{"entity": "journal", "iuid": "857318422126485d8eaf5e0c23adfb35", "timestamp": "2026-08-13T08:37:54.401Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Sci%20Adv.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Sci%20Adv"}}, "title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "publications_count": 67, "publications": [{"entity": "publication", "iuid": "36f8a81868eb4f9b983763556e8e7a6f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36f8a81868eb4f9b983763556e8e7a6f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36f8a81868eb4f9b983763556e8e7a6f"}}, "title": "Unheralded high MHC class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing.", "authors": [{"family": "Jamsandekar", "given": "Minal", "initials": "M", "orcid": "0000-0001-8678-9329", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5bfa164632d4084a7396c72b4c69da1.json"}}, {"family": "Mohamadnejad Sangdehi", "given": "Fahime", "initials": "F", "orcid": "0009-0006-0894-1659", "researcher": {"href": "https://publications.scilifelab.se/researcher/a191091424f947ee8009bfca59c84f05.json"}}, {"family": "Berg", "given": "Florian", "initials": "F", "orcid": "0000-0003-1543-8112", "researcher": {"href": "https://publications.scilifelab.se/researcher/902b6c39c4f5463ea25888c17732fc3e.json"}}, {"family": "Criscitiello", "given": "Michael F", "initials": "MF", "orcid": "0000-0003-4262-7832", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5b229b5134441e88da1ebff26bb8884.json"}}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Larsson", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0002-7855-9539", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c626e0c08ca449899cebece751e79cf.json"}}, {"family": "Li", "given": "Jingyi", "initials": "J", "orcid": "0000-0001-6775-5190", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b98cb0d4a11462787c60c54186bb828.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.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": "2026-07-24", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "30", "pages": "eaea2862", "issn-l": "2375-2548"}, "abstract": "Although major histocompatibility complex (MHC) genes are the most polymorphic genes in vertebrates, we still lack a clear understanding about the extent of polymorphism and selection mechanisms dominantly driving it. Here, we use 29 haploid genome assemblies resolved by long-read sequencing to characterize MHC II genes in Atlantic herring, a pelagic fish and one of the most abundant vertebrates on Earth. We found nine MHC II loci in total distributed on four chromosomes, three of which were extremely polymorphic because of high sequence diversity, in particular at peptide binding sites, along with high copy number variation. This study reveals that the herring MHC class II genes are among the most, if not the most, polymorphic so far described in vertebrates.", "doi": