64161a4558d8647c73b7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb41fa7668a64161a4558d8647c73b7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb41fa7668a64161a4558d8647c73b7e"}}, "title": "Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.", "authors": [{"family": "Sj\u00f6din", "given": "Kotryna Simonyt\u00e9", "initials": "KS", "orcid": "0000-0002-1323-9913", "researcher": {"href": "https://publications.scilifelab.se/researcher/f00fe6a2da9b447f949b5b2f26bda908.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "Ruszczy\u0144ski", "given": "Marek", "initials": "M"}, {"family": "Kristensen", "given": "Mette Bach", "initials": "MB"}, {"family": "Hernell", "given": "Olle", "initials": "O"}, {"family": "Szajewska", "given": "Hania", "initials": "H"}, {"family": "West", "given": "Christina E", "initials": "CE", "orcid": "0000-0001-9599-2580", "researcher": {"href": "https://publications.scilifelab.se/researcher/be2972e4afa744e5aa0525a4c9d89348.json"}}], "type": "randomized controlled trial", "published": "2023-02-20", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "issn-l": "1741-7007", "volume": "21", "issue": "1", "pages": "38"}, "abstract": "Formula-fed infants are at increased risk of infections. Due to the cross-talk between the mucosal systems of the gastrointestinal and respiratory tracts, adding synbiotics (prebiotics and probiotics) to infant formula may prevent infections even at distant sites. Infants that were born full term and weaned from breast milk were randomized to prebiotic formula (fructo- and galactooligosaccharides) or the same prebiotic formula with Lactobacillus paracasei ssp. paracasei F19 (synbiotics) from 1 to 6 months of age. The objective was to examine the synbiotic effects on gut microbiota development.\r\n\r\nFecal samples collected at ages 1, 4, 6, and 12 months were analyzed using 16S rRNA gene sequencing and a combination of untargeted gas chromatography-mass spectrometry/liquid chromatography-mass spectrometry. These analyses revealed that the synbiotic group had a lower abundance of Klebsiella, a higher abundance of Bifidobacterium breve compared to the prebiotic group, and increases in the anti-microbial metabolite d-3-phenyllactic acid. We also analyzed the fecal metagenome and antibiotic resistome in the 11 infants that had been diagnosed with lower respiratory tract infection (cases) and 11 matched controls using deep metagenomic sequencing. Cases with lower respiratory tract infection had a higher abundance of Klebsiella species and antimicrobial resistance genes related to Klebsiella pneumoniae, compared to controls. The results obtained using 16S rRNA gene amplicon and metagenomic sequencing were confirmed in silico by successful recovery of the metagenome-assembled genomes of the bacteria of interest.\r\n\r\nThis study demonstrates the additional benefit of feeding specific synbiotics to formula-fed infants over prebiotics only. Synbiotic feeding led to the underrepresentation of Klebsiella, enrichment of bifidobacteria, and increases in microbial degradation metabolites implicated in immune signaling and in the gut-lung and gut-skin axes. Our findings support future clinical evaluation of synbiotic formula in the prevention of infections and associated antibiotic treatment as a primary outcome when breastfeeding is not feasible.\r\n\r\nClinicalTrials.gov NCT01625273 . Retrospectively registered on 21 June 2012.", "doi": "10.1186/s12915-023-01531-3", "pmid": "36803508", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9940374"}, {"db": "pii", "key": "10.1186/s12915-023-01531-3"}, {"db": "ClinicalTrials.gov", "key": "NCT01625273"}], "notes": [], "created": "2023-08-30T07:07:12.511Z", "modified": "2025-10-17T13:03:14.225Z"}, {"entity": "publication", "iuid": "f3bbf73bbbd4488dbd6ed6b3b52fd575", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3bbf73bbbd4488dbd6ed6b3b52fd575.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3bbf73bbbd4488dbd6ed6b3b52fd575"}}, "title": "Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest.", "authors": [{"family": "Xu", "given": "Wenjia", "initials": "W", "orcid": "0000-0003-1945-4451", "researcher": {"href": "https://publications.scilifelab.se/researcher/20c6bb89f2a047328e12ef6f6f36fc91.json"}}, {"family": "Sato", "given": "Hikaru", "initials": "H", "orcid": "0000-0001-7628-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/910d1533dd744edcbb4950dfc7c7f7c6.json"}}, {"family": "Bente", "given": "Heinrich", "initials": "H", "orcid": "0000-0001-9229-5149", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf580937ed9c45a5b736c95699ccd8eb.json"}}, {"family": "Santos-Gonz\u00e1lez", "given": "Juan", "initials": "J", "orcid": "0000-0002-8712-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/d26cc8b837e64875aa2226cb9a8b8da3.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}], "type": "journal article", "published": "2023-02-20", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "35", "issue": "2", "pages": "874-888", "issn-l": "1040-4651"}, "abstract": "The endosperm is a nutritive tissue supporting embryo growth in flowering plants. Most commonly, the endosperm initially develops as a coenocyte (multinucleate cell) and then cellularizes. This process of cellularization is frequently disrupted in hybrid seeds generated by crosses between different flowering plant species or plants that differ in ploidy, resulting in embryo arrest and seed lethality. The reason for embryo arrest upon cellularization failure remains unclear. In this study, we show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signaling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA-induced endosperm cellularization and suppressed embryo growth arrest. Taking these results together, we propose that endosperm cellularization is required to establish dehydration tolerance in the developing embryo, ensuring its survival during seed maturation.", "doi": "10.1093/plcell/koac337", "pmid": "36427255", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9940880"}, {"db": "pii", "key": "6847301"}], "notes": [], "created": "2022-11-29T09:51:04.203Z", "modified": "2025-10-17T13:03:14.237Z"}, {"entity": "publication", "iuid": "d03cd66d9f694b8da2a36e70178b23f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d03cd66d9f694b8da2a36e70178b23f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d03cd66d9f694b8da2a36e70178b23f2"}}, "title": "Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent.", "authors": [{"family": "Bensch", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-8449-9843", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a204f1b0fe34b8999893abe65fb3e8c.json"}}, {"family": "Tolf", "given": "Conny", "initials": "C"}, {"family": "Waldenstr\u00f6m", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1152-4235", "researcher": {"href": "https://publications.scilifelab.se/researcher/53013aa313214e26abdb18ea0199371f.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Z\u00f6ttl", "given": "Markus", "initials": "M", "orcid": "0000-0002-5582-2306", "researcher": {"href": "https://publications.scilifelab.se/researcher/e262a41c07044bd88a4bd6f1dcc2f1eb.json"}}], "type": "journal article", "published": "2023-02-10", "journal": {"title": "Anim Microbiome", "issn": "2524-4671", "volume": "5", "issue": "1", "pages": "9", "issn-l": null}, "abstract": "In mammals, the gut microbiota has important effects on the health of their hosts. Recent research highlights that animal populations that live in captivity often differ in microbiota diversity and composition from wild populations. However, the changes that may occur when animals move to captivity remain difficult to predict and factors generating such differences are poorly understood. Here we compare the bacterial gut microbiota of wild and captive Damaraland mole-rats (Fukomys damarensis) originating from a population in the southern Kalahari Desert to characterise the changes of the gut microbiota that occur from one generation to the next generation in a long-lived, social rodent species.\n\nWe found a clear divergence in the composition of the gut microbiota of captive and wild Damaraland mole-rats. Although the dominating higher-rank bacterial taxa were the same in the two groups, captive animals had an increased ratio of relative abundance of Firmicutes to Bacteroidetes compared to wild animals. The Amplicon Sequence Variants (ASVs) that were strongly associated with wild animals were commonly members of the same bacterial families as those strongly associated with captive animals. Captive animals had much higher ASV richness compared to wild-caught animals, explained by an increased richness within the Firmicutes.\n\nWe found that the gut microbiota of captive hosts differs substantially from the gut microbiota composition of wild hosts. The largest differences between the two groups were found in shifts in relative abundances and diversity of Firmicutes and Bacteroidetes.", "doi": "10.1186/s42523-023-00231-1", "pmid": "36765400", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9912604"}, {"db": "pii", "key": "10.1186/s42523-023-00231-1"}], "notes": [], "created": "2023-11-29T11:42:36.598Z", "modified": "2023-11-29T11:42:36.636Z"}, {"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": "8d88408f966c47f889a1837ae4c1b936", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d88408f966c47f889a1837ae4c1b936.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d88408f966c47f889a1837ae4c1b936"}}, "title": "Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex.", "authors": [{"family": "Ottenburghs", "given": "Jente", "initials": "J"}, {"family": "Honka", "given": "Johanna", "initials": "J"}, {"family": "Heikkinen", "given": "Marja E", "initials": "ME"}, {"family": "Madsen", "given": "Jesper", "initials": "J"}, {"family": "M\u00fcskens", "given": "Gerhard J D M", "initials": "GJDM"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2023-01-19", "journal": {"title": "BMC Ecol Evol", "issn": "2730-7182", "volume": "23", "issue": "1", "pages": "2", "issn-l": null}, "abstract": "Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus).\n\nFirst, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree.\n\nThe evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.", "doi": "10.1186/s12862-023-02103-3", "pmid": "36658479", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9854053"}, {"db": "pii", "key": "10.1186/s12862-023-02103-3"}], "notes": [], "created": "2023-11-30T13:15:16.114Z", "modified": "2024-01-16T13:48:34.115Z"}, {"entity": "publication", "iuid": "8fdf3ddb19384b72b7184506e4a87f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fdf3ddb19384b72b7184506e4a87f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fdf3ddb19384b72b7184506e4a87f19"}}, "title": "Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.", "authors": [{"family": "Wang", "given": "Baolin", "initials": "B"}, {"family": "Hu", "given": "Haiyan", "initials": "H"}, {"family": "Bishop", "given": "Kevin", "initials": "K"}, {"family": "Buck", "given": "Moritz", "initials": "M"}, {"family": "Bj\u00f6rn", "given": "Erik", "initials": "E"}, {"family": "Skyllberg", "given": "Ulf", "initials": "U"}, {"family": "Nilsson", "given": "Mats B", "initials": "MB"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Bravo", "given": "Andrea G", "initials": "AG"}], "type": "journal article", "published": "2023-01-15", "journal": {"title": "J Hazard Mater", "issn": "1873-3336", "volume": "442", "pages": "130057", "issn-l": null}, "abstract": "Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change.", "doi": "10.1016/j.jhazmat.2022.130057", "pmid": "36179622", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0304-3894(22)01851-9"}], "notes": [], "created": "2022-11-29T12:19:05.196Z", "modified": "2024-01-16T13:48:34.134Z"}, {"entity": "publication", "iuid": "cb8bdac206dc430f8174e8cbcd6281cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb8bdac206dc430f8174e8cbcd6281cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb8bdac206dc430f8174e8cbcd6281cf"}}, "title": "PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.", "authors": [{"family": "Arendt", "given": "Maja Louise", "initials": "ML"}, {"family": "Sakthikumar", "given": "Sharadha", "initials": "S"}, {"family": "Melin", "given": "Malin", "initials": "M"}, {"family": "Elvers", "given": "Ingegerd", "initials": "I"}, {"family": "Rivera", "given": "Patricio", "initials": "P"}, {"family": "Larsen", "given": "Majbritt", "initials": "M"}, {"family": "Saellstr\u00f6m", "given": "Sara", "initials": "S"}, {"family": "Lingaas", "given": "Frode", "initials": "F"}, {"family": "R\u00f6nnberg", "given": "Henrik", "initials": "H"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2023-01-12", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "632", "issn-l": "2045-2322"}, "abstract": "Biological features of neoplastic disease affecting mammary gland tissue are shared between canines and humans. Research performed in either species has translational value and early phase clinical trials performed in canines with spontaneous disease could be informative for human trials. The purpose of this study was to investigate the somatic genetic aberrations occurring in canine mammary neoplasia by exome capture and next generation sequencing. Based on 55 tumor-normal pairs we identified the PIK3CA gene as the most commonly mutated gene in canine mammary tumors, with 25% of samples carrying mutations in this gene. A recurrent missense mutation was identified, p.H1047R, which is homologous to the human PIK3CA hotspot mutation found in different types of breast neoplasia. Mutations homologous to other known human mutation hotspots such as the PIK3CA p.E545K and the KRAS p.G12V/D were also identified. We identified copy number aberrations affecting important tumor suppressor and oncogenic pathways including deletions affecting the PTEN tumor suppressor gene. We suggest that activation of the KRAS or PIK3CA oncogenes or loss of the PTEN suppressor gene may be important for mammary tumor development in dogs. This data endorses the conservation of cancer across species and the validity of studying cancer in non-human species.", "doi": "10.1038/s41598-023-27664-7", "pmid": "36635367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9837039"}, {"db": "pii", "key": "10.1038/s41598-023-27664-7"}], "notes": [], "created": "2023-11-29T11:40:33.492Z", "modified": "2024-01-16T13:48:34.144Z"}, {"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": "dbd47bdc131a45f6866e697cbdbc8196", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbd47bdc131a45f6866e697cbdbc8196.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbd47bdc131a45f6866e697cbdbc8196"}}, "title": "Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones.", "authors": [{"family": "Scharf", "given": "Lydia", "initials": "L"}, {"family": "Axelsson", "given": "Hannes", "initials": "H"}, {"family": "Emmanouilidi", "given": "Aikaterini", "initials": "A"}, {"family": "Mathew", "given": "Nimitha R", "initials": "NR"}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ"}, {"family": "Leach", "given": "Susannah", "initials": "S"}, {"family": "Isakson", "given": "Pauline", "initials": "P"}, {"family": "Smirnov", "given": "Ilya V", "initials": "IV"}, {"family": "Marklund", "given": "Emelie", "initials": "E"}, {"family": "Miron", "given": "Nicolae", "initials": "N"}, {"family": "Andersson", "given": "Lars-Magnus", "initials": "LM"}, {"family": "Gissl\u00e9n", "given": "Magnus", "initials": "M"}, {"family": "Murrell", "given": "Ben", "initials": "B"}, {"family": "Lundgren", "given": "Anna", "initials": "A"}, {"family": "Bemark", "given": "Mats", "initials": "M"}, {"family": "Angeletti", "given": "Davide", "initials": "D"}], "type": "journal article", "published": "2023-01-10", "journal": {"title": "JCI Insight", "issn": "2379-3708", "volume": "8", "issue": "1", "issn-l": "2379-3708"}, "abstract": "Understanding persistence and evolution of B cell clones after COVID-19 infection and vaccination is crucial for predicting responses against emerging viral variants and optimizing vaccines. Here, we collected longitudinal samples from patients with severe COVID-19 every third to seventh day during hospitalization and every third month after recovery. We profiled their antigen-specific immune cell dynamics by combining single-cell RNA-Seq, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and B cell receptor-Seq (BCR-Seq) with oligo-tagged antigen baits. While the proportion of Spike receptor binding domain-specific memory B cells (MBC) increased from 3 months after infection, the other Spike- and Nucleocapsid-specific B cells remained constant. All patients showed ongoing class switching and sustained affinity maturation of antigen-specific cells, and affinity maturation was not significantly increased early after vaccine. B cell analysis revealed a polyclonal response with limited clonal expansion; nevertheless, some clones detected during hospitalization, as plasmablasts, persisted for up to 1 year, as MBC. Monoclonal antibodies derived from persistent B cell families increased their binding and neutralization breadth and started recognizing viral variants by 3 months after infection. Overall, our findings provide important insights into the clonal evolution and dynamics of antigen-specific B cell responses in longitudinally sampled patients infected with COVID-19.", "doi": "10.1172/jci.insight.165299", "pmid": "36445762", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9870078"}, {"db": "pii", "key": "165299"}], "notes": [], "created": "2023-11-29T11:33:16.662Z", "modified": "2023-11-29T11:33:16.666Z"}, {"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": "21d7e28b1789437a85310459cdaa7f7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21d7e28b1789437a85310459cdaa7f7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21d7e28b1789437a85310459cdaa7f7e"}}, "title": "Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas.", "authors": [{"family": "Weishaupt", "given": "Holger", "initials": "H"}, {"family": "\u010can\u010der", "given": "Matko", "initials": "M"}, {"family": "Ros\u00e9n", "given": "Gabriela", "initials": "G"}, {"family": "Holmberg", "given": "Karl O", "initials": "KO"}, {"family": "H\u00e4ggqvist", "given": "Susana", "initials": "S"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Jiang", "given": "Yiwen", "initials": "Y"}, {"family": "Sreedharan", "given": "Smitha", "initials": "S"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Becher", "given": "Oren J", "initials": "OJ"}, {"family": "Uhrbom", "given": "Lene", "initials": "L"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Swartling", "given": "Fredrik J", "initials": "FJ", "orcid": "0000-0002-8460-4367", "researcher": {"href": "https://publications.scilifelab.se/researcher/69679cebbc90496f9c5b32f56d966654.json"}}], "type": "journal article", "published": "2023-01-05", "journal": {"title": "Neuro-oncology", "issn": "1523-5866", "volume": "25", "issue": "1", "pages": "97-107", "issn-l": "1522-8517"}, "abstract": "Malignant gliomas, the most common malignant brain tumors in adults, represent a heterogeneous group of diseases with poor prognosis. Retroviruses can cause permanent genetic alterations that modify genes close to the viral integration site.\n\nHere we describe the use of a high-throughput pipeline coupled to the commonly used tissue-specific retroviral RCAS-TVA mouse tumor model system. Utilizing next-generation sequencing, we show that retroviral integration sites can be reproducibly detected in malignant stem cell lines generated from RCAS-PDGFB-driven glioma biopsies.\n\nA large fraction of common integration sites contained genes that have been dysregulated or misexpressed in glioma. Others overlapped with loci identified in previous glioma-related forward genetic screens, but several novel putative cancer-causing genes were also found. Integrating retroviral tagging and clinical data, Ppfibp1 was highlighted as a frequently tagged novel glioma-causing gene. Retroviral integrations into the locus resulted in Ppfibp1 upregulation, and Ppfibp1-tagged cells generated tumors with shorter latency on orthotopic transplantation. In human gliomas, increased PPFIBP1 expression was significantly linked to poor prognosis and PDGF treatment resistance.\n\nAltogether, the current study has demonstrated a novel approach to tagging glioma genes via forward genetics, validating previous results, and identifying PPFIBP1 as a putative oncogene in gliomagenesis.", "doi": "10.1093/neuonc/noac158", "pmid": "35738865", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Short read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9825320"}, {"db": "pii", "key": "6615415"}], "notes": [], "created": "2022-11-21T10:37:55.157Z", "modified": "2024-01-16T13:48:34.197Z"}, {"entity": "publication", "iuid": "18d1940c083c4e4780bea26c0c4df967", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967"}}, "title": "Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Stojkovi\u0107", "given": "Biljana", "initials": "B"}, {"family": "Savkovi\u0107", "given": "Uro\u0161", "initials": "U"}, {"family": "\u0110or\u0111evi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Liljestrand-R\u00f6nn", "given": "Johanna", "initials": "J"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "1", "pages": null}, "abstract": "The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.", "doi": "10.1093/gbe/evac177", "pmid": "36542472", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9830990"}, {"db": "pii", "key": "6948356"}], "notes": [], "created": "2023-12-01T12:26:26.019Z", "modified": "2024-07-01T06:04:47.982Z"}, {"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": "570bc081259441e1810c050f69061aa3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/570bc081259441e1810c050f69061aa3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/570bc081259441e1810c050f69061aa3"}}, "title": "The path to immortalization of cells starts by managing stress through gene duplications.", "authors": [{"family": "Lewerentz", "given": "Jacob", "initials": "J"}, {"family": "Johansson", "given": "Anna-Mia", "initials": "AM"}, {"family": "Stenberg", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2023-01-01", "journal": {"title": "Exp. Cell Res.", "issn": "1090-2422", "volume": "422", "issue": "1", "pages": "113431", "issn-l": "0014-4827"}, "abstract": "The genomes of immortalized cell lines (and cancer cells) are characterized by multiple types of aberrations, ranging from single nucleotide polymorphisms (SNPs) to structural rearrangements that have accumulated over time. Consequently, it is difficult to estimate the relative impact of different aberrations, the order of events, and which gene functions were under selective pressure at the early stage towards cellular immortalization. Here, we have established novel cell cultures derived from Drosophila melanogaster embryos that were sampled at multiple time points over a one-year period. Using short-read DNA sequencing, we show that copy-number gain in preferentially stress-related genes were acquired in a dominant fraction of cells in 300-days old cultures. Furthermore, transposable elements were active in cells of all cultures. Only a few (<1%) SNPs could be followed over time, and these showed no trend to increase or decrease. We conclude that the early cellular responses of a novel culture comprise sequence duplication and transposable element activity. During immortalization, positive selection first occurs on genes that are related to stress response before shifting to genes that are related to growth.", "doi": "10.1016/j.yexcr.2022.113431", "pmid": "36423660", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0014-4827(22)00424-4"}], "notes": [], "created": "2022-11-29T09:11:25.498Z", "modified": "2024-01-16T13:48:34.230Z"}, {"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": "7d5d646edfce4e7ca163863ea1e99260", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d5d646edfce4e7ca163863ea1e99260.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d5d646edfce4e7ca163863ea1e99260"}}, "title": "Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.", "authors": [{"family": "Cholleti", "given": "Harindranath", "initials": "H"}, {"family": "de Jong", "given": "Johnny", "initials": "J"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M", "orcid": "0000-0001-5779-3345", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf3060c6eae54268b8e5dee8cf0b7a19.json"}}], "type": "journal article", "published": "2022-12-21", "journal": {"title": "Pathogens", "issn": "2076-0817", "volume": "12", "issue": "1", "issn-l": null}, "abstract": "Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95-99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans.", "doi": "10.3390/pathogens12010012", "pmid": "36678360", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "pathogens12010012"}], "notes": [], "created": "2023-01-23T07:18:22.877Z", "modified": "2023-01-23T07:18:22.969Z"}, {"entity": "publication", "iuid": "1176beb197da4692837d803afde65d55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1176beb197da4692837d803afde65d55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1176beb197da4692837d803afde65d55"}}, "title": "Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells.", "authors": [{"family": "Najafi", "given": "Mojtaba", "initials": "M", "orcid": "0000-0002-5463-8873", "researcher": {"href": "https://publications.scilifelab.se/researcher/3411ca5b1bb944e88880f0a3d99c547f.json"}}, {"family": "Guo", "given": "Yongzhi", "initials": "Y"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Humblot", "given": "Patrice", "initials": "P"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E", "orcid": "0000-0002-1947-8288", "researcher": {"href": "https://publications.scilifelab.se/researcher/6970ca57259d498588ecf9e1ad28a9b0.json"}}], "type": "journal article", "published": "2022-12-12", "journal": {"title": "Genes", "issn": "2073-4425", "volume": "13", "issue": "12", "issn-l": "2073-4425"}, "abstract": "Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in the pathogenic processes leading to mastitis and metritis in animals such as dairy cattle. LPS causes cell proliferation associated with endometrium inflammation. Former in vitro studies have demonstrated that LPS induces an intense stimulation of the proliferation of a pure population of bovine endometrial epithelial cells. In a follow-up transcriptomic study based on RNA-sequencing data obtained after 24 h exposure of primary bovine endometrial epithelial cells to 0, 2, and 8 \u03bcg/mL LPS, 752 and 727 differentially expressed genes (DEGs) were detected between the controls and LPS-treated samples that encode proteins known to be associated with either proliferation or apoptosis, respectively. The present bioinformatic analysis was performed to decipher the gene networks involved to obtain a deeper understanding of the mechanisms underlying the proliferative and apoptosis processes. Our findings have revealed 116 putative transcription factors (TFs) and the most significant number of interactions between these TFs and DEGs belong to NFK\u03b21, TP53, STAT1, and HIF1A. Moreover, our results provide novel insights into the early signaling and metabolic pathways in bovine endometrial epithelial cells associated with the innate immune response and cell proliferation to Escherichia coli-LPS infection. The results further indicated that LPS challenge elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that are associated with a marked endometrial cancer, Toll-like receptor, NFK\u03b2, AKT, apoptosis, and MAPK signaling pathways. This effect may provide a mechanistic explanation for the relationship between LPS and cell proliferation.", "doi": "10.3390/genes13122342", "pmid": "36553609", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9778113"}, {"db": "pii", "key": "genes13122342"}], "notes": [], "created": "2022-12-27T07:30:58.773Z", "modified": "2022-12-27T07:30:58.916Z"}, {"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": "9004dc1628114cde8ae8db0a3a963600", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9004dc1628114cde8ae8db0a3a963600.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9004dc1628114cde8ae8db0a3a963600"}}, "title": "Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway.", "authors": [{"family": "Akhter", "given": "Shirin", "initials": "S", "orcid": "0000-0003-4238-3110", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbaba07c47b04b56bd303e120dd944b4.json"}}, {"family": "Westrin", "given": "Karl Johan", "initials": "KJ", "orcid": "0000-0002-6937-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/033a4b9be9db4317b11a1d31e5c9986b.json"}}, {"family": "Zivi", "given": "Nathan", "initials": "N"}, {"family": "Nordal", "given": "Veronika", "initials": "V"}, {"family": "Kretzschmar", "given": "Warren W", "initials": "WW", "orcid": "0000-0002-2575-0807", "researcher": {"href": "https://publications.scilifelab.se/researcher/a67389ef276a47cfacec7cbe50da37a7.json"}}, {"family": "Delhomme", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-3053-0796", "researcher": {"href": "https://publications.scilifelab.se/researcher/107fbbd40f1444fb838ad4c0365738fa.json"}}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.json"}}, {"family": "Nilsson", "given": "Ove", "initials": "O", "orcid": "0000-0002-1033-1909", "researcher": {"href": "https://publications.scilifelab.se/researcher/729146afe5e24eb0a6f107db10e95e01.json"}}, {"family": "Emanuelsson", "given": "Olof", "initials": "O", "orcid": "0000-0002-8879-9245", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e9c21102e97491bb88a25db8ae1b8d8.json"}}, {"family": "Sundstr\u00f6m", "given": "Jens F", "initials": "JF", "orcid": "0000-0003-2848-5284", "researcher": {"href": "https://publications.scilifelab.se/researcher/be85f558ad8a4f57b3b366812f1b5faa.json"}}], "type": "journal article", "published": "2022-12-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "236", "issue": "5", "pages": "1951-1963"}, "abstract": "Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots. We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees. A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation. In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.", "doi": "10.1111/nph.18449", "pmid": "36076311", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9825996"}, {"db": "RefSeq", "key": "AF064080"}], "notes": [], "created": "2022-11-09T15:42:14.878Z", "modified": "2024-01-16T13:48:34.395Z"}, {"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": "af709cc9882b4b46851b735254ff5af0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af709cc9882b4b46851b735254ff5af0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af709cc9882b4b46851b735254ff5af0"}}, "title": "Stage-specific transposon activity in the life cycle of the fairy-ring mushroom <i>Marasmius oreades<\/i>.", "authors": [{"family": "Hiltunen", "given": "Markus", "initials": "M", "orcid": "0000-0002-8880-872X", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b54361528b4c7c8f5122d91d58b36d.json"}}, {"family": "Ament-Vel\u00e1squez", "given": "Sandra Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Ryberg", "given": "Martin", "initials": "M", "orcid": "0000-0002-6795-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0a8578a1ace4105be91ec8116c84365.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-11-16", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "119", "issue": "46", "pages": "e2208575119"}, "abstract": "Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a <i>Marasmius oreades<\/i> fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.", "doi": "10.1073/pnas.2208575119", "pmid": "36343254", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9674265"}], "notes": [], "created": "2022-11-21T09:59:53.450Z", "modified": "2024-01-16T13:48:34.455Z"}, {"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": "c6cb0a80038d48c69c3e38c25d0ed018", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6cb0a80038d48c69c3e38c25d0ed018"}}, "title": "Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.", "authors": [{"family": "Sahraei", "given": "Shadi Eshghi", "initials": "SE", "orcid": "0000-0003-4741-5871", "researcher": {"href": "https://publications.scilifelab.se/researcher/98f7d11029704e33b61a8c27daa54378.json"}}, {"family": "S\u00e1nchez-Garc\u00eda", "given": "Marisol", "initials": "M", "orcid": "0000-0002-0635-6281", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ccb3584fa144e178750ff2fc4666cfe.json"}}, {"family": "Montoliu-Nerin", "given": "Merce", "initials": "M", "orcid": "0000-0002-5200-0411", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f89e94a04c6429db7e706b4d8d6626a.json"}}, {"family": "Manyara", "given": "David", "initials": "D", "orcid": "0000-0002-8370-2651", "researcher": {"href": "https://publications.scilifelab.se/researcher/2132548af20445b2b0561fa38b8f8b89.json"}}, {"family": "Bergin", "given": "Claudia", "initials": "C", "orcid": "0000-0001-7960-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdd58ab07d964bcfb865ce67f7826816.json"}}, {"family": "Rosendahl", "given": "S\u00f8ren", "initials": "S", "orcid": "0000-0001-5202-6585", "researcher": {"href": "https://publications.scilifelab.se/researcher/111116b3b09343f783385c30207fd9b3.json"}}, {"family": "Rosling", "given": "Anna", "initials": "A", "orcid": "0000-0002-7003-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4c4bbb9e6c343808e8fa9345b7c05b2.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Mycorrhiza", "issn": "1432-1890", "issn-l": "0940-6360", "volume": "32", "issue": "5-6", "pages": "361-371"}, "abstract": "Arbuscular mycorrhizal (AM) fungi are ubiquitous mutualistic symbionts of most terrestrial plants and many complete their lifecycles underground. Whole genome analysis of AM fungi has long been restricted to species and strains that can be maintained under controlled conditions that facilitate collection of biological samples. There is some evidence suggesting that AM fungi can adapt to culture resulting in phenotypic and possibly also genotypic changes in the fungi. In this study, we used field isolated spores of AM fungi and identified them as Funneliformis geosporum based on morphology and phylogenetic analyses. We separately assembled the genomes of two representative spores using DNA sequences of 19 and 22 individually amplified nuclei. The genomes were compared with previously published data from other members of Glomeraceae including two strains of F. mosseae. No significant differences were observed among the species in terms of gene content, while the single nucleotide polymorphism density was higher in the strains of F. geosporum than in the strains of F. mosseae. In this study, we demonstrate that it is possible to sequence and assemble genomes from AM fungal spores sampled in the field, which opens up the possibility to include uncultured AM fungi in phylogenomic and comparative genomic analysis and to study genomic variation in natural populations of these important plant symbionts.", "doi": "10.1007/s00572-022-01091-4", "pmid": "36161535", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Microbial Single Cell Genomics": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9560946"}, {"db": "pii", "key": "10.1007/s00572-022-01091-4"}], "notes": [], "created": "2022-11-29T12:15:19.004Z", "modified": "2024-01-16T13:48:34.535Z"}, {"entity": "publication", "iuid": "799166a7e02e4d8baee46b54d0b639e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/799166a7e02e4d8baee46b54d0b639e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/799166a7e02e4d8baee46b54d0b639e9"}}, "title": "Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sj\u00f6gren's Syndrome.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Wu", "given": "Yee Ling", "initials": "YL"}, {"family": "Lundstr\u00f6m", "given": "Emeli", "initials": "E"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Bucher", "given": "Sara", "initials": "S"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Auglaend Johnsen", "given": "Svein Joar", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT consortium, the ImmunoArray consortium", "given": "", "initials": ""}, {"family": "Yu", "given": "Chack-Yung", "initials": "CY"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "issn-l": "2326-5191", "volume": "74", "issue": "11", "pages": "1842-1850"}, "abstract": "Complete genetic deficiency of the complement component C2 is a strong risk factor for monogenic systemic lupus erythematosus (SLE), but whether heterozygous C2 deficiency adds to the risk of SLE or primary Sj\u00f6gren's syndrome (SS) has not been studied systematically. This study was undertaken to investigate potential associations of heterozygous C2 deficiency and C4 copy number variation with clinical manifestations in patients with SLE and patients with primary SS.\n\nThe presence of the common 28-bp C2 deletion rs9332736 and C4 copy number variation was examined in Scandinavian patients who had received a diagnosis of SLE (n = 958) or primary SS (n = 911) and in 2,262 healthy controls through the use of DNA sequencing. The concentration of complement proteins in plasma and classical complement function were analyzed in a subgroup of SLE patients.\n\nHeterozygous C2 deficiency-when present in combination with a low C4A copy number-substantially increased the risk of SLE (odds ratio [OR] 10.2 [95% confidence interval (95% CI) 3.5-37.0]) and the risk of primary SS (OR 13.0 [95% CI 4.5-48.4]) when compared to individuals with 2 C4A copies and normal C2. For patients heterozygous for rs9332736 with 1 C4A copy, the median age at diagnosis was 7 years earlier in patients with SLE and 12 years earlier in patients with primary SS when compared to patients with normal C2. Reduced C2 levels in plasma (P = 2 \u00d7 10-9 ) and impaired function of the classical complement pathway (P = 0.03) were detected in SLE patients with heterozygous C2 deficiency. Finally, in a primary SS patient homozygous for C2 deficiency, we observed low levels of anti-Scl-70, which suggests a risk of developing systemic sclerosis or potential overlap between primary SS and other systemic autoimmune diseases.\n\nWe demonstrate that a genetic pattern involving partial deficiencies of C2 and C4A in the classical complement pathway is a strong risk factor for SLE and for primary SS. Our results emphasize the central role of the complement system in the pathogenesis of both SLE and primary SS.", "doi": "10.1002/art.42270", "pmid": "35729719", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9828039"}], "notes": [], "created": "2022-11-02T11:56:01.128Z", "modified": "2024-01-16T13:48:34.645Z"}, {"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": "12159c4661c1445a9deed2ed84fce70f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12159c4661c1445a9deed2ed84fce70f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12159c4661c1445a9deed2ed84fce70f"}}, "title": "Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.", "authors": [{"family": "Yavuz", "given": "Sule", "initials": "S"}, {"family": "Pucholt", "given": "Pascal", "initials": "P", "orcid": "0000-0003-3342-1373", "researcher": {"href": "https://publications.scilifelab.se/researcher/61a214ff2d494b568cb6da944e858acf.json"}}, {"family": "Sandling", "given": "Johanna K", "initials": "JK", "orcid": "0000-0003-1382-2321", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c7bae5a05ac47eeac96547ca7336767.json"}}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Leonard", "given": "Dag", "initials": "D", "orcid": "0000-0002-6275-7282", "researcher": {"href": "https://publications.scilifelab.se/researcher/42ed25c2f495484db4757f4fef51abae.json"}}, {"family": "Bolin", "given": "Karin", "initials": "K"}, {"family": "Imgenberg-Kreuz", "given": "Juliana", "initials": "J"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV", "orcid": "0000-0001-6209-4100", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6be89ad73a14d66a3b9439efc9c4099.json"}}, {"family": "Lanata", "given": "Cristina M", "initials": "CM"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C", "orcid": "0000-0003-0900-2048", "researcher": {"href": "https://publications.scilifelab.se/researcher/fe4dd47b8ca1436e8a26fdea33f5e7f6.json"}}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E", "orcid": "0000-0003-3396-3244", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ab5989c3c604a96bf42b1b6f90434a0.json"}}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "Nititham", "given": "Joanne", "initials": "J"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L", "orcid": "0000-0001-9403-6503", "researcher": {"href": "https://publications.scilifelab.se/researcher/053ed3b657124a1bab3a78dc685556e6.json"}}], "type": "meta-analysis", "published": "2022-11-00", "journal": {"title": "Lupus Sci Med", "issn": "2053-8790", "volume": "9", "issue": "1", "issn-l": "2053-8790"}, "abstract": "Lupus nephritis (LN) is a common and severe manifestation of SLE. The genetic risk for nephritis and progression to end-stage renal disease (ESRD) in patients with LN remains unclear. Herein, we aimed to identify novel genetic associations with LN, focusing on subphenotypes and ESRD.\n\nWe analysed genomic data on 958 patients with SLE (discovery cohort: LN=338) with targeted sequencing data from 1832 immunological pathway genes. We used an independent multiethnic cohort comprising 1226 patients with SLE (LN=603) as a replication dataset. Detailed functional annotation and functional epigenomic enrichment analyses were applied to predict functional effects of the candidate variants.\n\nA genetic variant (rs56097910) within the MERTK gene was associated with ESRD in both cohorts, meta-analysis OR=5.4 (2.8 to 10.6); p=1.0\u00d710-6. We observed decreased methylation levels in peripheral blood cells from SLE patients with ESRD, compared with patients without renal SLE (p=2.7\u00d710-4), at one CpG site (cg16333401) in close vicinity to the transcription start site of MERTK and located in a DNAse hypersensitivity region in T and B cells. Rs56097910 is linked to altered MERTK expression in kidney tissue in public eQTL databases. Two loci were replicated for association with proliferative LN: PRDM1 (rs6924535, pmeta=1.6\u00d710-5, OR=0.58) and APOA1BP (NAXE) (rs942960, pmeta=1.2\u00d710-5, OR=2.64).\n\nWe identified a novel genetic risk locus, MERTK, associated with SLE-ESRD using the data from two large SLE cohorts. Through DNA methylation analysis and functional annotation, we showed that the risk could be mediated through regulation of gene expression. Our results suggest that variants in the MERTK gene are important for the risk of developing SLE-ESRD and suggest a role for PRDM1 and APOA1BP in proliferative LN.", "doi": "10.1136/lupus-2022-000752", "pmid": "36332927", "labels": {"NGI Short read": "Service", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9639142"}, {"db": "pii", "key": "9/1/e000752"}], "notes": [], "created": "2022-11-29T12:21:01.345Z", "modified": "2024-01-16T13:48:34.678Z"}, {"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": "d9be4ec5baae47499d9976f9b113a4d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9be4ec5baae47499d9976f9b113a4d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9be4ec5baae47499d9976f9b113a4d0"}}, "title": "Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.", "authors": [{"family": "Butler-Laporte", "given": "Guillaume", "initials": "G", "orcid": "0000-0001-5388-0396", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c165ac40c3c409b93acbb13ac63579a.json"}}, {"family": "Povysil", "given": "Gundula", "initials": "G", "orcid": "0000-0003-4625-5909", "researcher": {"href": "https://publications.scilifelab.se/researcher/78129fef5aad4ba8ad154d9a4908974f.json"}}, {"family": "Kosmicki", "given": "Jack A", "initials": "JA", "orcid": "0000-0003-1252-6192", "researcher": {"href": "https://publications.scilifelab.se/researcher/21b8896b49bd48a6b9b21b84a76cda41.json"}}, {"family": "Cirulli", "given": "Elizabeth T", "initials": "ET", "orcid": "0000-0001-7808-2809", "researcher": {"href": "https://publications.scilifelab.se/researcher/566755e2fb34412c93b01245e512f9fd.json"}}, {"family": "Drivas", "given": "Theodore", "initials": "T", "orcid": "0000-0002-8717-0111", "researcher": {"href": "https://publications.scilifelab.se/researcher/0adcb730c0f644ceb712e774801cb74a.json"}}, {"family": "Furini", "given": "Simone", "initials": "S"}, {"family": "Saad", "given": "Chadi", "initials": "C", "orcid": "0000-0001-6963-9126", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac0b588b98a7496aa8a422ce08dd89c9.json"}}, {"family": "Schmidt", "given": "Axel", "initials": "A", "orcid": "0000-0002-1185-3012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3708b225fbae4c239bdc3bea34beff17.json"}}, {"family": "Olszewski", "given": "Pawel", "initials": "P", "orcid": "0000-0003-1010-8843", "researcher": {"href": "https://publications.scilifelab.se/researcher/175cf3dd63e54f7c919ed3b1de3d4b11.json"}}, {"family": "Korotko", "given": "Urszula", "initials": "U", "orcid": "0000-0002-1779-8368", "researcher": {"href": "https://publications.scilifelab.se/researcher/9960078bdffa4561a9111e37390c44eb.json"}}, {"family": "Quinodoz", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-9841-4433", "researcher": {"href": "https://publications.scilifelab.se/researcher/140e63b09c3340a0ae6aeb8124ea15b1.json"}}, {"family": "\u00c7elik", "given": "Elifnaz", "initials": "E", "orcid": "0000-0002-0324-5228", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a15c971dbe44bda2ee9381196c6f23.json"}}, {"family": "Kundu", "given": "Kousik", "initials": "K", "orcid": "0000-0002-1019-8351", "researcher": {"href": "https://publications.scilifelab.se/researcher/55dbffb9b2234f8db2b17025bd053aa7.json"}}, {"family": "Walter", "given": "Klaudia", "initials": "K", "orcid": "0000-0003-4448-0301", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd5029beabb34e18869a535f9578bbd6.json"}}, {"family": "Jung", "given": "Junghyun", "initials": "J"}, {"family": "Stockwell", "given": "Amy D", "initials": "AD"}, {"family": "Sloofman", "given": "Laura G", "initials": "LG", "orcid": "0000-0001-7628-4378", "researcher": {"href": "https://publications.scilifelab.se/researcher/03b834030a6e4aef8e9340a0a8bab91d.json"}}, {"family": "Jordan", "given": "Daniel M", "initials": "DM", "orcid": "0000-0002-5318-8225", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5123b5265ee4ba5ab7e23ffaa9177ca.json"}}, {"family": "Thompson", "given": "Ryan C", "initials": "RC", "orcid": "0000-0002-0450-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/18e5041ace5249e9b5eda7ffd7e8fdbb.json"}}, {"family": "Del Valle", "given": "Diane", "initials": "D", "orcid": "0000-0001-6983-5362", "researcher": {"href": "https://publications.scilifelab.se/researcher/e63491ffb2b34e40b038c46206561813.json"}}, {"family": "Simons", "given": "Nicole", "initials": "N", "orcid": "0000-0002-3952-1458", "researcher": {"href": "https://publications.scilifelab.se/researcher/989038ff4ca94453a1c53435a13b0936.json"}}, {"family": "Cheng", "given": "Esther", "initials": "E"}, {"family": "Sebra", "given": "Robert", "initials": "R"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Kim-Schulze", "given": "Seunghee", "initials": "S"}, {"family": "Gnjatic", "given": "Sacha", "initials": "S"}, {"family": "Merad", "given": "Miriam", "initials": "M"}, {"family": "Buxbaum", "given": "Joseph D", "initials": "JD"}, {"family": "Beckmann", "given": "Noam D", "initials": "ND"}, {"family": "Charney", "given": "Alexander W", "initials": "AW"}, {"family": "Przychodzen", "given": "Bartlomiej", "initials": "B"}, {"family": "Chang", "given": "Timothy", "initials": "T", "orcid": "0000-0002-9225-9874", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a8e6da514524249bf7f659e6ac0fd37.json"}}, {"family": "Pottinger", "given": "Tess D", "initials": "TD"}, {"family": "Shang", "given": "Ning", "initials": "N"}, {"family": "Brand", "given": "Fabian", "initials": "F", "orcid": "0000-0003-1885-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/deeffbb73a484059b233f655a7ec9b2a.json"}}, {"family": "Fava", "given": "Francesca", "initials": "F"}, {"family": "Mari", "given": "Francesca", "initials": "F"}, {"family": "Chwialkowska", "given": "Karolina", "initials": "K", "orcid": "0000-0001-8053-8959", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f2e48406c854c07b36fdfd389669dca.json"}}, {"family": "Niemira", "given": "Magdalena", "initials": "M", "orcid": "0000-0002-0701-4961", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a5a941aefa1415da58a2e2c06a61475.json"}}, {"family": "Pula", "given": "Szymon", "initials": "S", "orcid": "0000-0002-5684-5358", "researcher": {"href": "https://publications.scilifelab.se/researcher/bee449a4cb304996919dc8bc4ef3cef3.json"}}, {"family": "Baillie", "given": "J Kenneth", "initials": "JK"}, {"family": "Stuckey", "given": "Alex", "initials": "A", "orcid": "0000-0001-8636-737X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e613c25c28c44551a51c6f5029ce429f.json"}}, {"family": "Salas", "given": "Antonio", "initials": "A"}, {"family": "Bello", "given": "Xabier", "initials": "X", "orcid": "0000-0002-4990-8496", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f6c5c66e6dc4bd9b17ea8f99dcdb1c3.json"}}, {"family": "Pardo-Seco", "given": "Jacobo", "initials": "J"}, {"family": "G\u00f3mez-Carballa", "given": "Alberto", "initials": "A"}, {"family": "Rivero-Calle", "given": "Irene", "initials": "I"}, {"family": "Martin\u00f3n-Torres", "given": "Federico", "initials": "F"}, {"family": "Ganna", "given": "Andrea", "initials": "A"}, {"family": "Karczewski", "given": "Konrad J", "initials": "KJ", "orcid": "0000-0003-2878-4671", "researcher": {"href": "https://publications.scilifelab.se/researcher/096bfb156b54478e9a3f9c9d7730bc43.json"}}, {"family": "Veerapen", "given": "Kumar", "initials": "K"}, {"family": "Bourgey", "given": "Mathieu", "initials": "M", "orcid": "0000-0002-8432-834X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7db054c6632438284888857aa54ada4.json"}}, {"family": "Bourque", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-3933-9656", "researcher": {"href": "https://publications.scilifelab.se/researcher/d72fde1b19d2491387b5df6429bb238e.json"}}, {"family": "Eveleigh", "given": "Robert Jm", "initials": "RJ", "orcid": "0000-0002-4147-382X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4455277bbf4f47df96377ca92c2e2c5d.json"}}, {"family": "Forgetta", "given": "Vincenzo", "initials": "V"}, {"family": "Morrison", "given": "David", "initials": "D", "orcid": "0000-0001-8380-3615", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cf4ef09fddb4438af55861445d796ef.json"}}, {"family": "Langlais", "given": "David", "initials": "D", "orcid": "0000-0003-4429-0110", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bc9421a0159458990b6bc1189cbb7fc.json"}}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Mooser", "given": "Vincent", "initials": "V", "orcid": "0000-0002-8632-0448", "researcher": {"href": "https://publications.scilifelab.se/researcher/97298e39568c461d9e174ff74c42e3f8.json"}}, {"family": "Nakanishi", "given": "Tomoko", "initials": "T", "orcid": "0000-0001-9510-5646", "researcher": {"href": "https://publications.scilifelab.se/researcher/156825097e204173b62131f9312b98b1.json"}}, {"family": "Frithiof", "given": "Robert", "initials": "R", "orcid": "0000-0003-2278-7951", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fec11dd18f941b7842610ad14237a35.json"}}, {"family": "Hultstr\u00f6m", "given": "Michael", "initials": "M", "orcid": "0000-0003-4675-1099", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a74d3380a24c31930e6e671e685b5b.json"}}, {"family": "Lipcsey", "given": "Miklos", "initials": "M", "orcid": "0000-0002-1976-4129", "researcher": {"href": "https://publications.scilifelab.se/researcher/81805f2324634628abefcf0ab6ce6a15.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Schiabor Barrett", "given": "Kelly M", "initials": "KM", "orcid": "0000-0001-6194-787X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e91dff1c84cb4accb893cbd711df3eb7.json"}}, {"family": "Lee", "given": "William", "initials": "W"}, {"family": "Bolze", "given": "Alexandre", "initials": "A", "orcid": "0000-0001-7399-2766", "researcher": {"href": "https://publications.scilifelab.se/researcher/99d7674f36d44b05b224d486d987521d.json"}}, {"family": "White", "given": "Simon", "initials": "S", "orcid": "0000-0001-6375-2363", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad52dae860c34ec9ab4ec9ebabffac7f.json"}}, {"family": "Riffle", "given": "Stephen", "initials": "S"}, {"family": "Tanudjaja", "given": "Francisco", "initials": "F"}, {"family": "Sandoval", "given": "Efren", "initials": "E"}, {"family": "Neveux", "given": "Iva", "initials": "I"}, {"family": "Dabe", "given": "Shaun", "initials": "S", "orcid": "0000-0002-2494-962X", "researcher": {"href": "https://publications.scilifelab.se/researcher/518051e39cdf4f20b202a8283421d0be.json"}}, {"family": "Casadei", "given": "Nicolas", "initials": "N", "orcid": "0000-0003-2209-0580", "researcher": {"href": "https://publications.scilifelab.se/researcher/7066abe2466d4b67b60bdffccd4a914c.json"}}, {"family": "Motameny", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1186-1108", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dacd0703dd34aa5b7a551cf32f609f3.json"}}, {"family": "Alaamery", "given": "Manal", "initials": "M"}, {"family": "Massadeh", "given": "Salam", "initials": "S", "orcid": "0000-0001-9193-0008", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffb8231147744c7481cc7ff3319fe497.json"}}, {"family": "Aljawini", "given": "Nora", "initials": "N"}, {"family": "Almutairi", "given": "Mansour S", "initials": "MS", "orcid": "0000-0003-2736-8991", "researcher": {"href": "https://publications.scilifelab.se/researcher/11a342f69f504ab1963435a94aa4424d.json"}}, {"family": "Arabi", "given": "Yaseen M", "initials": "YM", "orcid": "0000-0001-5735-6241", "researcher": {"href": "https://publications.scilifelab.se/researcher/39c27b87cc404c409fbca1b4ebcbddbc.json"}}, {"family": "Alqahtani", "given": "Saleh A", "initials": "SA"}, {"family": "Al Harthi", "given": "Fawz S", "initials": "FS"}, {"family": "Almutairi", "given": "Amal", "initials": "A"}, {"family": "Alqubaishi", "given": "Fatima", "initials": "F"}, {"family": "Alotaibi", "given": "Sarah", "initials": "S"}, {"family": "Binowayn", "given": "Albandari", "initials": "A"}, {"family": "Alsolm", "given": "Ebtehal A", "initials": "EA"}, {"family": "El Bardisy", "given": "Hadeel", "initials": "H"}, {"family": "Fawzy", "given": "Mohammad", "initials": "M", "orcid": "0000-0002-1318-9979", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f846217437d41e8aac1e350d7998f43.json"}}, {"family": "Cai", "given": "Fang", "initials": "F"}, {"family": "Soranzo", "given": "Nicole", "initials": "N", "orcid": "0000-0003-1095-3852", "researcher": {"href": "https://publications.scilifelab.se/researcher/da75fa9ee333474fad5aadcb99a63d8f.json"}}, {"family": "Butterworth", "given": "Adam", "initials": "A", "orcid": "0000-0002-6915-9015", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b8c140c80d942c4b1b684876e4d6180.json"}}, {"family": "COVID-19 Host Genetics Initiative", "given": "", "initials": ""}, {"family": "DeCOI Host Genetics Group", "given": "", "initials": ""}, {"family": "GEN-COVID Multicenter Study (Italy)", "given": "", "initials": ""}, {"family": "Mount Sinai Clinical Intelligence Center", "given": "", "initials": ""}, {"family": "GEN-COVID consortium (Spain)", "given": "", "initials": ""}, {"family": "GenOMICC Consortium", "given": "", "initials": ""}, {"family": "Japan COVID-19 Task Force", "given": "", "initials": ""}, {"family": "Regeneron Genetics Center", "given": "", "initials": ""}, {"family": "Geschwind", "given": "Daniel H", "initials": "DH"}, {"family": "Arteaga", "given": "Stephanie", "initials": "S", "orcid": "0000-0003-1441-8849", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b30c76180604ca1b81e4f3302ff7855.json"}}, {"family": "Stephens", "given": "Alexis", "initials": "A", "orcid": "0000-0002-5979-6838", "researcher": {"href": "https://publications.scilifelab.se/researcher/f053685d3fa74bfa819c0ebbb01dffa9.json"}}, {"family": "Butte", "given": "Manish J", "initials": "MJ"}, {"family": "Boutros", "given": "Paul C", "initials": "PC", "orcid": "0000-0003-0553-7520", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f627e3789d04a28aa270a5873c5f20b.json"}}, {"family": "Yamaguchi", "given": "Takafumi N", "initials": "TN", "orcid": "0000-0003-1082-3871", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc3e261be1794dfaa31f3a6e0e41d540.json"}}, {"family": "Tao", "given": "Shu", "initials": "S"}, {"family": "Eng", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5245-6507", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ddac6b0b1e4461a901a6f27222b95e5.json"}}, {"family": "Sanders", "given": "Timothy", "initials": "T"}, {"family": "Tung", "given": "Paul J", "initials": "PJ"}, {"family": "Broudy", "given": "Michael E", "initials": "ME"}, {"family": "Pan", "given": "Yu", "initials": "Y"}, {"family": "Gonzalez", "given": "Alfredo", "initials": "A", "orcid": "0000-0001-8963-3135", "researcher": {"href": "https://publications.scilifelab.se/researcher/f209f43c89874c8c9b3341a8b79da228.json"}}, {"family": "Chavan", "given": "Nikhil", "initials": "N"}, {"family": "Johnson", "given": "Ruth", "initials": "R", "orcid": "0000-0002-1929-0998", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f7714638b0546ba8a136a62b574897e.json"}}, {"family": "Pasaniuc", "given": "Bogdan", "initials": "B"}, {"family": "Yaspan", "given": "Brian", "initials": "B", "orcid": "0000-0002-3787-2510", "researcher": {"href": "https://publications.scilifelab.se/researcher/76252bb214f14e52ae844caee42092a6.json"}}, {"family": "Smieszek", "given": "Sandra", "initials": "S", "orcid": "0000-0002-8006-0454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3100d3272fa24461a048fb46fa488084.json"}}, {"family": "Rivolta", "given": "Carlo", "initials": "C", "orcid": "0000-0002-0733-9950", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cc230d3976e4008baf923b2bab1bc5f.json"}}, {"family": "Bibert", "given": "Stephanie", "initials": "S"}, {"family": "Bochud", "given": "Pierre-Yves", "initials": "P", "orcid": "0000-0002-2208-4757", "researcher": {"href": "https://publications.scilifelab.se/researcher/1316aaa3c5614d609e6c0c546f0e93ac.json"}}, {"family": "Dabrowski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-4150-3985", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4e1e77543b8409a92bc6f8f7feea490.json"}}, {"family": "Zawadzki", "given": "Pawel", "initials": "P", "orcid": "0000-0002-9032-2315", "researcher": {"href": "https://publications.scilifelab.se/researcher/55cb087eae464aefbbdbb45c23990bdb.json"}}, {"family": "Sypniewski", "given": "Mateusz", "initials": "M"}, {"family": "Kaja", "given": "El\u017cbieta", "initials": "E", "orcid": "0000-0003-1277-6140", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a893b26b52c4dc9890d4ada5f367a21.json"}}, {"family": "Chariyavilaskul", "given": "Pajaree", "initials": "P", "orcid": "0000-0003-1096-6020", "researcher": {"href": "https://publications.scilifelab.se/researcher/11808086b4b84a26a0bae2810e211399.json"}}, {"family": "Nilaratanakul", "given": "Voraphoj", "initials": "V", "orcid": "0000-0002-3964-5477", "researcher": {"href": "https://publications.scilifelab.se/researcher/49b8364a94c745beab463019b9a858cd.json"}}, {"family": "Hirankarn", "given": "Nattiya", "initials": "N", "orcid": "0000-0003-2224-6856", "researcher": {"href": "https://publications.scilifelab.se/researcher/0822723b25ed40b79fa0f8a6c26f1521.json"}}, {"family": "Shotelersuk", "given": "Vorasuk", "initials": "V", "orcid": "0000-0002-1856-0589", "researcher": {"href": "https://publications.scilifelab.se/researcher/645f2ef9414e4301af16d3fd7841b4a2.json"}}, {"family": "Pongpanich", "given": "Monnat", "initials": "M", "orcid": "0000-0003-3228-3351", "researcher": {"href": "https://publications.scilifelab.se/researcher/aae2487b5a5d421e8ebf4754d7a087ee.json"}}, {"family": "Phokaew", "given": "Chureerat", "initials": "C", "orcid": "0000-0002-4246-2604", "researcher": {"href": "https://publications.scilifelab.se/researcher/c27dd172310b4528b805467bcbc57be6.json"}}, {"family": "Chetruengchai", "given": "Wanna", "initials": "W", "orcid": "0000-0003-2495-6595", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1c1c00ff51b4eb185b62e2164047eec.json"}}, {"family": "Tokunaga", "given": "Katsushi", "initials": "K"}, {"family": "Sugiyama", "given": "Masaya", "initials": "M", "orcid": "0000-0002-9084-7197", "researcher": {"href": "https://publications.scilifelab.se/researcher/abfef9525e4d4b75babb1aa1cc663cc7.json"}}, {"family": "Kawai", "given": "Yosuke", "initials": "Y", "orcid": "0000-0003-0666-1224", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4cbad2923364bd8b32dcc4dcf1adb02.json"}}, {"family": "Hasegawa", "given": "Takanori", "initials": "T", "orcid": "0000-0001-7251-9950", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8679797c28149da9f1ee5d271a193c2.json"}}, {"family": "Naito", "given": "Tatsuhiko", "initials": "T"}, {"family": "Namkoong", "given": "Ho", "initials": "H", "orcid": "0000-0001-6181-4284", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9341eed6713468fbe38b03557824405.json"}}, {"family": "Edahiro", "given": "Ryuya", "initials": "R"}, {"family": "Kimura", "given": "Akinori", "initials": "A"}, {"family": "Ogawa", "given": "Seishi", "initials": "S", "orcid": "0000-0002-7778-5374", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbcc3b1b5f3045a7acd123222445449d.json"}}, {"family": "Kanai", "given": "Takanori", "initials": "T"}, {"family": "Fukunaga", "given": "Koichi", "initials": "K"}, {"family": "Okada", "given": "Yukinori", "initials": "Y", "orcid": "0000-0002-0311-8472", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b13860bfef41959c29be2de853b456.json"}}, {"family": "Imoto", "given": "Seiya", "initials": "S"}, {"family": "Miyano", "given": "Satoru", "initials": "S", "orcid": "0000-0002-1753-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e65512044c4965863ed41ef8aadd31.json"}}, {"family": "Mangul", "given": "Serghei", "initials": "S", "orcid": "0000-0003-4770-3443", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35a4535909643b2a532d3622f57e10f.json"}}, {"family": "Abedalthagafi", "given": "Malak S", "initials": "MS", "orcid": "0000-0003-2088-3632", "researcher": {"href": "https://publications.scilifelab.se/researcher/8dbb9410a1394132a0979e7cde5d1635.json"}}, {"family": "Zeberg", "given": "Hugo", "initials": "H", "orcid": "0000-0001-7118-1249", "researcher": {"href": "https://publications.scilifelab.se/researcher/090e842ed8ff4cf2a3fe5f8e58118e58.json"}}, {"family": "Grzymski", "given": "Joseph J", "initials": "JJ", "orcid": "0000-0003-2646-8958", "researcher": {"href": "https://publications.scilifelab.se/researcher/d309c535c04f40b39068df41546df2ab.json"}}, {"family": "Washington", "given": "Nicole L", "initials": "NL"}, {"family": "Ossowski", "given": "Stephan", "initials": "S", "orcid": "0000-0002-7416-9568", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df302939f5c4456927afdff5bdfb2eb.json"}}, {"family": "Ludwig", "given": "Kerstin U", "initials": "KU", "orcid": "0000-0002-8541-2519", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9e2b9bc9d114c93a4a545e5d6477ae0.json"}}, {"family": "Schulte", "given": "Eva C", "initials": "EC", "orcid": "0000-0003-3105-5672", "researcher": {"href": "https://publications.scilifelab.se/researcher/2443ead1e9564eb5a991ce8dfa7e851f.json"}}, {"family": "Riess", "given": "Olaf", "initials": "O"}, {"family": "Moniuszko", "given": "Marcin", "initials": "M"}, {"family": "Kwasniewski", "given": "Miroslaw", "initials": "M"}, {"family": "Mbarek", "given": "Hamdi", "initials": "H", "orcid": "0000-0002-1108-0371", "researcher": {"href": "https://publications.scilifelab.se/researcher/a50439a056e94688a64751e2bdc7c502.json"}}, {"family": "Ismail", "given": "Said I", "initials": "SI"}, {"family": "Verma", "given": "Anurag", "initials": "A", "orcid": "0000-0002-5063-9107", "researcher": {"href": "https://publications.scilifelab.se/researcher/556096ea8651491caa5daf52e10f79da.json"}}, {"family": "Goldstein", "given": "David B", "initials": "DB", "orcid": "0000-0001-7627-0259", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e797709a3f9473c851d79ababa3e680.json"}}, {"family": "Kiryluk", "given": "Krzysztof", "initials": "K", "orcid": "0000-0002-5047-6715", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6e7b5668c0141728599d5ebb68c8929.json"}}, {"family": "Renieri", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-0846-9220", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dbf990f1e0c4fd99e45c945915f25b0.json"}}, {"family": "Ferreira", "given": "Manuel A R", "initials": "MAR", "orcid": "0000-0001-9059-1825", "researcher": {"href": "https://publications.scilifelab.se/researcher/d27aef5015494b018b22352125c0225d.json"}}, {"family": "Richards", "given": "J Brent", "initials": "JB", "orcid": "0000-0002-3746-9086", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2c20c901fd041c194dae79b29b94ec2.json"}}], "type": "journal article", "published": "2022-11-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "issn-l": "1553-7390", "volume": "18", "issue": "11", "pages": "e1010367"}, "abstract": "Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.", "doi": "10.1371/journal.pgen.1010367", "pmid": "36327219", "labels": {"NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9632827"}, {"db": "pii", "key": "PGENETICS-D-22-00434"}], "notes": [], "created": "2022-11-29T14:02:16.675Z", "modified": "2023-06-16T12:55:14.973Z"}, {"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": "87091aedf5f94a5c86600d25244ac164", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87091aedf5f94a5c86600d25244ac164.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87091aedf5f94a5c86600d25244ac164"}}, "title": "ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.", "authors": [{"family": "Schuster", "given": "Jens", "initials": "J"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Khalfallah", "given": "Ayda", "initials": "A"}, {"family": "Laan", "given": "Loora", "initials": "L"}, {"family": "Hoeber", "given": "Jan", "initials": "J"}, {"family": "Fatima", "given": "Ambrin", "initials": "A"}, {"family": "Sequeira", "given": "Velin Marita", "initials": "VM"}, {"family": "Jin", "given": "Zhe", "initials": "Z"}, {"family": "Korol", "given": "Sergiy V", "initials": "SV"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Anderlid", "given": "Britt Marie", "initials": "BM"}, {"family": "Gallant", "given": "Caroline", "initials": "C"}, {"family": "Birnir", "given": "Bryndis", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2022-10-24", "journal": {"title": "Front Mol Neurosci", "issn": "1662-5099", "volume": "15", "pages": "988993", "issn-l": null}, "abstract": "Mowat-Wilson syndrome (MWS) is a severe neurodevelopmental disorder caused by heterozygous variants in the gene encoding transcription factor ZEB2. Affected individuals present with structural brain abnormalities, speech delay and epilepsy. In mice, conditional loss of Zeb2 causes hippocampal degeneration, altered migration and differentiation of GABAergic interneurons, a heterogeneous population of mainly inhibitory neurons of importance for maintaining normal excitability. To get insights into GABAergic development and function in MWS we investigated ZEB2 haploinsufficient induced pluripotent stem cells (iPSC) of MWS subjects together with iPSC of healthy donors. Analysis of RNA-sequencing data at two time points of GABAergic development revealed an attenuated interneuronal identity in MWS subject derived iPSC with enrichment of differentially expressed genes required for transcriptional regulation, cell fate transition and forebrain patterning. The ZEB2 haploinsufficient neural stem cells (NSCs) showed downregulation of genes required for ventral telencephalon specification, such as FOXG1, accompanied by an impaired migratory capacity. Further differentiation into GABAergic interneuronal cells uncovered upregulation of transcription factors promoting pallial and excitatory neurons whereas cortical markers were downregulated. The differentially expressed genes formed a neural protein-protein network with extensive connections to well-established epilepsy genes. Analysis of electrophysiological properties in ZEB2 haploinsufficient GABAergic cells revealed overt perturbations manifested as impaired firing of repeated action potentials. Our iPSC model of ZEB2 haploinsufficient GABAergic development thus uncovers a dysregulated gene network leading to immature interneurons with mixed identity and altered electrophysiological properties, suggesting mechanisms contributing to the neuropathogenesis and seizures in MWS.", "doi": "10.3389/fnmol.2022.988993", "pmid": "36353360", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "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": "PMC9637781"}], "notes": [], "created": "2022-11-29T12:21:58.551Z", "modified": "2024-01-16T13:48:34.689Z"}, {"entity": "publication", "iuid": "cf165c58527e41439582a10d2cc5f063", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf165c58527e41439582a10d2cc5f063.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf165c58527e41439582a10d2cc5f063"}}, "title": "Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Berdan", "given": "Emma L", "initials": "EL"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Losvik", "given": "Aleksandra", "initials": "A"}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Hughes", "given": "P William", "initials": "PW"}, {"family": "Foroozani", "given": "Alireza", "initials": "A"}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Pesquet", "given": "Edouard", "initials": "E"}, {"family": "Abdelaziz", "given": "Mohamed", "initials": "M"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Brennan", "given": "Adrian C", "initials": "AC"}, {"family": "Arroyo", "given": "Juan", "initials": "J"}, {"family": "Slotte", "given": "Tanja", "initials": "T"}], "type": "journal article", "published": "2022-10-24", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "issn-l": "0960-9822", "volume": "32", "issue": "20", "pages": "4360-4371.e6"}, "abstract": "Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.", "doi": "10.1016/j.cub.2022.08.042", "pmid": "36087578", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(22)01364-1"}], "notes": [], "created": "2022-09-22T18:45:15.012Z", "modified": "2024-01-16T13:48:34.696Z"}, {"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": "52583936c1024a468226e9c12527aaaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/52583936c1024a468226e9c12527aaaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/52583936c1024a468226e9c12527aaaa"}}, "title": "Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.", "authors": [{"family": "Behra", "given": "Phani Rama Krishna", "initials": "PRK"}, {"family": "Pettersson", "given": "B M Fredrik", "initials": "BMF"}, {"family": "Ramesh", "given": "Malavika", "initials": "M"}, {"family": "Das", "given": "Sarbashis", "initials": "S"}, {"family": "Dasgupta", "given": "Santanu", "initials": "S"}, {"family": "Kirsebom", "given": "Leif A", "initials": "LA"}], "type": "journal article", "published": "2022-10-15", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "issn-l": "1471-2164", "volume": "23", "issue": "1", "pages": "704"}, "abstract": "The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines.\r\n\r\nWe provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria.\r\n\r\nPhages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.", "doi": "10.1186/s12864-022-08927-5", "pmid": "36243697", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-022-08927-5"}, {"db": "pmc", "key": "PMC9569102"}], "notes": [], "created": "2022-11-21T10:04:26.689Z", "modified": "2024-01-16T13:48:34.732Z"}, {"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": "c27764ed4c514f2592c156cc59d23608", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c27764ed4c514f2592c156cc59d23608"}}, "title": "Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J", "orcid": "0000-0002-0151-8931", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2cb6f3cce5f4919959e18074d51256d.json"}}, {"family": "Lillie", "given": "Mette", "initials": "M", "orcid": "0000-0001-8714-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce02b2116c0417e8a4dcd578f45983b.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Grant", "given": "B Rosemary", "initials": "BR"}, {"family": "Grant", "given": "Peter R", "initials": "PR"}, {"family": "Andersson", "given": "Leif", "initials": "L", "orcid": "0000-0002-4085-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd3343c12f994b1fabcae23027d3a76d.json"}}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}], "type": "journal article", "published": "2022-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "6033"}, "abstract": "Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.", "doi": "10.1038/s41467-022-33723-w", "pmid": "36229469", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-33723-w"}, {"db": "pmc", "key": "PMC9562234"}], "notes": [], "created": "2022-11-09T16:00:11.231Z", "modified": "2024-01-16T13:48:34.742Z"}, {"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": "02ca612014284b319f023360ee4fefe4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02ca612014284b319f023360ee4fefe4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02ca612014284b319f023360ee4fefe4"}}, "title": "Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.", "authors": [{"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Li", "given": "Xiaoxiao", "initials": "X"}, {"family": "Yekta", "given": "Sepehr Shakeri", "initials": "SS"}, {"family": "Bj\u00f6rn", "given": "Annika", "initials": "A"}, {"family": "Mu", "given": "Bo-Zhong", "initials": "BZ"}, {"family": "Masuda", "given": "Laura Shizue Moriga", "initials": "LSM"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}, {"family": "Enrich-Prast", "given": "Alex", "initials": "A"}], "type": "journal article", "published": "2022-10-04", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "12", "issue": "1", "pages": "16570", "issn-l": "2045-2322"}, "abstract": "Natural environments with frequent drainage experience drying and rewetting events that impose fluctuations in water availability and oxygen exposure. These relatively dramatic cycles profoundly impact microbial activity in the environment and subsequent emissions of methane and carbon dioxide. In this study, we mimicked drying and rewetting events by submitting methanogenic communities from strictly anaerobic environments (anaerobic digestors) with different phylogenetic structures to consecutive desiccation events under aerobic (air) and anaerobic (nitrogen) conditions followed by rewetting. We showed that methane production quickly recovered after each rewetting, and surprisingly, no significant difference was observed between the effects of the aerobic or anaerobic desiccation events. There was a slight change in the microbial community structure and a decrease in methane production rates after consecutive drying and rewetting, which can be attributed to a depletion of the pool of available organic matter or the inhibition of the methanogenic communities. These observations indicate that in comparison to the drying and rewetting events or oxygen exposure, the initial phylogenetic structure and the organic matter quantity and quality exhibited a stronger influence on the methanogenic communities and overall microbial community responses. These results change the current paradigm of the sensitivity of strict anaerobic microorganisms to oxygen exposure.", "doi": "10.1038/s41598-022-20448-5", "pmid": "36195651", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9532411"}, {"db": "pii", "key": "10.1038/s41598-022-20448-5"}], "notes": [], "created": "2022-11-29T09:55:59.009Z", "modified": "2022-11-29T09:55:59.014Z"}, {"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": "b5b41e59d80945f0b7a009d2dd268562", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562"}}, "title": "A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "10", "pages": "e9440", "issn-l": "2045-7758"}, "abstract": "Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome-wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate-dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean F ST = 0.23-0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's D NS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (d XY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome-wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.", "doi": "10.1002/ece3.9440", "pmid": "36311399", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9608792"}, {"db": "pii", "key": "ECE39440"}], "notes": [], "created": "2022-11-29T09:34:26.276Z", "modified": "2022-11-29T09:34:26.313Z"}, {"entity": "publication", "iuid": "13e8aeb7d3f94c85981ecd78c1ad217a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13e8aeb7d3f94c85981ecd78c1ad217a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13e8aeb7d3f94c85981ecd78c1ad217a"}}, "title": "Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells.", "authors": [{"family": "Tsirigoti", "given": "Chrysoula", "initials": "C"}, {"family": "Ali", "given": "Mohamad Moustafa", "initials": "MM", "orcid": "0000-0002-4902-0550", "researcher": {"href": "https://publications.scilifelab.se/researcher/780c944670ff4d7489410895569ac257.json"}}, {"family": "Maturi", "given": "Varun", "initials": "V", "orcid": "0000-0003-1177-0839", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd84539b66b4e79964ec0330f1aefd7.json"}}, {"family": "Heldin", "given": "Carl-Henrik", "initials": "CH", "orcid": "0000-0002-9508-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f705f7c509904a1db721ace2267ca48f.json"}}, {"family": "Moustakas", "given": "Aristidis", "initials": "A", "orcid": "0000-0001-9131-3827", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c1626d991f3485e81232db174537e6d.json"}}], "type": "journal article", "published": "2022-09-28", "journal": {"title": "Cell Death Dis", "issn": "2041-4889", "volume": "13", "issue": "9", "pages": "832", "issn-l": "2041-4889"}, "abstract": "The transcription factor SNAI1 mediates epithelial-mesenchymal transition, fibroblast activation and controls inter-tissue migration. High SNAI1 expression characterizes metastatic triple-negative breast carcinomas, and its knockout by CRISPR/Cas9 uncovered an epithelio-mesenchymal phenotype accompanied by reduced signaling by the cytokine TGF\u03b2. The SNAI1 knockout cells exhibited plasticity in differentiation, drifting towards the luminal phenotype, gained stemness potential and could differentiate into acinar mammospheres in 3D culture. Loss of SNAI1 de-repressed the transcription factor FOXA1, a pioneering factor of mammary luminal progenitors. FOXA1 induced a specific gene program, including the androgen receptor (AR). Inhibiting AR via a specific antagonist regenerated the basal phenotype and blocked acinar differentiation. Thus, loss of SNAI1 in the context of triple-negative breast carcinoma cells promotes an intermediary luminal progenitor phenotype that gains differentiation plasticity based on the dual transcriptional action of FOXA1 and AR. This function of SNAI1 provides means to separate cell invasiveness from progenitor cell de-differentiation as independent cellular programs.", "doi": "10.1038/s41419-022-05280-z", "pmid": "36171192", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9519755"}, {"db": "pii", "key": "10.1038/s41419-022-05280-z"}], "notes": [], "created": "2022-11-29T09:54:47.071Z", "modified": "2024-01-16T13:48:34.962Z"}, {"entity": "publication", "iuid": "af3c88c82b9847cf8eb6003405006660", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af3c88c82b9847cf8eb6003405006660.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af3c88c82b9847cf8eb6003405006660"}}, "title": "A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Ali Abed", "given": "Salwan", "initials": "S", "orcid": "0000-0001-7347-3843", "researcher": {"href": "https://publications.scilifelab.se/researcher/df39e4e79acb469aa3d842fbb764b888.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2022-09-26", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X"}, "abstract": "We report the discovery of a novel neo-sex chromosome in an African warbler, Sylvietta brachyura (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome-sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single species-representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae and Leiothrichidae). In all three species, we confirmed the translocation of a part of chromosome 4A to the sex chromosomes, which originated basally in Sylvioidea. In S. brachyura, we found that a part of chromosome 8 has been translocated to the sex chromosomes, forming a unique neo-sex chromosome in this lineage. Furthermore, the non-recombining part of 4A in S. brachyura is smaller than in other Sylvioidea species, which suggests that recombination continued along this region after the fusion event in the Sylvioidea ancestor. These findings reveal additional sex chromosome diversity among the Sylvioidea, where five separate translocation events are now confirmed.", "doi": "10.1111/jeb.14096", "pmid": "36156325", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "RefSeq", "key": "GCF_003957565.1"}], "notes": [], "created": "2022-11-29T09:53:49.879Z", "modified": "2024-01-16T13:48:34.983Z"}, {"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": "fee6a328f53e4013a6ce31dfa9144540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fee6a328f53e4013a6ce31dfa9144540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fee6a328f53e4013a6ce31dfa9144540"}}, "title": "Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.", "authors": [{"family": "Stenberg", "given": "Hedvig", "initials": "H"}, {"family": "Hellman", "given": "Stina", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Lisa", "initials": "L"}, {"family": "Jacobson", "given": "Magdalena", "initials": "M"}, {"family": "Fossum", "given": "Caroline", "initials": "C"}, {"family": "Hayer", "given": "Juliette", "initials": "J"}, {"family": "Malmberg", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2022-09-16", "journal": {"title": "BMC Vet Res", "issn": "1746-6148", "issn-l": null, "volume": "18", "issue": "1", "pages": "348"}, "abstract": "Atypical porcine pestivirus (APPV) is a neurotropic virus associated with congenital tremor type A-II. A few experimental studies also indicate an association between APPV and splay leg. The overarching aim of the present study was to provide insights into the virome, local cytokine response, and histology of the CNS in piglets with signs of congenital tremor or splay leg.\r\n\r\nCharacterization of the cytokine profile and virome of the brain in piglets with signs of congenital tremor revealed an APPV-associated upregulation of Stimulator of interferon genes (STING). The upregulation of STING was associated with an increased expression of the gene encoding IFN-\u03b1 but no differential expression was recorded for the genes encoding CXCL8, IFN-\u03b2, IFN-\u03b3, IL-1\u03b2, IL-6, or IL-10. No viral agents or cytokine upregulation could be detected in the spinal cord of piglets with signs of splay leg or in the brain of piglets without an APPV-infection. The histopathological examination showed no lesions in the CNS that could be attributed to the APPV-infection, as no difference between sick and healthy piglets could be seen.\r\n\r\nThe results from this study provide evidence of an APPV-induced antiviral cytokine response but found no lesions related to the infection nor any support for a common causative agent.", "doi": "10.1186/s12917-022-03443-w", "pmid": "36109741", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12917-022-03443-w"}, {"db": "pmc", "key": "PMC9479355"}], "notes": [], "created": "2022-09-23T08:16:31.989Z", "modified": "2024-01-16T13:48:35.004Z"}, {"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": "5da648ba2e464fc99db858358c6e79e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5da648ba2e464fc99db858358c6e79e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5da648ba2e464fc99db858358c6e79e7"}}, "title": "Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.", "authors": [{"family": "Parrett", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0001-9141-1371", "researcher": {"href": "https://publications.scilifelab.se/researcher/74066c0ef87340f6b9f8479fd6fafdb1.json"}}, {"family": "Chmielewski", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-0719-4499", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d42c65e47fc4ffd844b997ed143960f.json"}}, {"family": "Aydogdu", "given": "Eylem", "initials": "E"}, {"family": "\u0141ukasiewicz", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-8038-8700", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e82002ce08541e187e286c0ab0d82c4.json"}}, {"family": "Rombauts", "given": "Stephane", "initials": "S", "orcid": "0000-0002-3985-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/78f2ecf95c174f0e927996e186c21f48.json"}}, {"family": "Szubert-Kruszy\u0144ska", "given": "Agnieszka", "initials": "A"}, {"family": "Babik", "given": "Wies\u0142aw", "initials": "W", "orcid": "0000-0002-1698-6615", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0314840d7fd469bbef8d1cbf05a830f.json"}}, {"family": "Konczal", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-7691-8075", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbd64205c1674cd5999b83f2e1032d95.json"}}, {"family": "Radwan", "given": "Jacek", "initials": "J", "orcid": "0000-0001-8503-5701", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b62da0fe50f4c0e80bca59e881ed63c.json"}}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "6", "issue": "9", "pages": "1330-1342", "issn-l": "2397-334X"}, "abstract": "The evolution of costly traits such as deer antlers and peacock trains, which drove the formation of Darwinian sexual selection theory, has been suggested to both reflect and affect patterns of genetic variance across the genome, but direct tests are missing. Here, we used an evolve and resequence approach to reveal patterns of genome-wide diversity associated with the expression of a sexually selected weapon that is dimorphic among males of the bulb mite, Rhizoglyphus robini. Populations selected for the weapon showed reduced genome-wide diversity compared to populations selected against the weapon, particularly in terms of the number of segregating non-synonymous positions, indicating enhanced purifying selection. This increased purifying selection reduced inbreeding depression, but outbred female fitness did not improve, possibly because any benefits were offset by increased sexual antagonism. Most single nucleotide polymorphisms (SNPs) that consistently diverged in response to selection were initially rare and overrepresented in exons, and enriched in regions under balancing or relaxed selection, suggesting they are probably moderately deleterious variants. These diverged SNPs were scattered across the genome, further demonstrating that selection for or against the weapon and the associated changes to the mating system can both capture and influence genome-wide variation.", "doi": "10.1038/s41559-022-01816-w", "pmid": "35851852", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-022-01816-w"}, {"db": "Dryad", "key": "10.5061/dryad.ncjsxksxg"}], "notes": [], "created": "2022-11-29T09:21:13.426Z", "modified": "2022-11-29T09:21:13.647Z"}, {"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": "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": "fa2c051345524172bdb5e411f318fc00", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fa2c051345524172bdb5e411f318fc00.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fa2c051345524172bdb5e411f318fc00"}}, "title": "Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.", "authors": [{"family": "Bier", "given": "Raven L", "initials": "RL"}, {"family": "Vass", "given": "M\u00e1t\u00e9", "initials": "M", "orcid": "0000-0003-0718-7659", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fed30af96e540269edcb565cb34bc39.json"}}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ", "orcid": "0000-0001-8063-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9b2d69cfd6a4f41a978b38ddf66c8d5.json"}}, {"family": "Langenheder", "given": "Silke", "initials": "S", "orcid": "0000-0002-5245-9935", "researcher": {"href": "https://publications.scilifelab.se/researcher/efa9e8f2174a4c7cb903b0f9b895a183.json"}}], "type": "journal article", "published": "2022-08-18", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "16", "issue": "12", "pages": "2635-2643"}, "abstract": "Understanding processes that determine community membership and abundance is important for many fields from theoretical community ecology to conservation. However, spatial community studies are often conducted only at a single timepoint despite the known influence of temporal variability on community assembly processes. Here we used a spatiotemporal study to determine how environmental fluctuation differences induced by mesocosm volumes (larger volumes were more stable) influence assembly processes of aquatic bacterial metacommunities along a press disturbance gradient. By combining path analysis and network approaches, we found mesocosm size categories had distinct relative influences of assembly process and environmental factors that determined spatiotemporal bacterial community composition, including dispersal and species sorting by conductivity. These processes depended on, but were not affected proportionately by, mesocosm size. Low fluctuation, large mesocosms primarily developed through the interplay of species sorting that became more important over time and transient priority effects as evidenced by more time-delayed associations. High fluctuation, small mesocosms had regular disruptions to species sorting and greater importance of ecological drift and dispersal limitation indicated by lower richness and higher taxa replacement. Together, these results emphasize that environmental fluctuations influence ecosystems over time and its impacts are modified by biotic properties intrinsic to ecosystem size.", "doi": "10.1038/s41396-022-01286-9", "pmid": "35982230", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41396-022-01286-9"}], "notes": [], "created": "2022-11-09T15:56:21.456Z", "modified": "2024-01-16T13:48:35.168Z"}, {"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": "26915f1cd4ba474aac0a8a591527744e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26915f1cd4ba474aac0a8a591527744e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26915f1cd4ba474aac0a8a591527744e"}}, "title": "Isolated Grauer's gorilla populations differ in diet and gut microbiome.", "authors": [{"family": "Michel", "given": "Alice", "initials": "A", "orcid": "0000-0002-0273-4097", "researcher": {"href": "https://publications.scilifelab.se/researcher/5300682d3a4e486d9403e970ca82f8e7.json"}}, {"family": "Minocher", "given": "Riana", "initials": "R"}, {"family": "Niehoff", "given": "Peter-Philip", "initials": "PP"}, {"family": "Li", "given": "Yuhong", "initials": "Y"}, {"family": "Nota", "given": "Kevin", "initials": "K"}, {"family": "Gadhvi", "given": "Maya A", "initials": "MA"}, {"family": "Su", "given": "Jiancheng", "initials": "J"}, {"family": "Iyer", "given": "Neetha", "initials": "N"}, {"family": "Porter", "given": "Amy", "initials": "A"}, {"family": "Ngobobo-As-Ibungu", "given": "Urbain", "initials": "U"}, {"family": "Binyinyi", "given": "Escobar", "initials": "E"}, {"family": "Nishuli Pekeyake", "given": "Radar", "initials": "R"}, {"family": "Parducci", "given": "Laura", "initials": "L"}, {"family": "Caillaud", "given": "Damien", "initials": "D"}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}], "type": "journal article", "published": "2022-08-17", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083"}, "abstract": "The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.", "doi": "10.1111/mec.16663", "pmid": "35976262", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-29T09:59:56.243Z", "modified": "2024-01-16T13:48:35.191Z"}, {"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": "f0f43f9275cf45ba9bedab180ad79085", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0f43f9275cf45ba9bedab180ad79085.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0f43f9275cf45ba9bedab180ad79085"}}, "title": "Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.", "authors": [{"family": "Zhao", "given": "Cheng", "initials": "C", "orcid": "0000-0003-0518-5924", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cd6a95b29e44b3fa8fed63033d26393.json"}}, {"family": "Biondic", "given": "Savana", "initials": "S"}, {"family": "Vandal", "given": "Katherine", "initials": "K"}, {"family": "Bj\u00f6rklund", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M"}, {"family": "Sommer", "given": "Theresa Maria", "initials": "TM"}, {"family": "Canizo", "given": "Jesica", "initials": "J"}, {"family": "Clark", "given": "Stephen", "initials": "S"}, {"family": "Raymond", "given": "Pascal", "initials": "P"}, {"family": "Zenklusen", "given": "Daniel R", "initials": "DR", "orcid": "0000-0002-0067-0093", "researcher": {"href": "https://publications.scilifelab.se/researcher/570efd02034b4c8c809c51476378da15.json"}}, {"family": "Rivron", "given": "Nicolas", "initials": "N"}, {"family": "Reik", "given": "Wolf", "initials": "W"}, {"family": "Petropoulos", "given": "Sophie", "initials": "S", "orcid": "0000-0003-2293-8238", "researcher": {"href": "https://publications.scilifelab.se/researcher/0766fd90df1f4199a000eb84b06e2d31.json"}}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Genome Res.", "issn": "1549-5469", "issn-l": "1088-9051", "volume": "32", "issue": "9", "pages": "1627-1641"}, "abstract": "The preconceptual, intrauterine, and early life environments can have a profound and long-lasting impact on the developmental trajectories and health outcomes of the offspring. Given the relatively low success rates of assisted reproductive technologies (ART; \u223c25%), additives and adjuvants, such as glucocorticoids, are used to improve the success rate. Considering the dynamic developmental events that occur during this window, these exposures may alter blastocyst formation at a molecular level, and as such, affect not only the viability of the embryo and the ability of the blastocyst to implant, but also the developmental trajectory of the first three cell lineages, ultimately influencing the physiology of the embryo. In this study, we present a comprehensive single-cell transcriptome, methylome, and small RNA atlas in the day 7 human embryo. We show that, despite no change in morphology and developmental features, preimplantation glucocorticoid exposure reprograms the molecular profile of the TE lineage, and these changes are associated with an altered metabolic and inflammatory response. Our data also suggest that glucocorticoids can precociously mature the TE sublineages, supported by the presence of extravillous trophoblast markers in the polar sublineage and presence of X Chromosome dosage compensation. Further, we have elucidated that epigenetic regulation-DNA methylation and microRNAs (miRNAs)-likely underlies the transcriptional changes observed. This study suggests that exposures to exogenous compounds during preimplantation may unintentionally reprogram the human embryo, possibly leading to suboptimal development and longer-term health outcomes.", "doi": "10.1101/gr.276665.122", "pmid": "35948369", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Single cell": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9528977"}, {"db": "pii", "key": "gr.276665.122"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2022-08-12T08:24:11.793Z", "modified": "2024-01-16T13:48:35.397Z"}, {"entity": "publication", "iuid": "83170949a3664c28be863b7ae471fc06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83170949a3664c28be863b7ae471fc06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83170949a3664c28be863b7ae471fc06"}}, "title": "Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.", "authors": [{"family": "Meunier", "given": "C\u00e9cile", "initials": "C"}, {"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Reimeg\u00e5rd", "given": "Johan", "initials": "J"}, {"family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.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": "20220971"}, "abstract": "Heterokaryosis is a system in which genetically distinct nuclei coexist within the same cytoplasm. While heterokaryosis dominates the life cycle of many fungal species, the transcriptomic changes associated with the transition from homokaryosis to heterokaryosis is not well understood. Here, we analyse gene expression profiles of homokaryons and heterokaryons from three phylogenetically and reproductively isolated lineages of the filamentous ascomycete Neurospora tetrasperma. We show that heterokaryons are transcriptionally distinct from homokaryons in the sexual stage of development, but not in the vegetative stage, suggesting that the phenotypic switch to fertility in heterokaryons is associated with major changes in gene expression. Heterokaryon expression is predominantly defined by additive effects of its two nuclear components. Furthermore, allele-specific expression analysis of heterokaryons with varying nuclear ratios show patterns of expression ratios strongly dependent on nuclear ratios in the vegetative stage. By contrast, in the sexual stage, strong deviations of expression ratios indicate a co-regulation of nuclear gene expression in all three lineages. Taken together, our results show two levels of expression control: additive effects suggest a nuclear level of expression, whereas co-regulation of gene expression indicate a heterokaryon level of control.", "doi": "10.1098/rspb.2022.0971", "pmid": "35946150", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9363985"}], "notes": [], "created": "2022-08-12T11:13:21.820Z", "modified": "2024-01-16T13:48:35.404Z"}, {"entity": "publication", "iuid": "e48911a20cdc402fb1cfcc754b80d040", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e48911a20cdc402fb1cfcc754b80d040.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e48911a20cdc402fb1cfcc754b80d040"}}, "title": "Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.", "authors": [{"family": "Nannapaneni", "given": "Priyanka", "initials": "P"}, {"family": "Sundh", "given": "John", "initials": "J"}, {"family": "Prast-Nielsen", "given": "Stefanie", "initials": "S"}, {"family": "Rhedin", "given": "Samuel", "initials": "S"}, {"family": "\u00d6rtqvist", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Naucler", "given": "Pontus", "initials": "P"}, {"family": "Henriques-Normark", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2022-08-10", "journal": {"title": "Am. J. Respir. Crit. Care Med.", "issn": "1535-4970", "issn-l": "1073-449X", "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1164/rccm.202203-0463LE", "pmid": "35947760", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-08-12T09:29:38.505Z", "modified": "2024-01-16T13:48:35.412Z"}, {"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": "4a28dd5860e7477c82ea19ebbdb98820", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a28dd5860e7477c82ea19ebbdb98820.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a28dd5860e7477c82ea19ebbdb98820"}}, "title": "Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.", "authors": [{"family": "Dahlqvist", "given": "Johanna", "initials": "J", "orcid": "0000-0002-6283-644X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fb2ab2d83b6437f9918f330e5fb81b2.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Nordin", "given": "Jessika", "initials": "J"}, {"family": "Karlsson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Hellbacher", "given": "Erik", "initials": "E"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S", "orcid": "0000-0001-8259-3863", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfca4bfdcf3946fda64397d3b7debc59.json"}}, {"family": "Berglin", "given": "Ewa", "initials": "E"}, {"family": "Stegmayr", "given": "Bernd", "initials": "B"}, {"family": "Baslund", "given": "Bo", "initials": "B"}, {"family": "Palm", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Haukeland", "given": "Hilde", "initials": "H"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Bruchfeld", "given": "Annette", "initials": "A", "orcid": "0000-0002-9752-9941", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc6ee3e8a4124c5f8d6506ab762949ae.json"}}, {"family": "Segelmark", "given": "M\u00e5rten", "initials": "M"}, {"family": "Ohlsson", "given": "Sophie", "initials": "S"}, {"family": "Mohammad", "given": "Aladdin J", "initials": "AJ", "orcid": "0000-0002-7169-6936", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7010c3f5b91415dbc26c87d6a923f68.json"}}, {"family": "Sv\u00e4rd", "given": "Anna", "initials": "A"}, {"family": "Pullerits", "given": "Rille", "initials": "R"}, {"family": "Herlitz", "given": "Hans", "initials": "H"}, {"family": "S\u00f6derbergh", "given": "Annika", "initials": "A"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}, {"family": "Hultin Rosenberg", "given": "Lina", "initials": "L"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Mur\u00e9n", "given": "Eva", "initials": "E"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "S\u00f6derkvist", "given": "Peter", "initials": "P"}, {"family": "Knight", "given": "Ann", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}], "type": "journal article", "published": "2022-08-03", "journal": {"title": "Rheumatology (Oxford)", "issn": "1462-0332", "volume": "61", "issue": "8", "pages": "3461-3470", "issn-l": "1462-0324"}, "abstract": "To identify and characterize genetic loci associated with the risk of developing ANCA-associated vasculitides (AAV).\n\nGenetic association analyses were performed after Illumina sequencing of 1853 genes and subsequent replication with genotyping of selected single nucleotide polymorphisms in a total cohort of 1110 Scandinavian cases with granulomatosis with polyangiitis or microscopic polyangiitis, and 1589 controls. A novel AAV-associated single nucleotide polymorphism was analysed for allele-specific effects on gene expression using luciferase reporter assay.\n\nPR3-ANCA+ AAV was significantly associated with two independent loci in the HLA-DPB1/HLA-DPA1 region [rs1042335, P = 6.3 \u00d7 10-61, odds ratio (OR) 0.10; rs9277341, P = 1.5 \u00d7 10-44, OR 0.22] and with rs28929474 in the SERPINA1 gene (P = 2.7 \u00d7 10-10, OR 2.9). MPO-ANCA+ AAV was significantly associated with the HLA-DQB1/HLA-DQA2 locus (rs9274619, P = 5.4 \u00d7 10-25, OR 3.7) and with a rare variant in the BACH2 gene (rs78275221, P = 7.9 \u00d7 10-7, OR 3.0), the latter a novel susceptibility locus for MPO-ANCA+ granulomatosis with polyangiitis/microscopic polyangiitis. The rs78275221-A risk allele reduced luciferase gene expression in endothelial cells, specifically, as compared with the non-risk allele.\n\nWe identified a novel susceptibility locus for MPO-ANCA+ AAV and propose that the associated variant is of mechanistic importance, exerting a regulatory function on gene expression in specific cell types.", "doi": "10.1093/rheumatology/keab912", "pmid": "34888651", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9348767"}, {"db": "pii", "key": "6458341"}], "notes": [], "created": "2021-12-16T12:04:03.431Z", "modified": "2024-01-16T13:48:35.466Z"}, {"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": "925dfb57c60840669f1589754cd95335", "links": {"self": {"href": "https://publications.scilifelab.se/publication/925dfb57c60840669f1589754cd95335.json"}, "display": {"href": "https://publications.scilifelab.se/publication/925dfb57c60840669f1589754cd95335"}}, "title": "A relationship between phages and organic carbon in wastewater treatment plant effluents.", "authors": [{"family": "Modin", "given": "Oskar", "initials": "O"}, {"family": "Fuad", "given": "Nafis", "initials": "N"}, {"family": "Abadikhah", "given": "Marie", "initials": "M"}, {"family": "I'Ons", "given": "David", "initials": "D"}, {"family": "Ossiansson", "given": "Elin", "initials": "E"}, {"family": "Gustavsson", "given": "David J I", "initials": "DJI"}, {"family": "Edefell", "given": "Ellen", "initials": "E"}, {"family": "Suarez", "given": "Carolina", "initials": "C"}, {"family": "Persson", "given": "Frank", "initials": "F"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}], "type": "journal article", "published": "2022-08-01", "journal": {"title": "Water Res X", "issn": "2589-9147", "volume": "16", "pages": "100146", "issn-l": null}, "abstract": "With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.", "doi": "10.1016/j.wroa.2022.100146", "pmid": "35761925", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9233278"}, {"db": "pii", "key": "S2589-9147(22)00016-0"}], "notes": [], "created": "2022-11-29T09:36:29.491Z", "modified": "2024-01-16T13:48:35.500Z"}, {"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": "9711136f1e1945caad4b5ed63968451c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9711136f1e1945caad4b5ed63968451c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9711136f1e1945caad4b5ed63968451c"}}, "title": "Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.", "authors": [{"family": "Lundtoft", "given": "Christian", "initials": "C"}, {"family": "Pucholt", "given": "Pascal", "initials": "P"}, {"family": "Martin", "given": "Myriam", "initials": "M"}, {"family": "Bianchi", "given": "Matteo", "initials": "M"}, {"family": "Lundstr\u00f6m", "given": "Emeli", "initials": "E"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Sj\u00f6wall", "given": "Christopher", "initials": "C"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Baecklund", "given": "Eva", "initials": "E"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}, {"family": "Hammenfors", "given": "Daniel", "initials": "D"}, {"family": "Forsblad-d'Elia", "given": "Helena", "initials": "H"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Mandl", "given": "Thomas", "initials": "T"}, {"family": "Magnusson Bucher", "given": "Sara", "initials": "S"}, {"family": "Norheim", "given": "Katrine B", "initials": "KB"}, {"family": "Auglaend Johnsen", "given": "Svein Joar", "initials": "SJ"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Notarnicola", "given": "Antonella", "initials": "A"}, {"family": "Andersson", "given": "Helena", "initials": "H"}, {"family": "Molberg", "given": "\u00d8yvind", "initials": "\u00d8"}, {"family": "Diederichsen", "given": "Louise Pyndt", "initials": "LP"}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC"}, {"family": "Kozyrev", "given": "Sergey V", "initials": "SV"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K"}, {"family": "DISSECT Consortium", "given": "", "initials": ""}, {"family": "ImmunoArray Development Consortium", "given": "", "initials": ""}, {"family": "Nilsson", "given": "Bo", "initials": "B"}, {"family": "Blom", "given": "Anna M", "initials": "AM"}, {"family": "Lundberg", "given": "Ingrid E", "initials": "IE"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Diaz-Gallo", "given": "Lina Marcela", "initials": "LM"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "Arthritis & rheumatology (Hoboken, N.J.)", "issn": "2326-5205", "volume": "74", "issue": "8", "pages": "1440-1450", "issn-l": "2326-5191"}, "abstract": "Copy number variation of the C4 complement components, C4A and C4B, has been associated with systemic inflammatory autoimmune diseases. This study was undertaken to investigate whether C4 copy number variation is connected to the autoimmune repertoire in systemic lupus erythematosus (SLE), primary Sj\u00f6gren's syndrome (SS), or myositis.\n\nUsing targeted DNA sequencing, we determined the copy number and genetic variants of C4 in 2,290 well-characterized Scandinavian patients with SLE, primary SS, or myositis and 1,251 healthy controls.\n\nA prominent relationship was observed between C4A copy number and the presence of SSA/SSB autoantibodies, which was shared between the 3 diseases. The strongest association was detected in patients with autoantibodies against both SSA and SSB and 0 C4A copies when compared to healthy controls (odds ratio [OR] 18.0 [95% confidence interval (95% CI) 10.2-33.3]), whereas a weaker association was seen in patients without SSA/SSB autoantibodies (OR 3.1 [95% CI 1.7-5.5]). The copy number of C4 correlated positively with C4 plasma levels. Further, a common loss-of-function variant in C4A leading to reduced plasma C4 was more prevalent in SLE patients with a low copy number of C4A. Functionally, we showed that absence of C4A reduced the individuals' capacity to deposit C4b on immune complexes.\n\nWe show that a low C4A copy number is more strongly associated with the autoantibody repertoire than with the clinically defined disease entities. These findings may have implications for understanding the etiopathogenetic mechanisms of systemic inflammatory autoimmune diseases and for patient stratification when taking the genetic profile into account.", "doi": "10.1002/art.42122", "pmid": "35315244", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9543510"}], "notes": [], "created": "2022-09-06T15:12:48.456Z", "modified": "2024-01-16T13:48:35.558Z"}, {"entity": "publication", "iuid": "9c68253c983c4dd8b33da093c868b3ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c68253c983c4dd8b33da093c868b3ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c68253c983c4dd8b33da093c868b3ba"}}, "title": "A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.", "authors": [{"family": "Gramlich", "given": "Susanne", "initials": "S", "orcid": "0000-0003-1224-0514", "researcher": {"href": "https://publications.scilifelab.se/researcher/49a7319974c04884b77987640ab92994.json"}}, {"family": "Liu", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-8839-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/fabce70bd90a4bfe8923d6167e236cff.json"}}, {"family": "Favre", "given": "Adrien", "initials": "A", "orcid": "0000-0001-6132-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6992fd6e45a41ffb6fe4aa2a11e812a.json"}}, {"family": "Buerkle", "given": "C Alex", "initials": "CA", "orcid": "0000-0003-4222-8858", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f8582095a674055b811170719618d0b.json"}}, {"family": "Karrenberg", "given": "Sophie", "initials": "S", "orcid": "0000-0002-7146-588X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a982636b44f4b93b7ec0bd64e5d6bfb.json"}}], "type": "journal article", "published": "2022-08-00", "journal": {"title": "New Phytol.", "issn": "1469-8137", "issn-l": "0028-646X", "volume": "235", "issue": "4", "pages": "1641-1652"}, "abstract": "Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.", "doi": "10.1111/nph.18260", "pmid": "35586969", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9544174"}, {"db": "Dryad", "key": "10.5061/dryad.4tmpg4fcn"}], "notes": [], "created": "2022-11-09T15:42:31.295Z", "modified": "2024-01-16T13:48:35.574Z"}, {"entity": "publication", "iuid": "425bcad722be4cf8b20047dcd31f3141", "links": {"self": {"href": "https://publications.scilifelab.se/publication/425bcad722be4cf8b20047dcd31f3141.json"}, "display": {"href": "https://publications.scilifelab.se/publication/425bcad722be4cf8b20047dcd31f3141"}}, "title": "Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.", "authors": [{"family": "Cholleti", "given": "Harindranath", "initials": "H"}, {"family": "de Jong", "given": "Johnny", "initials": "J"}, {"family": "Blomstr\u00f6m", "given": "Anne-Lie", "initials": "AL"}, {"family": "Berg", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2022-07-28", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "14", "issue": "8", "issn-l": "1999-4915"}, "abstract": "Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78-99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88-94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.", "doi": "10.3390/v14081654", "pmid": "36016275", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9415950"}, {"db": "pii", "key": "v14081654"}], "notes": [], "created": "2022-09-06T05:44:09.655Z", "modified": "2024-01-16T13:48:35.624Z"}, {"entity": "publication", "iuid": "796f460ce9794c089a8bdd175c3a9b65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/796f460ce9794c089a8bdd175c3a9b65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/796f460ce9794c089a8bdd175c3a9b65"}}, "title": "Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies.", "authors": [{"family": "Swaegers", "given": "Janne", "initials": "J", "orcid": "0000-0003-1952-3170", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cb5191ea7e94e8696e42fc15e854ce8.json"}}, {"family": "S\u00e1nchez-Guill\u00e9n", "given": "Rosa Ana", "initials": "RA", "orcid": "0000-0001-6024-8321", "researcher": {"href": "https://publications.scilifelab.se/researcher/c03f95fe4ced4dd690950ab8bb656710.json"}}, {"family": "Chauhan", "given": "Pallavi", "initials": "P", "orcid": "0000-0002-5160-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2ca3733447d4e38ae5cce50d1b4d165.json"}}, {"family": "Wellenreuther", "given": "Maren", "initials": "M", "orcid": "0000-0002-2764-8291", "researcher": {"href": "https://publications.scilifelab.se/researcher/82e9b593bf0f4535a7b9231608b1e27d.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2022-07-27", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "issn-l": "0962-8452", "volume": "289", "issue": "1979", "pages": "20220968"}, "abstract": "Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and may shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridization. Moreover, they are thought to contribute to Haldane's rule, which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes, and (ii) that males are underrepresented among admixed individuals, as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data add to the few studies on species with X0 sex determination system and contradict the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.", "doi": "10.1098/rspb.2022.0968", "pmid": "35855603", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9297008"}, {"db": "Dryad", "key": "10.5061/dryad.gqnk98sp8"}], "notes": [], "created": "2022-11-09T15:50:07.860Z", "modified": "2024-01-16T13:48:35.646Z"}, {"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": "ae81f81f52cb4fbc9ea20d482d20a8b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae81f81f52cb4fbc9ea20d482d20a8b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae81f81f52cb4fbc9ea20d482d20a8b6"}}, "title": "Proliferation and Immune Response Gene Signatures Associated with Clinical Outcome to Immunotherapy and Targeted Therapy in Metastatic Cutaneous Malignant Melanoma.", "authors": [{"family": "Costa Svedman", "given": "Fernanda", "initials": "F", "orcid": "0000-0001-8065-3375", "researcher": {"href": "https://publications.scilifelab.se/researcher/468b2e407aeb49a88b1ef0f7b1e02ce7.json"}}, {"family": "Das", "given": "Ishani", "initials": "I"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Darai Ramqvist", "given": "Eva", "initials": "E"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}, {"family": "Egyhazi Brage", "given": "Suzanne", "initials": "S"}], "type": "journal article", "published": "2022-07-22", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "14", "issue": "15", "issn-l": "2072-6694"}, "abstract": "Targeted therapy (TT), together with immune checkpoint inhibitors (ICI), has significantly improved clinical outcomes for patients with advanced cutaneous malignant melanoma (CMM) during the last decade. However, the magnitude and the duration of response vary considerably. There is still a paucity of predictive biomarkers to identify patients who benefit most from treatment. To address this, we performed targeted transcriptomics of CMM tumors to identify biomarkers associated with clinical outcomes. Pre-treatment tumor samples from 28 patients with advanced CMM receiving TT (n = 13) or ICI (n = 15) were included in the study. Targeted RNA sequencing was performed using Ion AmpliSeq \u2122, followed by gene set enrichment analysis (GSEA) using MSigDB's Hallmark Gene Set Collection to identify gene expression signatures correlating with treatment outcome. The GSEA demonstrated that up-regulation of allograft rejection genes, together with down-regulation of E2F and MYC targets as well as G2M checkpoint genes, significantly correlated with longer progression-free survival on ICI while IFN\u03b3 and inflammatory response genes were associated with a better clinical outcome on TT. In conclusion, we identify novel genes and their expression signatures as potential predictive biomarkers for TT and ICI in patients with metastatic CMM, paving the way for clinical use following larger validation studies.", "doi": "10.3390/cancers14153587", "pmid": "35892846", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "cancers14153587"}, {"db": "pmc", "key": "PMC9331037"}], "notes": [], "created": "2022-09-05T07:12:08.602Z", "modified": "2022-09-05T07:12:08.643Z"}, {"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": "45433b3cce4846679af7f62c08acb69b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/45433b3cce4846679af7f62c08acb69b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/45433b3cce4846679af7f62c08acb69b"}}, "title": "Lipoxins reduce obesity-induced adipose tissue inflammation in 3D-cultured human adipocytes and explant cultures.", "authors": [{"family": "Sot\u00e1k", "given": "Mat\u00fa\u0161", "initials": "M"}, {"family": "Rajan", "given": "Meenu Rohini", "initials": "MR"}, {"family": "Clark", "given": "Madison", "initials": "M"}, {"family": "Harms", "given": "Matthew", "initials": "M"}, {"family": "Rani", "given": "Alankrita", "initials": "A"}, {"family": "Kraft", "given": "Jamie D", "initials": "JD"}, {"family": "Tandio", "given": "David", "initials": "D"}, {"family": "Shen", "given": "Tong", "initials": "T"}, {"family": "Borkowski", "given": "Kamil", "initials": "K"}, {"family": "Fiehn", "given": "Oliver", "initials": "O"}, {"family": "Newman", "given": "John W", "initials": "JW"}, {"family": "Quiding-J\u00e4rbrink", "given": "Marianne", "initials": "M"}, {"family": "Bi\u00f6rserud", "given": "Christina", "initials": "C"}, {"family": "Apelgren", "given": "Peter", "initials": "P"}, {"family": "Staalesen", "given": "Trude", "initials": "T"}, {"family": "Hagberg", "given": "Carolina E", "initials": "CE"}, {"family": "Boucher", "given": "Jeremie", "initials": "J"}, {"family": "Wallenius", "given": "Ville", "initials": "V"}, {"family": "Lange", "given": "Stephan", "initials": "S"}, {"family": "B\u00f6rgeson", "given": "Emma", "initials": "E"}], "type": "journal article", "published": "2022-07-15", "journal": {"title": "iScience", "issn": "2589-0042", "volume": "25", "issue": "7", "pages": "104602", "issn-l": "2589-0042"}, "abstract": "Adipose tissue inflammation drives obesity-related cardiometabolic diseases. Enhancing endogenous resolution mechanisms through administration of lipoxin A4, a specialized pro-resolving lipid mediator, was shown to reduce adipose inflammation and subsequently protects against obesity-induced systemic disease in mice. Here, we demonstrate that lipoxins reduce inflammation in 3D-cultured human adipocytes and adipose tissue explants from obese patients. Approximately 50% of patients responded particularly well to lipoxins by reducing inflammatory cytokines and promoting an anti-inflammatory M2 macrophage phenotype. Responding patients were characterized by elevated systemic levels of C-reactive protein, which causes inflammation in cultured human adipocytes. Responders appeared more prone to producing anti-inflammatory oxylipins and displayed elevated prostaglandin D2 levels, which has been interlinked with transcription of lipoxin-generating enzymes. Using explant cultures, this study provides the first proof-of-concept evidence supporting the therapeutic potential of lipoxins in reducing human adipose tissue inflammation. Our data further indicate that lipoxin treatment may require a tailored personalized-medicine approach.", "doi": "10.1016/j.isci.2022.104602", "pmid": "35789845", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9249816"}, {"db": "pii", "key": "S2589-0042(22)00874-4"}], "notes": [], "created": "2022-11-29T09:47:56.917Z", "modified": "2022-11-29T09:47:56.920Z"}, {"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": "64ad69b112e8486882a7f3720623a583", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64ad69b112e8486882a7f3720623a583"}}, "title": "Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.", "authors": [{"family": "Selvin", "given": "Tove", "initials": "T"}, {"family": "Fasterius", "given": "Erik", "initials": "E"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Andersson", "given": "Claes R", "initials": "CR"}], "type": "journal article", "published": "2022-07-13", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "11960"}, "abstract": "Understanding the immunological effects of chemotherapy is of great importance, especially now that we have entered an era where ever-increasing pre-clinical and clinical efforts are put into combining chemotherapy and immunotherapy to combat cancer. Single-cell RNA sequencing (scRNA-seq) has proved to be a powerful technique with a broad range of applications, studies evaluating drug effects in co-cultures of tumor and immune cells are however scarce. We treated a co-culture comprised of human colorectal cancer (CRC) cells and peripheral blood mononuclear cells (PBMCs) with the nucleoside analogue trifluridine (FTD) and used scRNA-seq to analyze posttreatment gene expression profiles in thousands of individual cancer and immune cells concurrently. ScRNA-seq recapitulated major mechanisms of action previously described for FTD and provided new insight into possible treatment-induced effects on T-cell mediated antitumor responses.", "doi": "10.1038/s41598-022-16077-7", "pmid": "35831404", "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Single cell": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9279337"}, {"db": "pii", "key": "10.1038/s41598-022-16077-7"}], "notes": [], "created": "2022-08-22T07:53:44.772Z", "modified": "2024-01-16T13:48:35.689Z"}, {"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": "6ac7c7975ef94079a12757f6846f20a6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ac7c7975ef94079a12757f6846f20a6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ac7c7975ef94079a12757f6846f20a6"}}, "title": "Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes", "authors": [{"family": "Hoffman", "given": "Tove", "initials": "T", "orcid": "0000-0003-2239-9078", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8baafa073c34cfcbdfb513392373b3f.json"}}, {"family": "Sj\u00f6din", "given": "Andreas", "initials": "A", "orcid": "0000-0001-5350-4219", "researcher": {"href": "https://publications.scilifelab.se/researcher/6398d7c06a414ea6bcaf2579a8587452.json"}}, {"family": "\u00d6hrman", "given": "Caroline", "initials": "C", "orcid": "0000-0001-8489-757X", "researcher": {"href": "https://publications.scilifelab.se/researcher/804b654aa0be4d7a9ecdf113487fe443.json"}}, {"family": "Karlsson", "given": "Linda", "initials": "L"}, {"family": "McDonough", "given": "Ryelan Francis", "initials": "RF"}, {"family": "Sahl", "given": "Jason W", "initials": "JW"}, {"family": "Birdsell", "given": "Dawn", "initials": "D"}, {"family": "Wagner", "given": "David M", "initials": "DM", "orcid": "0000-0003-2684-6007", "researcher": {"href": "https://publications.scilifelab.se/researcher/04dbf7488dc54ca3b7031571b9acc982.json"}}, {"family": "Carra", "given": "Laura G", "initials": "LG"}, {"family": "Wilhelmsson", "given": "Peter", "initials": "P"}, {"family": "Pettersson", "given": "John H O", "initials": "JHO"}, {"family": "Barboutis", "given": "Christos", "initials": "C", "orcid": "0000-0002-5644-4327", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c4a150259c44fe1a79914c1c0605130.json"}}, {"family": "Figuerola", "given": "Jordi", "initials": "J", "orcid": "0000-0002-4664-9011", "researcher": {"href": "https://publications.scilifelab.se/researcher/3832a2f08cec48848cf289134a105840.json"}}, {"family": "Onrubia", "given": "Alejandro", "initials": "A", "orcid": "0000-0001-8860-3524", "researcher": {"href": "https://publications.scilifelab.se/researcher/c73213860576464fafb5b1565d7299cc.json"}}, {"family": "Kiat", "given": "Yosef", "initials": "Y", "orcid": "0000-0002-3485-3517", "researcher": {"href": "https://publications.scilifelab.se/researcher/40519e89d3e44b47bf402078e687a45a.json"}}, {"family": "Piacentini", "given": "Dario", "initials": "D"}, {"family": "Jaenson", "given": "Thomas G T", "initials": "TGT"}, {"family": "Lindgren", "given": "Per Eric", "initials": "PE", "orcid": "0000-0003-2767-3638", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4a6e70c9c514a48a40c3edf446ab5ce.json"}}, {"family": "Moutailler", "given": "Sara", "initials": "S", "orcid": "0000-0003-3010-6968", "researcher": {"href": "https://publications.scilifelab.se/researcher/b332d118556846808a1df98dbd5da020.json"}}, {"family": "Fransson", "given": "Thord", "initials": "T", "orcid": "0000-0002-9721-7024", "researcher": {"href": "https://publications.scilifelab.se/researcher/d17e09b5057d47eb87174f839d16c257.json"}}, {"family": "Forsman", "given": "Mats", "initials": "M", "orcid": "0000-0002-4466-5325", "researcher": {"href": "https://publications.scilifelab.se/researcher/b52b5a759a3e452b80728241c50c76dd.json"}}, {"family": "Nilsson", "given": "Kenneth", "initials": "K"}, {"family": "Lundkvist", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0001-8608-6551", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c4bcad692e48dfb25a551f014d8482.json"}}, {"family": "Olsen", "given": "Bj\u00f6rn", "initials": "B"}], "type": "journal-article", "published": "2022-07-11", "journal": {"title": "Microorganisms", "issn": "2076-2607", "issn-l": "2076-2607", "volume": "10", "issue": "7", "pages": "1393"}, "abstract": "The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species Francisella tularensis, the genus Francisella, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick samples that putatively tested positive for F. tularensis during initial screenings. Hyalomma rufipes was the most common tick species and had a high prevalence of Francisella, including co-occurrence of Francisella and SFGR. Metagenomic analysis of total DNA extracted from two H. rufipes confirmed the presence of Francisella, Rickettsia, and Midichloria. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a Francisella-like endosymbiont (FLE), Rickettsia aeschlimannii, and Midichloria mitochondrii. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) H. rufipes likely is not involved in transmission of F. tularensis in the AWPR, and (iii) a dual endosymbiosis of FLEs and Midichloria may support some of the nutritional requirements of H. rufipes.", "doi": "10.3390/microorganisms10071393", "pmid": "35889112", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9323704"}, {"db": "pii", "key": "microorganisms10071393"}], "notes": [], "created": "2022-11-09T15:44:20.894Z", "modified": "2024-01-16T13:48:35.835Z"}, {"entity": "publication", "iuid": "42b992446dbf48e7aa157bc279607840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42b992446dbf48e7aa157bc279607840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42b992446dbf48e7aa157bc279607840"}}, "title": "Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms.", "authors": [{"family": "Varg", "given": "Javier Edo", "initials": "JE", "orcid": "0000-0002-7895-4563", "researcher": {"href": "https://publications.scilifelab.se/researcher/72cb1019516e49f7b8f39b18924babc2.json"}}, {"family": "Outomuro", "given": "David", "initials": "D"}, {"family": "Kunce", "given": "Warren", "initials": "W"}, {"family": "Kuehrer", "given": "Lukas", "initials": "L"}, {"family": "Svanb\u00e4ck", "given": "Richard", "initials": "R"}, {"family": "Johansson", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2022-07-06", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "17", "issue": "1", "pages": "36", "issn-l": null}, "abstract": "Microplastics are a pervasive pollutant widespread in the sea and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic organisms and on their microbiota. Few studies have explored the combined effects of microplastics and pesticides on the host-microbiome, and more importantly, the effects across multiple trophic levels. In this work, we studied the effects of exposure to microplastics and the pesticide deltamethrin on the diversity and abundance of the host-microbiome across a three-level food chain: daphnids-damselfly-dragonflies. Daphnids were the only organism exposed to 1 \u00b5m microplastic beads, and they were fed to damselfly larvae. Those damselfly larvae were exposed to deltamethrin and then fed to the dragonfly larvae. The microbiotas of the daphnids, damselflies, and dragonflies were analyzed.\n\nExposure to microplastics and deltamethrin had a direct effect on the microbiome of the species exposed to these pollutants. An indirect effect was also found since exposure to the pollutants at lower trophic levels showed carry over effects on the diversity and abundance of the microbiome on higher trophic levels, even though the organisms at these levels where not directly exposed to the pollutants. Moreover, the exposure to deltamethrin on the damselflies negatively affected their survival rate in the presence of the dragonfly predator, but no such effects were found on damselflies fed with daphnids that had been exposed to microplastics.\n\nOur study highlights the importance of evaluating ecotoxicological effects at the community level. Importantly, the indirect exposure to microplastics and pesticides through diet can potentially have bottom-up effects on the trophic webs.", "doi": "10.1186/s40793-022-00429-x", "pmid": "35794681", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9258161"}, {"db": "pii", "key": "10.1186/s40793-022-00429-x"}], "notes": [], "created": "2022-11-29T09:37:16.537Z", "modified": "2022-11-29T09:37:16.572Z"}, {"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": "6f309d38fa3443c59966f673a7b43fdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f309d38fa3443c59966f673a7b43fdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f309d38fa3443c59966f673a7b43fdb"}}, "title": "Practical application of a Bayesian network approach to poultry epigenetics and stress.", "authors": [{"family": "Videla Rodriguez", "given": "Emiliano A", "initials": "EA"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Mitchell", "given": "John B O", "initials": "JBO"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Smith", "given": "V Anne", "initials": "VA"}], "type": "journal article", "published": "2022-07-01", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "23", "issue": "1", "pages": "261", "issn-l": "1471-2105"}, "abstract": "Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide array of possibilities in Bayesian network analysis is limited. Our study aimed to apply a BN approach, while clearly laying out our analysis choices as an example for future researchers, in order to provide further insights into the relationships among epigenetic features and a stressful condition in chickens (Gallus gallus).\n\nChickens raised under control conditions (n = 22) and chickens exposed to a social isolation protocol (n = 24) were used to identify differentially methylated regions (DMRs). A total of 60 DMRs were selected by a threshold, after bioinformatic pre-processing and analysis. The treatment was included as a binary variable (control = 0; stress = 1). Thereafter, a BN approach was applied: initially, a pre-filtering test was used for identifying pairs of features that must not be included in the process of learning the structure of the network; then, the average probability values for each arc of being part of the network were calculated; and finally, the arcs that were part of the consensus network were selected. The structure of the BN consisted of 47 out of 61 features (60 DMRs and the stressful condition), displaying 43 functional relationships. The stress condition was connected to two DMRs, one of them playing a role in tight and adhesive intracellular junctions in organs such as ovary, intestine, and brain.\n\nWe clearly explain our steps in making each analysis choice, from discrete BN models to final generation of a consensus network from multiple model averaging searches. The epigenetic BN unravelled functional relationships among the DMRs, as well as epigenetic features in close association with the stressful condition the chickens were exposed to. The DMRs interacting with the stress condition could be further explored in future studies as possible biomarkers of stress in poultry species.", "doi": "10.1186/s12859-022-04800-0", "pmid": "35778683", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9250184"}, {"db": "pii", "key": "10.1186/s12859-022-04800-0"}], "notes": [], "created": "2022-11-29T09:52:41.045Z", "modified": "2024-01-16T13:48:35.948Z"}, {"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": "903a0d4b47c0422abb32f266006c4d51", "links": {"self": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51.json"}, "display": {"href": "https://publications.scilifelab.se/publication/903a0d4b47c0422abb32f266006c4d51"}}, "title": "Allorecognition genes drive reproductive isolation in Podospora anserina.", "authors": [{"family": "Ament-Vel\u00e1squez", "given": "S Lorena", "initials": "SL", "orcid": "0000-0003-3371-9292", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d54ef94f91c4c1c85d5dc3a846023e5.json"}}, {"family": "Vogan", "given": "Aaron A", "initials": "AA", "orcid": "0000-0003-2013-7445", "researcher": {"href": "https://publications.scilifelab.se/researcher/71c6d460e3b44712a1a9dc19066211a4.json"}}, {"family": "Granger-Farbos", "given": "Alexandra", "initials": "A"}, {"family": "Bastiaans", "given": "Eric", "initials": "E", "orcid": "0000-0003-1502-0947", "researcher": {"href": "https://publications.scilifelab.se/researcher/870bd6035e54489187ef1d5131d14108.json"}}, {"family": "Martinossi-Allibert", "given": "Ivain", "initials": "I"}, {"family": "Saupe", "given": "Sven J", "initials": "SJ"}, {"family": "de Groot", "given": "Suzette", "initials": "S"}, {"family": "Lascoux", "given": "Martin", "initials": "M", "orcid": "0000-0003-1699-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ad3fadfb69448f397ad3bf55b2d2cb3.json"}}, {"family": "Debets", "given": "Alfons J M", "initials": "AJM", "orcid": "0000-0002-1799-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/b95b282c02d44a1a9f4d3d2aa7578b8a.json"}}, {"family": "Clav\u00e9", "given": "Corinne", "initials": "C"}, {"family": "Johannesson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-6359-9856", "researcher": {"href": "https://publications.scilifelab.se/researcher/36e8fe278e01470e8cddaaccc5dad596.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "issn-l": "2397-334X", "volume": "6", "issue": "7", "pages": "910-923"}, "abstract": "Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.", "doi": "10.1038/s41559-022-01734-x", "pmid": "35551248", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-022-01734-x"}, {"db": "pmc", "key": "PMC9262711"}], "notes": [], "created": "2022-11-09T15:43:47.396Z", "modified": "2024-01-16T13:48:36.025Z"}, {"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": "4b97923e6cd647c4aff7feec91201142", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b97923e6cd647c4aff7feec91201142.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b97923e6cd647c4aff7feec91201142"}}, "title": "Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.", "authors": [{"family": "Law", "given": "Simon R", "initials": "SR", "orcid": "0000-0003-0389-6650", "researcher": {"href": "https://publications.scilifelab.se/researcher/eec5f3e0d7f640f7948c4caec1f31802.json"}}, {"family": "Serrano", "given": "Alonso R", "initials": "AR", "orcid": "0000-0002-1635-6410", "researcher": {"href": "https://publications.scilifelab.se/researcher/bbb5a3f8e00542adb782f0671294f746.json"}}, {"family": "Daguerre", "given": "Yohann", "initials": "Y", "orcid": "0000-0003-4233-8926", "researcher": {"href": "https://publications.scilifelab.se/researcher/39d3e87a528b41a6b64d7d981d58f8f7.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Schneider", "given": "Andreas N", "initials": "AN", "orcid": "0000-0001-5431-955X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1859c02ba19541528bdfb9036119672c.json"}}, {"family": "Stangl", "given": "Zsofia R", "initials": "ZR"}, {"family": "Castro", "given": "David", "initials": "D", "orcid": "0000-0003-0836-6624", "researcher": {"href": "https://publications.scilifelab.se/researcher/04be48fb09cc4c868f2dbdb90e461a23.json"}}, {"family": "Grabherr", "given": "Manfred", "initials": "M", "orcid": "0000-0001-8792-6508", "researcher": {"href": "https://publications.scilifelab.se/researcher/70359af8bb7e4bd2b35d45ab7af0d7cc.json"}}, {"family": "N\u00e4sholm", "given": "Torgny", "initials": "T"}, {"family": "Street", "given": "Nathaniel R", "initials": "NR", "orcid": "0000-0001-6031-005X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb9ceb237a724046a1454179a32de1b0.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": "2022-06-28", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "issn-l": "0027-8424", "volume": "119", "issue": "26", "pages": "e2118852119"}, "abstract": "Carbon storage and cycling in boreal forests-the largest terrestrial carbon store-is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree-microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host-microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.", "doi": "10.1073/pnas.2118852119", "pmid": "35727987", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9245616"}], "notes": [], "created": "2022-06-29T12:19:10.889Z", "modified": "2024-01-16T13:48:36.106Z"}, {"entity": "publication", "iuid": "060874a4da484eb1bb146a7d3c2a60be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/060874a4da484eb1bb146a7d3c2a60be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/060874a4da484eb1bb146a7d3c2a60be"}}, "title": "MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.", "authors": [{"family": "Blixt", "given": "Maria K E", "initials": "MKE"}, {"family": "Hellsand", "given": "Minas", "initials": "M", "orcid": "0000-0002-1459-0377", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa1e2f60d8c4fcd97c54b23246f55f2.json"}}, {"family": "Konjusha", "given": "Dardan", "initials": "D", "orcid": "0000-0002-6959-8376", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfa3697dd35c422a993a87be8d50c40b.json"}}, {"family": "Zhang", "given": "Hanzhao", "initials": "H"}, {"family": "Stenfelt", "given": "Sonya", "initials": "S"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}, {"family": "Rafati", "given": "Nima", "initials": "N", "orcid": "0000-0002-3687-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/8b5c32bab72f430a80485c0312ca0e21.json"}}, {"family": "Tararuk", "given": "Tatsiana", "initials": "T"}, {"family": "St\u00e5lhammar", "given": "Gustav", "initials": "G"}, {"family": "All-Eriksson", "given": "Charlotta", "initials": "C"}, {"family": "Ring", "given": "Henrik", "initials": "H"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F", "orcid": "0000-0001-7552-187X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fd6bad55b67431c82e2e54e5b007917.json"}}], "type": "journal article", "published": "2022-06-21", "journal": {"title": "Oncogenesis", "issn": "2157-9024", "issn-l": null, "volume": "11", "issue": "1", "pages": "34"}, "abstract": "Retinoblastoma is a rare, intraocular paediatric cancer that originates in the neural retina and is most frequently caused by bi-allelic loss of RB1 gene function. Other oncogenic mutations, such as amplification and increased expression of the MYCN gene, have been found even with proficient RB1 function. In this study, we investigated whether MYCN over-expression can drive carcinogenesis independently of RB1 loss-of-function mutations. The aim was to elucidate the events that result in carcinogenesis and identify the cancer cell-of-origin. We used the chicken retina, a well-established model for studying retinal neurogenesis, and established human embryonic stem cell-derived retinal organoids as model systems. We over-expressed MYCN by electroporation of piggyBac genome-integrating expression vectors. We found that over-expression of MYCN induced tumorigenic growth with high frequency in RB1-proficient chicken retinas and human organoids. In both systems, the tumorigenic cells expressed markers for undifferentiated cone photoreceptor/horizontal cell progenitors. The over-expression resulted in metastatic retinoblastoma within 7-9 weeks in chicken. Cells expressing MYCN could be grown in vitro and, when orthotopically injected, formed tumours that infiltrated the sclera and optic nerve and expressed markers for cone progenitors. Investigation of the tumour cell phenotype determined that the potential for neoplastic growth was embryonic stage-dependent and featured a cell-specific resistance to apoptosis in the cone/horizontal cell lineage, but not in ganglion or amacrine cells. We conclude that MYCN over-expression is sufficient to drive tumorigenesis and that a cell-specific resistance to apoptosis in the cone/horizontal cell lineage mediates the cancer phenotype.", "doi": "10.1038/s41389-022-00409-3", "pmid": "35729105", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9213451"}, {"db": "pii", "key": "10.1038/s41389-022-00409-3"}], "notes": [], "created": "2022-11-09T15:38:35.302Z", "modified": "2024-01-16T13:48:36.126Z"}, {"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": "73f79f2fc206426caa16aafb578b1761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/73f79f2fc206426caa16aafb578b1761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/73f79f2fc206426caa16aafb578b1761"}}, "title": "CRISPR-Cas9 treatment partially restores amyloid-\u03b2 42/40 in human fibroblasts with the Alzheimer's disease PSEN 1 M146L mutation.", "authors": [{"family": "Konstantinidis", "given": "Evangelos", "initials": "E"}, {"family": "Molisak", "given": "Agnieszka", "initials": "A"}, {"family": "Perrin", "given": "Florian", "initials": "F"}, {"family": "Streubel-Gallasch", "given": "Linn", "initials": "L"}, {"family": "Fayad", "given": "Sarah", "initials": "S"}, {"family": "Kim", "given": "Daniel Y", "initials": "DY"}, {"family": "Petri", "given": "Karl", "initials": "K"}, {"family": "Aryee", "given": "Martin J", "initials": "MJ"}, {"family": "Aguilar", "given": "Ximena", "initials": "X"}, {"family": "Gy\u00f6rgy", "given": "Bence", "initials": "B"}, {"family": "Giedraitis", "given": "Vilmantas", "initials": "V"}, {"family": "Joung", "given": "J Keith", "initials": "JK"}, {"family": "Pattanayak", "given": "Vikram", "initials": "V"}, {"family": "Essand", "given": "Magnus", "initials": "M"}, {"family": "Erlandsson", "given": "Anna", "initials": "A"}, {"family": "Berezovska", "given": "Oksana", "initials": "O"}, {"family": "Ingelsson", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2022-06-14", "journal": {"title": "Mol Ther Nucleic Acids", "issn": "2162-2531", "volume": "28", "pages": "450-461", "issn-l": "2162-2531"}, "abstract": "Presenilin 1 (PS1) is a central component of \u03b3-secretase, an enzymatic complex involved in the generation of the amyloid-\u03b2 (A\u03b2) peptide that deposits as plaques in the Alzheimer's disease (AD) brain. The M146L mutation in the PS1 gene (PSEN1) leads to an autosomal dominant form of early-onset AD by promoting a relative increase in the generation of the more aggregation-prone A\u03b242. This change is evident not only in the brain but also in peripheral cells of mutation carriers. In this study we used the CRISPR-Cas9 system from Streptococcus pyogenes to selectively disrupt the PSEN1 allele in human fibroblasts. A disruption of more than 50% of mutant alleles was observed in all CRISPR-Cas9-treated samples, resulting in reduced extracellular A\u03b242/40 ratios. Fluorescence resonance energy transfer-based conformation and western blot analyses indicated that CRISPR-Cas9 treatment also affects the overall PS1 conformation and reduces PS1 levels. Moreover, our guide RNA did not lead to any detectable editing at the highest-ranking candidate off-target sites identified by ONE-seq and CIRCLE-seq. Overall, our data support the effectiveness of CRISPR-Cas9 in selectively targeting the M146LPSEN1 allele and counteracting the AD-associated phenotype. We believe that this system could be developed into a therapeutic strategy for patients with this and other dominant mutations leading to early-onset AD.M146L", "doi": "10.1016/j.omtn.2022.03.022", "pmid": "35505961", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9043867"}, {"db": "pii", "key": "S2162-2531(22)00071-3"}], "notes": [], "created": "2022-11-28T10:49:45.806Z", "modified": "2022-11-28T10:49:45.810Z"}, {"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": "93a04540a4c2419ca466a44ebbe062b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93a04540a4c2419ca466a44ebbe062b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93a04540a4c2419ca466a44ebbe062b8"}}, "title": "The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.", "authors": [{"family": "Ma", "given": "Lijiang", "initials": "L", "orcid": "0000-0001-6498-5556", "researcher": {"href": "https://publications.scilifelab.se/researcher/f000e91a6c8c4ab081846c120683edc2.json"}}, {"family": "Bryce", "given": "Nicole S", "initials": "NS", "orcid": "0000-0001-9799-7393", "researcher": {"href": "https://publications.scilifelab.se/researcher/78e70822e0584633874053649f608dd1.json"}}, {"family": "Turner", "given": "Adam W", "initials": "AW"}, {"family": "Di Narzo", "given": "Antonio F", "initials": "AF", "orcid": "0000-0002-4033-5038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c826b7a4f7cb446cb60410e167150312.json"}}, {"family": "Rahman", "given": "Karishma", "initials": "K", "orcid": "0000-0002-7675-9596", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fa895ec4c8449b0b6e0841259ab7101.json"}}, {"family": "Xu", "given": "Yang", "initials": "Y", "orcid": "0000-0003-4669-0003", "researcher": {"href": "https://publications.scilifelab.se/researcher/0b571d6393af4cacbc53cf9208201266.json"}}, {"family": "Ermel", "given": "Raili", "initials": "R"}, {"family": "Sukhavasi", "given": "Katyayani", "initials": "K", "orcid": "0000-0001-5627-0163", "researcher": {"href": "https://publications.scilifelab.se/researcher/147dcf0d2b604e219e5b9b5cd7089a55.json"}}, {"family": "d'Escamard", "given": "Valentina", "initials": "V"}, {"family": "Chandel", "given": "Nirupama", "initials": "N"}, {"family": "V'Gangula", "given": "Bhargavi", "initials": "B"}, {"family": "Wolhuter", "given": "Kathryn", "initials": "K", "orcid": "0000-0001-6293-9820", "researcher": {"href": "https://publications.scilifelab.se/researcher/363b5011d58d412290824444e3e51399.json"}}, {"family": "Kadian-Dodov", "given": "Daniella", "initials": "D"}, {"family": "Franzen", "given": "Oscar", "initials": "O"}, {"family": "Ruusalepp", "given": "Arno", "initials": "A"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Miller", "given": "Clint L", "initials": "CL", "orcid": "0000-0003-4276-3607", "researcher": {"href": "https://publications.scilifelab.se/researcher/f126f09351544045a13bae1ff4391e78.json"}}, {"family": "Bj\u00f6rkegren", "given": "Johan L M", "initials": "JLM"}, {"family": "Kovacic", "given": "Jason C", "initials": "JC", "orcid": "0000-0003-4555-769X", "researcher": {"href": "https://publications.scilifelab.se/researcher/caefcca7394142918b01b3660da6551d.json"}}], "type": "journal article", "published": "2022-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "18", "issue": "6", "pages": "e1010261", "issn-l": "1553-7390"}, "abstract": "Genome wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of common disorders. However, since the large majority of these risk SNPs reside outside gene-coding regions, GWAS generally provide no information about causal mechanisms regarding the specific gene(s) that are affected or the tissue(s) in which these candidate gene(s) exert their effect. The 'gold standard' method for understanding causal genes and their mechanisms of action are laborious basic science studies often involving sophisticated knockin or knockout mouse lines, however, these types of studies are impractical as a high-throughput means to understand the many risk variants that cause complex diseases like coronary artery disease (CAD). As a solution, we developed a streamlined, data-driven informatics pipeline to gain mechanistic insights on complex genetic loci. The pipeline begins by understanding the SNPs in a given locus in terms of their relative location and linkage disequilibrium relationships, and then identifies nearby expression quantitative trait loci (eQTLs) to determine their relative independence and the likely tissues that mediate their disease-causal effects. The pipeline then seeks to understand associations with other disease-relevant genes, disease sub-phenotypes, potential causality (Mendelian randomization), and the regulatory and functional involvement of these genes in gene regulatory co-expression networks (GRNs). Here, we applied this pipeline to understand a cluster of SNPs associated with CAD within and immediately adjacent to the gene encoding HDAC9. Our pipeline demonstrated, and validated, that this locus is causal for CAD by modulation of TWIST1 expression levels in the arterial wall, and by also governing a GRN related to metabolic function in skeletal muscle. Our results reconciled numerous prior studies, and also provided clear evidence that this locus does not govern HDAC9 expression, structure or function. This pipeline should be considered as a powerful and efficient way to understand GWAS risk loci in a manner that better reflects the highly complex nature of genetic risk associated with common disorders.", "doi": "10.1371/journal.pgen.1010261", "pmid": "35714152", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9246173"}, {"db": "pii", "key": "PGENETICS-D-21-01392"}], "notes": [], "created": "2022-11-29T12:12:39.019Z", "modified": "2022-11-29T12:12:39.361Z"}, {"entity": "publication", "iuid": "0b04ba3887a041eab29ed76faa76295d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b04ba3887a041eab29ed76faa76295d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b04ba3887a041eab29ed76faa76295d"}}, "title": "Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R", "orcid": "0000-0002-2283-786X", "researcher": {"href": "https://publications.scilifelab.se/researcher/12601745d2c74562bf83d22879f212eb.json"}}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Biloglav", "given": "Andrea", "initials": "A"}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Paulsson", "given": "Kajsa", "initials": "K", "orcid": "0000-0001-7950-222X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2033b23811f1432c90ad860dd993e7a8.json"}}, {"family": "Johansson", "given": "Bertil", "initials": "B"}], "type": "letter", "published": "2022-06-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "volume": "36", "issue": "6", "pages": "1681-1684", "issn-l": "0887-6924"}, "abstract": null, "doi": "10.1038/s41375-022-01552-x", "pmid": "35365774", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9162923"}, {"db": "pii", "key": "10.1038/s41375-022-01552-x"}], "notes": [], "created": "2022-11-29T09:20:02.714Z", "modified": "2022-11-29T09:20:02.768Z"}, {"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": "c2b2bd4639fc4fee871c6ab8e77b0a9f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2b2bd4639fc4fee871c6ab8e77b0a9f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2b2bd4639fc4fee871c6ab8e77b0a9f"}}, "title": "Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.", "authors": [{"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Boroffka", "given": "Nikolaus", "initials": "N"}, {"family": "Schr\u00f6der", "given": "Oskar", "initials": "O"}, {"family": "Sverchkov", "given": "Leonid", "initials": "L"}, {"family": "Benecke", "given": "Norbert", "initials": "N"}, {"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": "2022-06-00", "journal": {"title": "R. Soc. open sci.", "issn": "2054-5703", "volume": "9", "issue": "6", "pages": "220104", "issn-l": "2054-5703"}, "abstract": "Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, supporting hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data do represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.", "doi": "10.1098/rsos.220104", "pmid": "35719876", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9198508"}, {"db": "pii", "key": "rsos220104"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.6024060"}], "notes": [], "created": "2022-11-29T12:33:09.400Z", "modified": "2024-01-16T13:48:36.352Z"}, {"entity": "publication", "iuid": "304b49e6219a4beb9a932d515c6e1453", "links": {"self": {"href": "https://publications.scilifelab.se/publication/304b49e6219a4beb9a932d515c6e1453.json"}, "display": {"href": "https://publications.scilifelab.se/publication/304b49e6219a4beb9a932d515c6e1453"}}, "title": "Development of gut microbiota during the first 2 years of life.", "authors": [{"family": "Wernroth", "given": "Mona-Lisa", "initials": "ML"}, {"family": "Peura", "given": "Sari", "initials": "S"}, {"family": "Hedman", "given": "Anna M", "initials": "AM"}, {"family": "Hetty", "given": "Susanne", "initials": "S"}, {"family": "Vicenzi", "given": "Silvia", "initials": "S"}, {"family": "Kennedy", "given": "Beatrice", "initials": "B"}, {"family": "Fall", "given": "Katja", "initials": "K"}, {"family": "Svennblad", "given": "Bodil", "initials": "B"}, {"family": "Andolf", "given": "Ellika", "initials": "E"}, {"family": "Pershagen", "given": "G\u00f6ran", "initials": "G"}, {"family": "Theorell-Hagl\u00f6w", "given": "Jenny", "initials": "J"}, {"family": "Nguyen", "given": "Diem", "initials": "D"}, {"family": "Sayols-Baixeras", "given": "Sergi", "initials": "S"}, {"family": "Dekkers", "given": "Koen F", "initials": "KF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Almqvist", "given": "Catarina", "initials": "C"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Fall", "given": "Tove", "initials": "T"}], "type": "journal article", "published": "2022-05-31", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "12", "issue": "1", "pages": "9080"}, "abstract": "Although development of microbiota in childhood has been linked to chronic immune-related conditions, early childhood determinants of microbiota development have not been fully elucidated. We used 16S rRNA sequencing to analyse faecal and saliva samples from 83 children at four time-points during their first 2 years of life and from their mothers. Our findings confirm that gut microbiota in infants have low diversity and highlight that some properties are shared with the oral microbiota, although inter-individual differences are present. A considerable convergence in gut microbiota composition was noted across the first 2 years of life, towards a more diverse adult-like microbiota. Mode of delivery accounted for some of the inter-individual variation in early childhood, but with a pronounced attenuation over time. Our study extends previous research with further characterization of the major shift in gut microbiota composition during the first 2 years of life.", "doi": "10.1038/s41598-022-13009-3", "pmid": "35641542", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-022-13009-3"}, {"db": "pmc", "key": "PMC9156670"}], "notes": [], "created": "2022-06-03T06:21:52.597Z", "modified": "2024-01-16T13:48:36.379Z"}, {"entity": "publication", "iuid": "265d3081559d435081d2d22b8a2e97da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/265d3081559d435081d2d22b8a2e97da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/265d3081559d435081d2d22b8a2e97da"}}, "title": "An empirical evaluation of genotype imputation of ancient DNA.", "authors": [{"family": "Ausmees", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-6212-539X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d6a0fd5017647a7acb70bf4c667c73e.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications.scilifelab.se/researcher/c300f2900aff429d8a3bbc72ee006df7.json"}}], "type": "journal article", "published": "2022-05-30", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "12", "issue": "6", "issn-l": "2160-1836"}, "abstract": "With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1\u00d7 coverage, and similar levels of accuracy and reference bias at levels as low as 0.75\u00d7. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1\u00d7. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.", "doi": "10.1093/g3journal/jkac089", "pmid": "35482488", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9157144"}, {"db": "pii", "key": "6575448"}], "notes": [], "created": "2022-11-29T09:07:08.055Z", "modified": "2024-01-16T13:48:36.386Z"}, {"entity": "publication", "iuid": "bc12467f5df540deb9a014812f7caf7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc12467f5df540deb9a014812f7caf7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc12467f5df540deb9a014812f7caf7d"}}, "title": "Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.", "authors": [{"family": "Fineschi", "given": "Serena", "initials": "S"}, {"family": "Klar", "given": "Joakim", "initials": "J"}, {"family": "Gustafsson", "given": "Kristin Ayoola", "initials": "KA"}, {"family": "Jonsson", "given": "Kent", "initials": "K"}, {"family": "Karlsson", "given": "Bo", "initials": "B"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2022-05-26", "journal": {"title": "Front Immunol", "issn": "1664-3224", "volume": "13", "pages": "874490", "issn-l": "1664-3224"}, "abstract": "Fibromyalgia (FM) is an idiopathic chronic disease characterized by widespread musculoskeletal pain, hyperalgesia and allodynia, often accompanied by fatigue, cognitive dysfunction and other symptoms. Autoimmunity and neuroinflammatory mechanisms have been suggested to play important roles in the pathophysiology of FM supported by recently identified interferon signatures in affected individuals. However, the contribution of different components in the immune system, such as the B-lymphocytes, in the progression to FM are yet unknown. Furthermore, there is a great need for biomarkers that may improve diagnostics of FM. Herein, we investigated the gene expression profile in peripheral B-cells, as well as a panel of inflammatory serum proteins, in 30 FM patients and 23 healthy matched control individuals. RNA sequence analysis revealed 60 differentially expressed genes when comparing the two groups. The group of FM patients showed increased expression of twenty-five interferon-regulated genes, such as S100A8 and S100A9, VCAM, CD163, SERPINA1, ANXA1, and an increased interferon score. Furthermore, FM was associated with elevated levels of 19 inflammatory serum proteins, such as IL8, AXIN1, SIRT2 and STAMBP, that correlated with the FM severity score. Together, the results shows that FM is associated with an interferon signature in B-cells and increased levels of a set of inflammatory serum proteins. Our findings bring further support for immune activation in the pathogenesis of FM and highlight candidate biomarkers for diagnosis and intervention in the management of FM.", "doi": "10.3389/fimmu.2022.874490", "pmid": "35693781", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "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": "PMC9177944"}], "notes": [], "created": "2022-06-13T14:53:56.387Z", "modified": "2024-01-16T13:48:36.443Z"}, {"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": "585a9c3c56ab443caaaccac60747db0f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/585a9c3c56ab443caaaccac60747db0f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/585a9c3c56ab443caaaccac60747db0f"}}, "title": "Quantitative Analysis of the Transcriptome of Two Commonly Used Human Monocytic Cell Lines-THP-1 and Mono Mac 6-Reveals Their Arrest during Early Monocyte/Neutrophil Differentiation.", "authors": [{"family": "Akula", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-6628-1640", "researcher": {"href": "https://publications.scilifelab.se/researcher/22e673e8a5b945509424e84b5f75ba7f.json"}}, {"family": "Lara", "given": "Sandra", "initials": "S", "orcid": "0000-0002-1637-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/35660d640cca4c2c87dbed84ff0501f0.json"}}, {"family": "Olsson", "given": "Anna-Karin", "initials": "AK"}, {"family": "Hellman", "given": "Lars", "initials": "L", "orcid": "0000-0003-1459-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7048f04e30642889d744fb42420fd88.json"}}], "type": "journal article", "published": "2022-05-22", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "23", "issue": "10", "issn-l": null}, "abstract": "Cell lines of monocyte/macrophage origin are often used as model systems to study monocyte/macrophage biology. A relevant question is how similar these cell lines are to their in vivo counterparts? To address this issue, we performed a detailed analysis of the transcriptome of two commonly used human monocyte/macrophage cell lines, Mono Mac 6 and THP-1. Both of these cell lines originate from leukemic cells with myelo-monocytic characteristics. We found that both Mono Mac 6 and THP-1 represent cells of very immature origin. Their transcriptomes show more similarities to immature neutrophils than cells of the monocyte/macrophage lineage. They express significant levels of N-elastase, proteinase 3, cathepsin G, and azurocidin but very low levels of CD14, ficolin, and complement factor P. All major MHC class II genes are also expressed at low levels. They show high levels of lysozyme and low levels of one of the immunoglobulin Fc receptors, FCGRIIA, which is characteristic of both neutrophils and monocytes. THP-1, but not Mono Mac 6, also expresses the high-affinity receptor for IgG, FCGRIA. Both cell lines lack the expression of the connective tissue components fibronectin, proteoglycan 4, and syndecan 3, which are characteristics of tissue macrophages but are absent in blood monocytes, indicating that they originate from bone marrow precursors and not yolk sac-derived hematopoietic cells. Both of these cell lines seem, therefore, to represent cells arrested during early myelo-monocytic development, at a branch point between neutrophil and monocyte differentiation. Their very immature phenotype indicates that great care should be taken when using these cell lines as models for normal monocyte/macrophage biology.", "doi": "10.3390/ijms23105818", "pmid": "35628628", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "ijms23105818"}, {"db": "pmc", "key": "PMC9145822"}], "notes": [], "created": "2022-09-05T07:15:13.414Z", "modified": "2022-09-05T07:15:13.535Z"}, {"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": "25a29e9b946b4f01b58409c5d20272c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/25a29e9b946b4f01b58409c5d20272c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/25a29e9b946b4f01b58409c5d20272c4"}}, "title": "Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.", "authors": [{"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Radersma", "given": "Reinder", "initials": "R"}, {"family": "Vasquez", "given": "Louella", "initials": "L"}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Tobi", "given": "Elmar W", "initials": "EW"}, {"family": "Heijmans", "given": "Bastiaan T", "initials": "BT"}, {"family": "Uller", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2022-05-20", "journal": {"title": "iScience", "issn": "2589-0042", "issn-l": "2589-0042", "volume": "25", "issue": "5", "pages": "104303"}, "abstract": "Transgenerational inheritance of environmentally induced epigenetic marks can have significant impacts on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. We used whole-genome bisulfite sequencing of individual water fleas (Daphnia magna) to assess whether environmentally induced DNA methylation is transgenerationally inherited. Genetically identical females were exposed to one of three natural stressors, or a de-methylating drug, and their offspring were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) in F1 individuals whose mothers were exposed to a natural stressor. Roughly half of these environmentally induced DMPs persisted until generation F4. In contrast, treatment with the drug demonstrated that pervasive hypomethylation upon exposure is reset almost completely after one generation. These results suggest that environmentally induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of freshwater communities.", "doi": "10.1016/j.isci.2022.104303", "pmid": "35573201", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Short read": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S2589-0042(22)00573-9"}, {"db": "pmc", "key": "PMC9097707"}, {"db": "Dryad", "key": "10.5061/dryad.f4qrfj6xq"}], "notes": [], "created": "2022-05-06T10:42:50.020Z", "modified": "2024-01-16T13:48:36.473Z"}, {"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": "a037a3c54c4049f5abc112ffb15baca4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a037a3c54c4049f5abc112ffb15baca4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a037a3c54c4049f5abc112ffb15baca4"}}, "title": "Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro.", "authors": [{"family": "Dube", "given": "Faruk", "initials": "F", "orcid": "0000-0003-1340-9123", "researcher": {"href": "https://publications.scilifelab.se/researcher/efd709b6ebf04946bf70f1ab4c8c5cbf.json"}}, {"family": "Hinas", "given": "Andrea", "initials": "A"}, {"family": "Roy", "given": "Shweta", "initials": "S"}, {"family": "Martin", "given": "Frida", "initials": "F"}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M"}, {"family": "Sv\u00e4rd", "given": "Staffan", "initials": "S"}, {"family": "Tyd\u00e9n", "given": "Eva", "initials": "E"}], "type": "journal article", "published": "2022-05-05", "journal": {"title": "Parasit Vectors", "issn": "1756-3305", "volume": "15", "issue": "1", "pages": "158", "issn-l": "1756-3305"}, "abstract": "The nematode Parascaris univalens is one of the most prevalent parasitic pathogens infecting horses but anthelmintic resistance undermines treatment approaches. The molecular mechanisms underlying drug activity and resistance remain poorly understood in this parasite since experimental in vitro models are lacking. The aim of this study was to evaluate the use of Caenorhabditis elegans as a model for P. univalens drug metabolism/resistance studies by a comparative gene expression approach after in vitro exposure to the anthelmintic drug ivermectin (IVM).\n\nTwelve adult P. univalens worms in groups of three were exposed to ivermectin (IVM, 10-13 M, 10-11 M, 10-9 M) or left unexposed for 24 h at 37 \u00b0C, and total RNA, extracted from the anterior end of the worms, was sequenced using Illumina NovaSeq. Differentially expressed genes (DEGs) involved in metabolism, transportation, or gene expression with annotated Caernorhabditis elegans orthologues were identified as candidate genes to be involved in IVM metabolism/resistance. Similarly, groups of 300 adult C. elegans worms were exposed to IVM (10-9 M, 10-8 M and 10-7 M) or left unexposed for 4 h at 20 \u00b0C. Quantitative RT-PCR of RNA extracted from the C. elegans worm pools was used to compare against the expression of selected P. univalens candidate genes after drug treatment.\n\nAfter IVM exposure, 1085 DEGs were found in adult P. univalens worms but the relative gene expression changes were small and large variabilities were found between different worms. Fifteen of the DEGs were chosen for further characterization in C. elegans after comparative bioinformatics analyses. Candidate genes, including the putative drug target lgc-37, responded to IVM in P. univalens, but marginal to no responses were observed in C. elegans despite dose-dependent behavioral effects observed in C. elegans after IVM exposure. Thus, the overlap in IVM-induced gene expression in this small set of genes was minor in adult worms of the two nematode species.\n\nThis is the first time to our knowledge that a comparative gene expression approach has evaluated C. elegans as a model to understand IVM metabolism/resistance in P. univalens. Genes in P. univalens adults that responded to IVM treatment were identified. However, identifying conserved genes in P. univalens and C. elegans involved in IVM metabolism/resistance by comparing gene expression of candidate genes proved challenging. The approach appears promising but was limited by the number of genes studied (n = 15). Future studies comparing a larger number of genes between the two species may result in identification of additional candidate genes involved in drug metabolism and/or resistance.", "doi": "10.1186/s13071-022-05260-4", "pmid": "35513885", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9074254"}, {"db": "pii", "key": "10.1186/s13071-022-05260-4"}], "notes": [], "created": "2022-11-29T12:03:10.370Z", "modified": "2024-01-16T13:48:36.731Z"}, {"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": "959380267d6149ad8c41e56a069865c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/959380267d6149ad8c41e56a069865c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/959380267d6149ad8c41e56a069865c6"}}, "title": "Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.", "authors": [{"family": "Darolti", "given": "Iulia", "initials": "I"}, {"family": "Almeida", "given": "Pedro", "initials": "P"}, {"family": "Wright", "given": "Alison E", "initials": "AE"}, {"family": "Mank", "given": "Judith E", "initials": "JE", "orcid": "0000-0002-2450-513X", "researcher": {"href": "https://publications.scilifelab.se/researcher/42f3e1ac3beb4d9cb0c6687ec7d94c68.json"}}], "type": "journal article", "published": "2022-05-04", "journal": {"title": "J. Evol. Biol.", "issn": "1420-9101", "issn-l": "1010-061X", "volume": "35", "issue": "12", "pages": "1646-1658"}, "abstract": "Studies of sex chromosome systems at early stages of divergence are key to understanding the initial process and underlying causes of recombination suppression. However, identifying signatures of divergence in homomorphic sex chromosomes can be challenging due to high levels of sequence similarity between the X and the Y. Variations in methodological precision and underlying data can make all the difference between detecting subtle divergence patterns or missing them entirely. Recent efforts to test for X-Y sequence differentiation in the guppy have led to contradictory results. Here, we apply different analytical methodologies to the same data set to test for the accuracy of different approaches in identifying patterns of sex chromosome divergence in the guppy. Our comparative analysis reveals that the most substantial source of variation in the results of the different analyses lies in the reference genome used. Analyses using custom-made genome assemblies for the focal population or species successfully recover a signal of divergence across different methodological approaches. By contrast, using the distantly related Xiphophorus reference genome results in variable patterns, due to both sequence evolution and structural variations on the sex chromosomes between the guppy and Xiphophorus. Changes in mapping and filtering parameters can additionally introduce noise and obscure the signal. Our results illustrate how analytical differences can alter perceived results and we highlight best practices for the study of nascent sex chromosomes.", "doi": "10.1111/jeb.14013", "pmid": "35506576", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-29T11:58:52.373Z", "modified": "2022-12-07T08:53:17.615Z"}, {"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": "28a281acd45f4ed7a0999df336aa4840", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28a281acd45f4ed7a0999df336aa4840.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28a281acd45f4ed7a0999df336aa4840"}}, "title": "Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.", "authors": [{"family": "Rojas", "given": "Laura", "initials": "L"}, {"family": "Gr\u00fcttner", "given": "Jana", "initials": "J"}, {"family": "Ma'ayeh", "given": "Showgy", "initials": "S"}, {"family": "Xu", "given": "Feifei", "initials": "F"}, {"family": "Sv\u00e4rd", "given": "Staffan G", "initials": "SG"}], "type": "journal article", "published": "2022-04-27", "journal": {"title": "Front. Cell. Infect. Microbiol.", "issn": "2235-2988", "volume": "12", "pages": "862211", "issn-l": "2235-2988"}, "abstract": "Giardia intestinalis is a protozoan parasite causing diarrheal disease, giardiasis, after extracellular infection of humans and other mammals' intestinal epithelial cells (IECs) of the upper small intestine. The parasite has two main life cycle stages: replicative trophozoites and transmissive cysts. Differentiating parasites (encysting cells) and trophozoites have recently been shown to be present in the same regions of the upper small intestine, whereas most mature cysts are found further down in the intestinal system. To learn more about host-parasite interactions during Giardia infections, we used an in vitro model of the parasite's interaction with host IECs (differentiated Caco-2 cells) and Giardia WB trophozoites, early encysting cells (7 h), and cysts. Dual RNA sequencing (Dual RNAseq) was used to identify differentially expressed genes (DEGs) in both Giardia and the IECs, which might relate to establishing infection and disease induction. In the human cells, the largest gene expression changes were found in immune and MAPK signaling, transcriptional regulation, apoptosis, cholesterol metabolism and oxidative stress. The different life cycle stages of Giardia induced a core of similar DEGs but at different levels and there are many life cycle stage-specific DEGs. The metabolic protein PCK1, the transcription factors HES7, HEY1 and JUN, the peptide hormone CCK and the mucins MUC2 and MUC5A are up-regulated in the IECs by trophozoites but not cysts. Cysts specifically induce the chemokines CCL4L2, CCL5 and CXCL5, the signaling protein TRKA and the anti-bacterial protein WFDC12. The parasite, in turn, up-regulated a large number of hypothetical genes, high cysteine membrane proteins (HCMPs) and oxidative stress response genes. Early encysting cells have unique DEGs compared to trophozoites (e.g. several uniquely up-regulated HCMPs) and interaction of these cells with IECs affected the encystation process. Our data show that different life cycle stages of Giardia induce different gene expression responses in the host cells and that the IECs in turn differentially affect the gene expression in trophozoites and early encysting cells. This life cycle stage-specific host-parasite cross-talk is an important aspect to consider during further studies of Giardia's molecular pathogenesis.", "doi": "10.3389/fcimb.2022.862211", "pmid": "35573800", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9094438"}], "notes": [], "created": "2022-11-29T12:13:42.089Z", "modified": "2022-11-29T12:13:42.093Z"}, {"entity": "publication", "iuid": "d42d2a62ff4a4fd492c94539d79ed06f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d42d2a62ff4a4fd492c94539d79ed06f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d42d2a62ff4a4fd492c94539d79ed06f"}}, "title": "Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.", "authors": [{"family": "Lu", "given": "Xi", "initials": "X", "orcid": "0000-0002-1650-9974", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2fc905a0497492c964e10e0f1f82f4c.json"}}, {"family": "Maturi", "given": "Naga Prathyusha", "initials": "NP", "orcid": "0000-0002-7726-8617", "researcher": {"href": "https://publications.scilifelab.se/researcher/12f69dfe618f48c9bd4aa6075525975c.json"}}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Yildirim", "given": "Irem", "initials": "I", "orcid": "0000-0003-3602-5544", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29421803962496880443d5772f4c97a.json"}}, {"family": "Dang", "given": "Yonglong", "initials": "Y"}, {"family": "Zhao", "given": "Linxuan", "initials": "L"}, {"family": "Xie", "given": "Yuan", "initials": "Y"}, {"family": "Tan", "given": "E-Jean", "initials": "EJ", "orcid": "0000-0002-4631-174X", "researcher": {"href": "https://publications.scilifelab.se/researcher/03d12f8cf5714430a7297ed0c3f0e1f6.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Uhrbom", "given": "Lene", "initials": "L", "orcid": "0000-0001-8595-5698", "researcher": {"href": "https://publications.scilifelab.se/researcher/67bb8672ad514a9bb5f86c8d6b494269.json"}}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef7ddc09e57745909175e41ac2d1b647.json"}}], "type": "journal article", "published": "2022-04-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "13", "issue": "1", "pages": "2236", "issn-l": "2041-1723"}, "abstract": "There is ample support for developmental regulation of glioblastoma stem cells. To examine how cell lineage controls glioblastoma stem cell function, we present a cross-species epigenome analysis of mouse and human glioblastoma stem cells. We analyze and compare the chromatin-accessibility landscape of nine mouse glioblastoma stem cell cultures of three defined origins and 60 patient-derived glioblastoma stem cell cultures by assay for transposase-accessible chromatin using sequencing. This separates the mouse cultures according to cell of origin and identifies three human glioblastoma stem cell clusters that show overlapping characteristics with each of the mouse groups, and a distribution along an axis of proneural to mesenchymal phenotypes. The epigenetic-based human glioblastoma stem cell clusters display distinct functional properties and can separate patient survival. Cross-species analyses reveals conserved epigenetic regulation of mouse and human glioblastoma stem cells. We conclude that epigenetic control of glioblastoma stem cells primarily is dictated by developmental origin which impacts clinically relevant glioblastoma stem cell properties and patient survival.", "doi": "10.1038/s41467-022-29912-2", "pmid": "35469026", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-022-29912-2"}], "notes": [], "created": "2022-04-29T09:50:33.950Z", "modified": "2022-04-29T09:50:34.131Z"}, {"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": "3607abce5d57420abd7f4b3689913959", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3607abce5d57420abd7f4b3689913959.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3607abce5d57420abd7f4b3689913959"}}, "title": "Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.", "authors": [{"family": "Shakeri Yekta", "given": "Sepehr", "initials": "S"}, {"family": "Elreedy", "given": "Ahmed", "initials": "A"}, {"family": "Liu", "given": "Tong", "initials": "T"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Isaksson", "given": "Simon", "initials": "S"}, {"family": "Fujii", "given": "Manabu", "initials": "M"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2022-04-15", "journal": {"title": "Sci. Total Environ.", "issn": "1879-1026", "issn-l": "0048-9697", "volume": "817", "issue": null, "pages": "152967"}, "abstract": "This study aims to elucidate the role of sulfide and its precursors in anaerobic digestion (i.e., cysteine, representing sulfur-containing amino acids, and sulfate) on microbial oleate conversion to methane. Serine, with a similar structure to cysteine but with a hydroxyl group instead of a thiol, was included as a control to assess potential effects on methane formation that were not related to sulfur functionalities. The results showed that copresence of sulfide and oleate in anaerobic batch assays accelerated the methane formation compared to assays with only oleate and mitigated negative effect on methane formation caused by increased sulfide level. Nuclear magnetic resonance spectroscopy of sulfide-exposed oleate suggested that sulfide reaction with oleate double bonds likely contributed to negation of the negative effect on the methanogenic activity. Methane formation from oleate was also accelerated in the presence of cysteine or serine, while sulfate decreased the cumulative methane formation from oleate. Neither cysteine nor serine was converted to methane, and their accelerating effects was associated to different mechanisms due to establishment of microbial communities with different structures, as evidenced by high-throughput sequencing of 16S rRNA gene. These outcomes contribute with new knowledge to develop strategies for optimum use of sulfur- and lipid-rich wastes in anaerobic digestion processes.", "doi": "10.1016/j.scitotenv.2022.152967", "pmid": "35016947", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0048-9697(22)00056-0"}], "notes": [], "created": "2022-01-13T16:12:31.063Z", "modified": "2025-10-17T13:03:54.839Z"}, {"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": "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": "d43e6d14232747caa43602a9dbe3b086", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d43e6d14232747caa43602a9dbe3b086.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d43e6d14232747caa43602a9dbe3b086"}}, "title": "Inflammation and neutrophil extracellular traps in cerebral cavernous malformation.", "authors": [{"family": "Yau", "given": "Anthony C Y", "initials": "ACY", "orcid": "0000-0002-1570-7813", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d050ac252ce4b8e82ae73ed9f4aa6b4.json"}}, {"family": "Globisch", "given": "Maria Ascencion", "initials": "MA", "orcid": "0000-0002-2251-9810", "researcher": {"href": "https://publications.scilifelab.se/researcher/eec1b44eb73f410f8c27f642ec061a67.json"}}, {"family": "Onyeogaziri", "given": "Favour Chinyere", "initials": "FC"}, {"family": "Conze", "given": "Lei L", "initials": "LL", "orcid": "0000-0001-8698-3842", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff4ce9ba49a5461f9247f3d1220bed18.json"}}, {"family": "Smith", "given": "Ross", "initials": "R", "orcid": "0000-0003-4239-3204", "researcher": {"href": "https://publications.scilifelab.se/researcher/a464f28ad47c4706a08645b9616198b7.json"}}, {"family": "Jauhiainen", "given": "Suvi", "initials": "S"}, {"family": "Corada", "given": "Monica", "initials": "M", "orcid": "0000-0001-8220-0871", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e75cbe437524e2d87d202eaefc0ccca.json"}}, {"family": "Orsenigo", "given": "Fabrizio", "initials": "F", "orcid": "0000-0001-9135-8478", "researcher": {"href": "https://publications.scilifelab.se/researcher/f03f2f483b8f491582245a256bef8ccb.json"}}, {"family": "Huang", "given": "Hua", "initials": "H", "orcid": "0000-0002-0914-6562", "researcher": {"href": "https://publications.scilifelab.se/researcher/35186228c92646e891ea31b4cf65a577.json"}}, {"family": "Herre", "given": "Melanie", "initials": "M"}, {"family": "Olsson", "given": "Anna-Karin", "initials": "AK", "orcid": "0000-0002-5438-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/57ec91022afd4c1390433d6383a06fc0.json"}}, {"family": "Malinverno", "given": "Matteo", "initials": "M", "orcid": "0000-0001-8242-7937", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb8715aae8fe48f6b2cbacb997401749.json"}}, {"family": "Sundell", "given": "Veronica", "initials": "V"}, {"family": "Rezai Jahromi", "given": "Behnam", "initials": "B", "orcid": "0000-0003-3937-2816", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b1eedb302484555b1451aa283157a04.json"}}, {"family": "Niemel\u00e4", "given": "Mika", "initials": "M", "orcid": "0000-0003-1526-0684", "researcher": {"href": "https://publications.scilifelab.se/researcher/41d032a4f170424f8c24657bb282a48e.json"}}, {"family": "Laakso", "given": "Aki", "initials": "A", "orcid": "0000-0002-5312-4926", "researcher": {"href": "https://publications.scilifelab.se/researcher/d34aba099f9044c88997da8ab113a7c2.json"}}, {"family": "Garlanda", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-1510-7703", "researcher": {"href": "https://publications.scilifelab.se/researcher/c40dc1a52b364e2194ac072873d5efc9.json"}}, {"family": "Mantovani", "given": "Alberto", "initials": "A", "orcid": "0000-0001-5578-236X", "researcher": {"href": "https://publications.scilifelab.se/researcher/99eeed4b00c6456d8d4fc1b6832f677b.json"}}, {"family": "Lampugnani", "given": "Maria Grazia", "initials": "MG", "orcid": "0000-0002-4802-7064", "researcher": {"href": "https://publications.scilifelab.se/researcher/9aca420b37904fceac0b4bbc7f634c70.json"}}, {"family": "Dejana", "given": "Elisabetta", "initials": "E", "orcid": "0000-0002-0007-0426", "researcher": {"href": "https://publications.scilifelab.se/researcher/44cc4a690a194c5bbc2193213c98c5e1.json"}}, {"family": "Magnusson", "given": "Peetra U", "initials": "PU", "orcid": "0000-0003-1142-854X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b1a74b677b145fc81a2d4bd7f3bf498.json"}}], "type": "journal article", "published": "2022-03-25", "journal": {"title": "Cell. Mol. Life Sci.", "issn": "1420-9071", "volume": "79", "issue": "4", "pages": "206", "issn-l": "1420-682X"}, "abstract": "Cerebral Cavernous Malformation (CCM) is a brain vascular disease with various neurological symptoms. In this study, we describe the inflammatory profile in CCM and show for the first time the formation of neutrophil extracellular traps (NETs) in rodents and humans with CCM. Through RNA-seq analysis of cerebellum endothelial cells from wild-type mice and mice with an endothelial cell-specific ablation of the Ccm3 gene (Ccm3iECKO), we show that endothelial cells from Ccm3iECKO mice have an increased expression of inflammation-related genes. These genes encode proinflammatory cytokines and chemokines, as well as adhesion molecules, which promote recruitment of inflammatory and immune cells. Similarly, immunoassays showed elevated levels of these cytokines and chemokines in the cerebellum of the Ccm3iECKO mice. Consistently, both flow cytometry and immunofluorescence analysis showed infiltration of different subsets of leukocytes into the CCM lesions. Neutrophils, which are known to fight against infection through different strategies, including the formation of NETs, represented the leukocyte subset within the most pronounced increase in CCM. Here, we detected elevated levels of NETs in the blood and the deposition of NETs in the cerebral cavernomas of Ccm3iECKO mice. Degradation of NETs by DNase I treatment improved the vascular barrier. The deposition of NETs in the cavernomas of patients with CCM confirms the clinical relevance of NETs in CCM.", "doi": "10.1007/s00018-022-04224-2", "pmid": "35333979", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8949649"}, {"db": "pii", "key": "10.1007/s00018-022-04224-2"}], "notes": [], "created": "2022-11-29T09:50:27.050Z", "modified": "2022-11-29T09:50:27.560Z"}, {"entity": "publication", "iuid": "8f169041de1f4c60ad274706cf0739bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f169041de1f4c60ad274706cf0739bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f169041de1f4c60ad274706cf0739bc"}}, "title": "Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence.", "authors": [{"family": "Mart\u00edn-Hern\u00e1ndez", "given": "Giselle C", "initials": "GC", "orcid": "0000-0003-1497-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/5289a4b7aa8e476eaadb6d7773be8db8.json"}}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B", "orcid": "0000-0002-0030-7710", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c1cb5bfdb1a4ceaa551d5908b54e062.json"}}, {"family": "Brandt", "given": "Christian", "initials": "C", "orcid": "0000-0002-7199-3957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f760c98ca3844c50a684346e41733263.json"}}, {"family": "H\u00f6lzer", "given": "Martin", "initials": "M", "orcid": "0000-0001-7090-8717", "researcher": {"href": "https://publications.scilifelab.se/researcher/87dee9193083480d9be8784de5431626.json"}}, {"family": "Viehweger", "given": "Adrian", "initials": "A"}, {"family": "Passoth", "given": "Volkmar", "initials": "V", "orcid": "0000-0002-2059-9044", "researcher": {"href": "https://publications.scilifelab.se/researcher/b44de438fbf14bda83267d133a19f488.json"}}], "type": "journal article", "published": "2022-03-22", "journal": {"title": "JoF", "issn": "2309-608X", "volume": "8", "issue": "4", "issn-l": null}, "abstract": "The genus Rhodotorula includes basidiomycetous oleaginous yeast species. Rhodotorula babjevae can produce compounds of biotechnological interest such as lipids, carotenoids, and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058, at chromosomal level. Both genomes are 21 Mbp in size and have a GC content of 68.2%. Allele frequency analysis indicates that both strains are tetraploid. The genomes consist of a maximum of 21 chromosomes with a size of 0.4 to 2.4 Mbp. In both assemblies, the mitochondrial genome was recovered in a single contig, that shared 97% pairwise identity. Pairwise identity between most chromosomes ranges from 82 to 87%. We also found indications for strain-specific extrachromosomal endogenous DNA. A total of 7591 and 7481 protein-coding genes were annotated in CBS 7808 and DBVPG 8058, respectively. CBS 7808 accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes. Genome divergence values between the two strains indicate that they may belong to different species.", "doi": "10.3390/jof8040323", "pmid": "35448555", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9027234"}, {"db": "pii", "key": "jof8040323"}], "notes": [], "created": "2022-11-29T12:27:36.058Z", "modified": "2022-11-29T12:27:36.232Z"}, {"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": "595bc0af097f4c82b88f2b3184d72f42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/595bc0af097f4c82b88f2b3184d72f42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/595bc0af097f4c82b88f2b3184d72f42"}}, "title": "Weakened resilience of benthic microbial communities in the face of climate change", "authors": [{"family": "Seidel", "given": "Laura", "initials": "L", "orcid": "0000-0002-2620-914X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d0923436cd0a42cea933771b57ae8c94.json"}}, {"family": "Ketzer", "given": "Marcelo", "initials": "M", "orcid": "0000-0003-4796-8177", "researcher": {"href": "https://publications.scilifelab.se/researcher/5224e1bded3a4866802b863ed32cb10e.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications.scilifelab.se/researcher/63826da04a1f4f80bc3229df12bac9b7.json"}}, {"family": "Shahabi-Ghahfarokhi", "given": "Sina", "initials": "S"}, {"family": "Rahmati-Abkenar", "given": "Mahboubeh", "initials": "M", "orcid": "0000-0002-3193-9331", "researcher": {"href": "https://publications.scilifelab.se/researcher/f64c520b937a4871ba129141b01042b9.json"}}, {"family": "Turner", "given": "Stephanie", "initials": "S"}, {"family": "St\u00e5hle", "given": "Magnus", "initials": "M"}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K"}, {"family": "Manoharan", "given": "Lokeshwaran", "initials": "L", "orcid": "0000-0001-9751-5745", "researcher": {"href": "https://publications.scilifelab.se/researcher/000321fd81b9457db66140246bbd9066.json"}}, {"family": "Ali", "given": "Ashfaq", "initials": "A"}, {"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": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.json"}}], "type": "journal-article", "published": "2022-03-08", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "2", "issue": "1", "pages": null}, "abstract": null, "doi": "10.1038/s43705-022-00104-9", "pmid": null, "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-03-28T08:58:38.250Z", "modified": "2024-01-16T13:48:37.272Z"}, {"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": "2ac617985f284c5da4d79ca90e3b6931", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ac617985f284c5da4d79ca90e3b6931.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ac617985f284c5da4d79ca90e3b6931"}}, "title": "Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.", "authors": [{"family": "Viluma", "given": "Agnese", "initials": "A", "orcid": "0000-0003-3388-5020", "researcher": {"href": "https://publications.scilifelab.se/researcher/1df731227e824bb5a8dade435f9571aa.json"}}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "\u00c5kesson", "given": "Mikael", "initials": "M"}, {"family": "Wikenros", "given": "Camilla", "initials": "C"}, {"family": "Sand", "given": "H\u00e5kan", "initials": "H"}, {"family": "Wabakken", "given": "Petter", "initials": "P"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2022-03-00", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "32", "issue": "3", "pages": "449-458", "issn-l": "1088-9051"}, "abstract": "Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.", "doi": "10.1101/gr.276070.121", "pmid": "35135873", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8896455"}, {"db": "pii", "key": "gr.276070.121"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2022-09-28T13:51:59.123Z", "modified": "2024-01-16T13:48:37.319Z"}, {"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": "70304e2e74c14f8c98b28d736df71cf4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70304e2e74c14f8c98b28d736df71cf4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70304e2e74c14f8c98b28d736df71cf4"}}, "title": "The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.", "authors": [{"family": "Oliver", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-5231-7910", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fdb426c5e2e48e985eb8939a1c40d6e.json"}}, {"family": "Annacondia", "given": "Maria Luz", "initials": "ML", "orcid": "0000-0001-7998-8362", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4d89a422254e47a38fe438fe99bdaf.json"}}, {"family": "Wang", "given": "Zhenxing", "initials": "Z", "orcid": "0000-0001-5102-7121", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b6c9f88c65d4fbc94da6d7598102335.json"}}, {"family": "Jullien", "given": "Pauline E", "initials": "PE", "orcid": "0000-0003-1212-3246", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a97f95d2f1046b3a7027dedf5a31082.json"}}, {"family": "Slotkin", "given": "R Keith", "initials": "RK", "orcid": "0000-0001-9582-3533", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac639e0390ef4140a566e5cbbf65084a.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Martinez", "given": "German", "initials": "G", "orcid": "0000-0002-5215-0866", "researcher": {"href": "https://publications.scilifelab.se/researcher/591f629ea8ed44c2bd9cd417dcebd8bc.json"}}], "type": "journal article", "published": "2022-02-03", "journal": {"title": "Plant Cell", "issn": "1532-298X", "volume": "34", "issue": "2", "pages": "784-801", "issn-l": "1040-4651"}, "abstract": "Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.", "doi": "10.1093/plcell/koab280", "pmid": "34755870", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8824631"}, {"db": "pii", "key": "6424912"}], "notes": [], "created": "2022-11-29T09:51:29.116Z", "modified": "2022-11-29T09:51:29.270Z"}, {"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": "47a4b84cdcfc498c8e898c032a1c6b57", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47a4b84cdcfc498c8e898c032a1c6b57.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47a4b84cdcfc498c8e898c032a1c6b57"}}, "title": "Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.", "authors": [{"family": "Edvardsen", "given": "Rolf Brudvik", "initials": "RB", "orcid": "0000-0001-8430-8042", "researcher": {"href": "https://publications.scilifelab.se/researcher/07efd6f7e7b04bbd8af5221f78e982c7.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O", "orcid": "0000-0003-1037-7904", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b32e1cfd3084b10a4c220416a6bc589.json"}}, {"family": "Furmanek", "given": "Tomasz", "initials": "T", "orcid": "0000-0001-8577-9604", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a02b990970e46409613ca730ced5914.json"}}, {"family": "Kleppe", "given": "Lene", "initials": "L"}, {"family": "Jern", "given": "Patric", "initials": "P", "orcid": "0000-0003-3393-5825", "researcher": {"href": "https://publications.scilifelab.se/researcher/8baed28572fd470ba1e7b18fccd2e275.json"}}, {"family": "Wallberg", "given": "Andreas", "initials": "A", "orcid": "0000-0002-9081-9663", "researcher": {"href": "https://publications.scilifelab.se/researcher/b67a52aca631482d8b8f58e525a82d14.json"}}, {"family": "Kj\u00e6rner-Semb", "given": "Erik", "initials": "E", "orcid": "0000-0001-7160-6710", "researcher": {"href": "https://publications.scilifelab.se/researcher/44013d14287f43a29ca482f5dcdc988a.json"}}, {"family": "M\u00e6hle", "given": "Stig", "initials": "S"}, {"family": "Olausson", "given": "Sara Karolina", "initials": "SK"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E", "orcid": "0000-0001-9526-8541", "researcher": {"href": "https://publications.scilifelab.se/researcher/20f87b64e71b4a00a9474ec4d898601d.json"}}, {"family": "Harboe", "given": "Torstein", "initials": "T"}, {"family": "Mangor-Jensen", "given": "Ragnfrid", "initials": "R"}, {"family": "M\u00f8gster", "given": "Margareth", "initials": "M"}, {"family": "Perrichon", "given": "Prescilla", "initials": "P", "orcid": "0000-0002-1410-878X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd8005cb7ec44f569ffc2d457d6e8bf9.json"}}, {"family": "Norberg", "given": "Birgitta", "initials": "B", "orcid": "0000-0003-1550-5725", "researcher": {"href": "https://publications.scilifelab.se/researcher/c178dcf0ef364f14b6cdb7661540070f.json"}}, {"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "18", "issue": "2", "pages": "e1010011", "issn-l": "1553-7390"}, "abstract": "Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly from a male and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed that all chromosomes exhibit heterochiasmy, i.e. male-only and female-only meiotic recombination regions (MRR/FRR). We show that FRR/MRR intervals differ in nucleotide diversity and repeat class content and that this is true also for other Pleuronectidae species. We further show that remnants of a Gypsy-like transposable element insertion on chr13 promotes early male specific expression of gonadal somatic cell derived factor (gsdf). Less than 4.5 MYA, this male-determining element evolved on an autosomal FRR segment featuring pre-existing male meiotic recombination barriers, thereby creating a Y chromosome. Our findings indicate that heterochiasmy may facilitate the evolution of genetic sex determination systems relying on linkage of sexually antagonistic loci to a sex-determining factor.", "doi": "10.1371/journal.pgen.1010011", "pmid": "35134055", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8824383"}, {"db": "pii", "key": "PGENETICS-D-21-00885"}], "notes": [], "created": "2022-11-29T09:16:18.063Z", "modified": "2024-01-16T13:48:37.634Z"}, {"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": "c7e444c1c6864297b04b31cb10b66b98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7e444c1c6864297b04b31cb10b66b98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7e444c1c6864297b04b31cb10b66b98"}}, "title": "A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host \u03b2-pinene monoterpene.", "authors": [{"family": "Rafiei", "given": "Vahideh", "initials": "V", "orcid": "0000-0003-0021-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c453e43d63594937aa2efd03e37bee1e.json"}}, {"family": "Ruffino", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-7039-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/acfbbc82f59b4fbc8a9ea0e6b8515e51.json"}}, {"family": "Persson Hod\u00e9n", "given": "Kristian", "initials": "K", "orcid": "0000-0003-0354-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b41e8e41574ee6bcb55df3b0d145d9.json"}}, {"family": "Tornkvist", "given": "Anna", "initials": "A", "orcid": "0000-0002-6215-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36e5404f2a841019aa1aeac9c8c7ec9.json"}}, {"family": "Mozuraitis", "given": "Raimondas", "initials": "R", "orcid": "0000-0002-1719-2294", "researcher": {"href": "https://publications.scilifelab.se/researcher/213ecb5deb7d4d06901f461424d964cf.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "volume": "23", "issue": "2", "pages": "291-303", "issn-l": null}, "abstract": "Terpenes constitute a major part of secondary metabolites secreted by plants in the rhizosphere. However, their specific functions in fungal-plant interactions have not been investigated thoroughly. In this study we investigated the role of monoterpenes in interactions between oilseed rape (Brassica napus) and the soilborne pathogen Verticillium longisporum. We identified seven monoterpenes produced by B. napus, and production of \u03b1-pinene, \u03b2-pinene, 3-carene, and camphene was significantly increased upon fungal infection. Among them, \u03b2-pinene was chosen for further analysis. Transcriptome analysis of V. longisporum on exposure to \u03b2-pinene resulted in identification of two highly expressed pleotropic drug transporters paralog genes named VlAbcG1a and VlAbcG1b. Overexpression of VlAbcG1a in Saccharomyces cerevisiae increased tolerance to \u03b2-pinene, while deletion of the VlAbcG1a homologous gene in Verticillium dahliae resulted in mutants with increased sensitivity to certain monoterpenes. Furthermore, the VlAbcG1a overexpression strain displayed an increased tolerance to \u03b2-pinene and increased virulence in tomato plants. Data from this study give new insights into the roles of terpenes in plant-fungal pathogen interactions and the mechanisms fungi deploy to cope with the toxicity of these secondary metabolites.", "doi": "10.1111/mpp.13162", "pmid": "34825755", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8743018"}], "notes": [], "created": "2022-11-29T09:34:58.011Z", "modified": "2022-11-29T09:34:58.198Z"}, {"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": "e0d583dfe4c3412cbdc9356197a1f6ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0d583dfe4c3412cbdc9356197a1f6ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0d583dfe4c3412cbdc9356197a1f6ac"}}, "title": "Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.", "authors": [{"family": "Stratmann", "given": "Svea", "initials": "S", "orcid": "0000-0002-7438-9093", "researcher": {"href": "https://publications.scilifelab.se/researcher/3927efe3aaf84399b26355d92c3a15cf.json"}}, {"family": "Yones", "given": "Sara A", "initials": "SA", "orcid": "0000-0002-7201-2604", "researcher": {"href": "https://publications.scilifelab.se/researcher/17817db9549947578bbe96ba93524cf5.json"}}, {"family": "Garbulowski", "given": "Mateusz", "initials": "M", "orcid": "0000-0002-2497-194X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad0d6d37b2a04400a8dc407fc78523ec.json"}}, {"family": "Sun", "given": "Jitong", "initials": "J"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Norgren", "given": "Nina", "initials": "N", "orcid": "0000-0002-3823-1555", "researcher": {"href": "https://publications.scilifelab.se/researcher/a14a423eff78442daffe57aff0130f33.json"}}, {"family": "Herlin", "given": "Morten Krogh", "initials": "MK", "orcid": "0000-0001-7179-4643", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc2efb7b874d46879e3f34e3d7a1b8ef.json"}}, {"family": "Sundstr\u00f6m", "given": "Christer", "initials": "C", "orcid": "0000-0002-8160-5647", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfac750a70664f9986b3cc06334638cc.json"}}, {"family": "Eriksson", "given": "Anna", "initials": "A"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J"}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K"}, {"family": "Munthe-Kaas", "given": "Monica Cheng", "initials": "MC"}, {"family": "Zeller", "given": "Bernward", "initials": "B"}, {"family": "Tamm", "given": "Katja Pokrovskaja", "initials": "KP"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Holmfeldt", "given": "Linda", "initials": "L", "orcid": "0000-0003-4140-3423", "researcher": {"href": "https://publications.scilifelab.se/researcher/12b8b368e61e48d3b800516f006fbb7d.json"}}], "type": "journal article", "published": "2022-01-11", "journal": {"title": "Blood Adv", "issn": "2473-9537", "issn-l": "2473-9529", "volume": "6", "issue": "1", "pages": "152-164"}, "abstract": "Numerous studies have been performed over the last decade to exploit the complexity of genomic and transcriptomic lesions driving the initiation of acute myeloid leukemia (AML). These studies have helped improve risk classification and treatment options. Detailed molecular characterization of longitudinal AML samples is sparse, however; meanwhile, relapse and therapy resistance represent the main challenges in AML care. To this end, we performed transcriptome-wide RNA sequencing of longitudinal diagnosis, relapse, and/or primary resistant samples from 47 adult and 23 pediatric AML patients with known mutational background. Gene expression analysis revealed the association of short event-free survival with overexpression of GLI2 and IL1R1, as well as downregulation of ST18. Moreover, CR1 downregulation and DPEP1 upregulation were associated with AML relapse both in adults and children. Finally, machine learning-based and network-based analysis identified overexpressed CD6 and downregulated INSR as highly copredictive genes depicting important relapse-associated characteristics among adult patients with AML. Our findings highlight the importance of a tumor-promoting inflammatory environment in leukemia progression, as indicated by several of the herein identified differentially expressed genes. Together, this knowledge provides the foundation for novel personalized drug targets and has the potential to maximize the benefit of current treatments to improve cure rates in AML.", "doi": "10.1182/bloodadvances.2021004962", "pmid": "34619772", "labels": {"Clinical Genomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8753201"}, {"db": "pii", "key": "477210"}], "notes": [], "created": "2021-12-06T08:28:43.286Z", "modified": "2024-01-16T13:48:37.758Z"}, {"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": "6afe7eb5e9a94df680b83253610f4fcf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6afe7eb5e9a94df680b83253610f4fcf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6afe7eb5e9a94df680b83253610f4fcf"}}, "title": "Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.", "authors": [{"family": "Guti\u00e9rrez-Valencia", "given": "Juanita", "initials": "J"}, {"family": "Fracassetti", "given": "Marco", "initials": "M"}, {"family": "Horvath", "given": "Robert", "initials": "R", "orcid": "0000-0002-3221-8835", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd1f411c815a49bf91ada0eac39dee8b.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "D\u00e9samore", "given": "Aur\u00e9lie", "initials": "A"}, {"family": "Drouzas", "given": "Andreas D", "initials": "AD"}, {"family": "Friberg", "given": "Magne", "initials": "M"}, {"family": "Kol\u00e1\u0159", "given": "Filip", "initials": "F"}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2022-01-07", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "39", "issue": "1", "pages": null}, "abstract": "Fertilization in angiosperms involves the germination of pollen on the stigma, followed by the extrusion of a pollen tube that elongates through the style and delivers two sperm cells to the embryo sac. Sexual selection could occur throughout this process when male gametophytes compete for fertilization. The strength of sexual selection during pollen competition should be affected by the number of genotypes deposited on the stigma. As increased self-fertilization reduces the number of mating partners, and the genetic diversity and heterozygosity of populations, it should thereby reduce the intensity of sexual selection during pollen competition. Despite the prevalence of mating system shifts, few studies have directly compared the molecular signatures of sexual selection during pollen competition in populations with different mating systems. Here we analyzed whole-genome sequences from natural populations of Arabis alpina, a species showing mating system variation across its distribution, to test whether shifts from cross- to self-fertilization result in molecular signatures consistent with sexual selection on genes involved in pollen competition. We found evidence for efficient purifying selection on genes expressed in vegetative pollen, and overall weaker selection on sperm-expressed genes. This pattern was robust when controlling for gene expression level and specificity. In agreement with the expectation that sexual selection intensifies under cross-fertilization, we found that the efficacy of purifying selection on male gametophyte-expressed genes was significantly stronger in genetically more diverse and outbred populations. Our results show that intra-sexual competition shapes the evolution of pollen-expressed genes, and that its strength fades with increasing self-fertilization rates.", "doi": "10.1093/molbev/msab349", "pmid": "34878144", "labels": {"Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8788238"}, {"db": "pii", "key": "6456311"}], "notes": [], "created": "2022-02-17T12:52:26.583Z", "modified": "2024-01-16T13:48:37.803Z"}, {"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": "a8f05f12d3914490af074ff93cd54013", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8f05f12d3914490af074ff93cd54013.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8f05f12d3914490af074ff93cd54013"}}, "title": "Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.", "authors": [{"family": "Mennuni", "given": "Mara", "initials": "M", "orcid": "0000-0001-6199-6233", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d3b8d76aacd4f47ae62d0de66e9222a.json"}}, {"family": "Filograna", "given": "Roberta", "initials": "R", "orcid": "0000-0002-6581-9426", "researcher": {"href": "https://publications.scilifelab.se/researcher/7d215cffe2dc48a18d051a2229c8ce9f.json"}}, {"family": "Felser", "given": "Andrea", "initials": "A"}, {"family": "Bonekamp", "given": "Nina A", "initials": "NA", "orcid": "0000-0001-9748-8089", "researcher": {"href": "https://publications.scilifelab.se/researcher/786f4a3ca29a4033b3252e014e6785df.json"}}, {"family": "Giavalisco", "given": "Patrick", "initials": "P", "orcid": "0000-0002-4636-1827", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b3ada5024b4a23a32cdc392f92fb81.json"}}, {"family": "Lytovchenko", "given": "Oleksandr", "initials": "O", "orcid": "0000-0003-1032-2612", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fb9454d524a470196c06792d4b47a7c.json"}}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "N"}], "type": "journal article", "published": "2022-01-05", "journal": {"title": "EMBO Rep.", "issn": "1469-3178", "issn-l": "1469-221X", "volume": "23", "issue": "1", "pages": "e53054"}, "abstract": "Cancer cells depend on mitochondria to sustain their increased metabolic need and mitochondria therefore constitute possible targets for cancer treatment. We recently developed small-molecule inhibitors of mitochondrial transcription (IMTs) that selectively impair mitochondrial gene expression. IMTs have potent antitumor properties in vitro and in vivo, without affecting normal tissues. Because therapy-induced resistance is a major constraint to successful cancer therapy, we investigated mechanisms conferring resistance to IMTs. We employed a CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats)-(CRISP-associated protein 9) whole-genome screen to determine pathways conferring resistance to acute IMT1 treatment. Loss of genes belonging to von Hippel-Lindau (VHL) and mammalian target of rapamycin complex 1 (mTORC1) pathways caused resistance to acute IMT1 treatment and the relevance of these pathways was confirmed by chemical modulation. We also generated cells resistant to chronic IMT treatment to understand responses to persistent mitochondrial gene expression impairment. We report that IMT1-acquired resistance occurs through a compensatory increase of mitochondrial DNA (mtDNA) expression and cellular metabolites. We found that mitochondrial transcription factor A (TFAM) downregulation and inhibition of mitochondrial translation impaired survival of resistant cells. The identified susceptibility and resistance mechanisms to IMTs may be relevant for different types of mitochondria-targeted therapies.", "doi": "10.15252/embr.202153054", "pmid": "34779571", "labels": {"CRISPR Functional Genomics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8728608"}], "notes": [], "created": "2022-06-20T12:50:08.214Z", "modified": "2022-08-19T09:49:54.313Z"}, {"entity": "publication", "iuid": "d42a9507c5ac44fa9396fc9e67645fe3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d42a9507c5ac44fa9396fc9e67645fe3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d42a9507c5ac44fa9396fc9e67645fe3"}}, "title": "Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.", "authors": [{"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Abdulla", "given": "Maysaa", "initials": "M"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Berglund", "given": "Mattias", "initials": "M"}, {"family": "Ednersson", "given": "Susanne Bram", "initials": "SB"}, {"family": "Andersson", "given": "Per-Ola", "initials": "PO"}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Amini", "given": "Rose-Marie", "initials": "RM"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}], "type": "journal article", "published": "2022-01-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1098-2264", "issn-l": "1045-2257", "volume": "61", "issue": "1", "pages": "27-36"}, "abstract": "Formalin-fixed, paraffin-embedded (FFPE) specimens are an underutilized resource in medical research, particularly in the setting of transcriptome sequencing, as RNA from these samples is often degraded. We took advantage of an exome capture-based RNA-sequencing protocol to explore global gene expression in paired fresh-frozen (FF) and FFPE samples from 16 diffuse large B-cell lymphoma (DLBCL) patients. While FFPE samples generated fewer mapped reads compared to their FF counterparts, these reads captured the same library complexity and had a similar number of genes expressed on average. Furthermore, gene expression demonstrated a high correlation when comparing housekeeping genes only or across the entire transcriptome (r = 0.99 for both comparisons). Differences in gene expression were primarily seen in lowly expressed genes and genes with small or large coding sequences. Using cell-of-origin classifiers and clinically relevant gene expression signatures for DLBCL, FF, and FFPE samples from the same biopsy paired nearly perfectly in clustering analysis. This was further confirmed in a validation cohort of 50 FFPE DLBCL samples. In summary, we found the biological differences between tumors to be far greater than artifacts created as a result of degraded RNA. We conclude that exome capture transcriptome sequencing data from archival samples can confidently be used for cell-of-origin classification of DLBCL samples.", "doi": "10.1002/gcc.23002", "pmid": "34647650", "labels": {"Clinical Genomics Uppsala": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "National Genomics Infrastructure": "Technology development", "NGI Short read": "Technology development", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T08:28:42.125Z", "modified": "2023-06-20T15:58:04.919Z"}, {"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": "728cc0ed8d014a65b15817c2235987b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/728cc0ed8d014a65b15817c2235987b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/728cc0ed8d014a65b15817c2235987b9"}}, "title": "Genome-wide spatial expression profiling in formalin-fixed tissues.", "authors": [{"family": "Gracia Villacampa", "given": "Eva", "initials": "E", "orcid": "0000-0003-0353-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/eaf72d81feea4b7899197c67131a85ba.json"}}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications.scilifelab.se/researcher/22f1a6ef554a48a49733cc129f50d052.json"}}, {"family": "Andersson", "given": "Alma", "initials": "A"}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Kokaraki", "given": "Georgia", "initials": "G"}, {"family": "Monteil", "given": "Vanessa", "initials": "V"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Appelberg", "given": "Karin Sofia", "initials": "KS"}, {"family": "Montserrat", "given": "Nuria", "initials": "N"}, {"family": "Zhang", "given": "Haibo", "initials": "H"}, {"family": "Penninger", "given": "Josef M", "initials": "JM"}, {"family": "Miesbach", "given": "Wolfgang", "initials": "W"}, {"family": "Mirazimi", "given": "Ali", "initials": "A"}, {"family": "Carlson", "given": "Joseph", "initials": "J", "orcid": "0000-0002-3006-4107", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb81cad4b24d4692bc21bda7305f21f1.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": "2021-12-08", "journal": {"title": "Cell Genomics", "issn": "2666-979X", "volume": "1", "issue": "3", "pages": "100065", "issn-l": null}, "abstract": "Formalin-fixed paraffin embedding (FFPE) is the most widespread long-term tissue preservation approach. Here, we report a procedure to perform genome-wide spatial analysis of mRNA in FFPE-fixed tissue sections, using well-established, commercially available methods for imaging and spatial barcoding using slides spotted with barcoded oligo(dT) probes to capture the 3' end of mRNA molecules in tissue sections. We applied this method for expression profiling and cell type mapping in coronal sections from the mouse brain to demonstrate the method's capability to delineate anatomical regions from a molecular perspective. We also profiled the spatial composition of transcriptomic signatures in two ovarian carcinosarcoma samples, exemplifying the method's potential to elucidate molecular mechanisms in heterogeneous clinical samples. Finally, we demonstrate the applicability of the assay to characterize human lung and kidney organoids and a human lung biopsy specimen infected with SARS-CoV-2. We anticipate that genome-wide spatial gene expression profiling in FFPE biospecimens will be used for retrospective analysis of biobank samples, which will facilitate longitudinal studies of biological processes and biomarker discovery.", "doi": "10.1016/j.xgen.2021.100065", "pmid": "36776149", "labels": {"NGI Spatial omics": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9903805"}, {"db": "pii", "key": "S2666-979X(21)00081-1"}], "notes": [], "created": "2023-01-03T14:49:59.765Z", "modified": "2023-06-02T10:33:04.298Z"}, {"entity": "publication", "iuid": "3611028adfd841ac88242da67bb97158", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3611028adfd841ac88242da67bb97158.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3611028adfd841ac88242da67bb97158"}}, "title": "Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis.", "authors": [{"family": "M\u00e4kinen", "given": "Artturi", "initials": "A"}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Mehtonen", "given": "Juha", "initials": "J"}, {"family": "Teppo", "given": "Susanna", "initials": "S"}, {"family": "Oksa", "given": "Laura", "initials": "L"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Pohjolainen", "given": "Virva", "initials": "V"}, {"family": "Laukkanen", "given": "Saara", "initials": "S"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M"}, {"family": "Paavonen", "given": "Timo", "initials": "T"}, {"family": "Lohi", "given": "Olli", "initials": "O"}], "type": "journal article", "published": "2021-12-00", "journal": {"title": "Pathology", "issn": "1465-3931", "issn-l": null, "volume": "53", "issue": "7", "pages": "875-882"}, "abstract": "B-cell lineage acute lymphoblastic leukaemia (B-ALL) is the most common paediatric malignancy. Transcription factor B-cell lymphoma 6 (BCL6) is essential to germinal centre formation and antibody affinity maturation and plays a major role in mature B-cell malignancies. More recently, it was shown to act as a critical downstream regulator in pre-BCR+ B-ALL. We investigated the expression of the BCL6 protein in a population-based cohort of paediatric B-ALL cases and detected moderate to strong positivity through immunohistochemistry in 7% of cases (8/117); however, only two of eight BCL6 cases (25%) co-expressed the ZAP70 protein. In light of these data, the subtype with active pre-BCR signalling constitutes a rare entity in paediatric B-ALL. In three independent larger cohorts with gene expression data, high BCL6 mRNA levels were associated with the TCF3-PBX1, Ph-like, NUTM1, MEF2D and PAX5-alt subgroups and the 'metagene' signature for pre-BCR-associated genes. However, higher-than-median BCL6 mRNA level alone was associated with favourable event free survival in the Nordic paediatric cohort, indicating that using BCL6 as a diagnostic marker requires careful design, and evaluation of protein level is needed alongside the genetic or transcriptomic data.", "doi": "10.1016/j.pathol.2021.02.013", "pmid": "34049715", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0031-3025(21)00109-4"}], "notes": [], "created": "2021-12-10T10:33:38.923Z", "modified": "2023-05-22T14:24:21.445Z"}, {"entity": "publication", "iuid": "e2e0b1cdb60c40dabbccb4597711b1ea", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e2e0b1cdb60c40dabbccb4597711b1ea.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e2e0b1cdb60c40dabbccb4597711b1ea"}}, "title": "Comparison of EM-seq and PBAT methylome library methods for low-input DNA.", "authors": [{"family": "Han", "given": "Yanan", "initials": "Y", "orcid": "0000-0002-3464-2656", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dbd01317d224156a002d298de5112ac.json"}}, {"family": "Zheleznyakova", "given": "Galina Yurevna", "initials": "GY"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Kakhki", "given": "Majid Pahlevan", "initials": "MP"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Needhamsen", "given": "Maria", "initials": "M"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}], "type": "journal article", "published": "2021-11-17", "journal": {"title": "Epigenetics", "issn": "1559-2308", "issn-l": "1559-2294", "volume": "17", "issue": "10", "pages": "1195-1204"}, "abstract": "DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.", "doi": "10.1080/15592294.2021.1997406", "pmid": "34709110", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Short read": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-10T11:22:58.275Z", "modified": "2022-11-29T09:19:22.428Z"}, {"entity": "publication", "iuid": "1fafeea0c1fc4b21b45c073667f92be3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fafeea0c1fc4b21b45c073667f92be3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fafeea0c1fc4b21b45c073667f92be3"}}, "title": "Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.", "authors": [{"family": "Sigeman", "given": "Hanna", "initials": "H", "orcid": "0000-0002-1457-4174", "researcher": {"href": "https://publications.scilifelab.se/researcher/f75fea472d1d495a92228c50bd63891e.json"}}, {"family": "Strandh", "given": "Maria", "initials": "M"}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E"}, {"family": "Kutschera", "given": "Verena E", "initials": "VE"}, {"family": "Ponnikas", "given": "Suvi", "initials": "S"}, {"family": "Zhang", "given": "Hongkai", "initials": "H"}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Tarka", "given": "Maja", "initials": "M"}, {"family": "Hasselquist", "given": "Dennis", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Westerdahl", "given": "Helena", "initials": "H"}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2021-09-20", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "38", "issue": "12", "pages": "5275-5291"}, "abstract": "How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (Myr) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event \u223c24 Myr ago formed \"neo-sex chromosomes\" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and while the added-Z has remained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for non-random maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex-linkage.", "doi": "10.1093/molbev/msab277", "pmid": "34542640", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6372697"}], "notes": [], "created": "2021-10-29T14:04:51.682Z", "modified": "2024-01-16T13:48:38.463Z"}, {"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": "55e97ce1989c4bb184fae3027bb2bf9c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55e97ce1989c4bb184fae3027bb2bf9c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55e97ce1989c4bb184fae3027bb2bf9c"}}, "title": "Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.", "authors": [{"family": "Guo", "given": "Yongzhi", "initials": "Y", "orcid": "0000-0002-5057-9095", "researcher": {"href": "https://publications.scilifelab.se/researcher/8040d6c76eb6467585d054d55a1965fe.json"}}, {"family": "van Schaik", "given": "Tom", "initials": "T", "orcid": "0000-0001-7850-5074", "researcher": {"href": "https://publications.scilifelab.se/researcher/79ccfcbccc214a7591e33d611edf0e8a.json"}}, {"family": "Jhamat", "given": "Naveed", "initials": "N"}, {"family": "Niazi", "given": "Adnan", "initials": "A", "orcid": "0000-0003-0311-5279", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9e07c9891804a60980eb07956a7cd0d.json"}}, {"family": "Chanrot", "given": "Metasu", "initials": "M"}, {"family": "Charpigny", "given": "Gilles", "initials": "G"}, {"family": "Valarcher", "given": "Jean Francois", "initials": "JF"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Humblot", "given": "Patrice", "initials": "P"}], "type": "journal article", "published": "2019-09-05", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "14", "issue": "9", "pages": "e0222081", "issn-l": "1932-6203"}, "abstract": "Lipopolysaccharide (LPS) expressed on the surface of Gram-negative bacteria activates pro-inflammatory pathways, dys-regulates the function of endometrial cells and is a key player in the mechanisms involved in endometritis. This study aimed to investigate the effects of LPS on bovine endometrial epithelial cells (bEEC) from whole transcriptome with a special focus on genes involved in embryo-maternal interactions. Following in vitro culture, bEEC from three cows were exposed to 0, 2, and 8 \u03bcg/mL LPS for 24h. RNA samples extracted at 0 and 24 hours were analyzed by RNA sequencing (RNA-seq). At 24h, 2035 differentially expressed genes (DEGs) were identified between controls and samples treated with 2 \u03bcg/mL LPS. Gene ontology analysis showed that over-expressed DEGs were associated to immune response, response to stress and external stimuli, catalytic activity, and cell cycle. Genes associated with cell membrane and cell adhesion pathways were under-expressed. LPS induced changes in expression of specific genes related to embryo-maternal interactions including under-expression of eight members of the cadherin superfamily, over-expression of six members of the mucin family, and differential expression of a large set of genes binding the above molecules and of more than 20 transcripts coding for cytokines and their receptors. Type I interferon-\u03c4 dependent genes were also over-expressed. From a sub-set of 19 genes, (biological replicates of bEEC from cows taken at time 6 (n = 3), 24 (n = 6) and 48 hours (n = 3), and 2 technical replicates per sample) differential gene expression was confirmed by RT2-qPCR (r2 between fold changes at 24 hours by RT2-qPCR and RNA-seq = 0.97). These results indicate that LPS affects the function of bEEC in many ways by differential transcription, glycolytic metabolism and oxidative stress. Many transcriptomic signatures related to implantation and embryo maternal interactions were strongly affected by LPS. These results pave the way for further studies to investigate the duration of these changes and their possible impact on endometrial function and fertility.", "doi": "10.1371/journal.pone.0222081", "pmid": "31487323", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6728075"}, {"db": "pii", "key": "PONE-D-19-15238"}], "notes": [], "created": "2024-09-30T06:07:45.782Z", "modified": "2024-09-30T06:07:46.035Z"}, {"entity": "publication", "iuid": "15ef40b017654d21a684bf04354b27db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15ef40b017654d21a684bf04354b27db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15ef40b017654d21a684bf04354b27db"}}, "title": "Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.", "authors": [{"family": "Jovanovic", "given": "Braslav", "initials": "B"}, {"family": "Egyhazi", "given": "Suzanne", "initials": "S"}, {"family": "Eskandarpour", "given": "Malihe", "initials": "M"}, {"family": "Ghiorzo", "given": "Paola", "initials": "P"}, {"family": "Palmer", "given": "Jane M", "initials": "JM"}, {"family": "Bianchi Scarr\u00e0", "given": "Giovanna", "initials": "G"}, {"family": "Hayward", "given": "Nicholas K", "initials": "NK"}, {"family": "Hansson", "given": "Johan", "initials": "J"}], "type": "letter", "published": "2010-02-00", "journal": {"title": "J. Invest. Dermatol.", "issn": "1523-1747", "issn-l": "0022-202X", "volume": "130", "issue": "2", "pages": "618-620"}, "abstract": null, "doi": "10.1038/jid.2009.287", "pmid": "19759551", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-202X(15)34686-8"}, {"db": "pmc", "key": "PMC3665509"}, {"db": "mid", "key": "NIHMS468846"}], "notes": [], "created": "2017-05-04T14:57:11.959Z", "modified": "2022-08-19T09:04:31.750Z"}]}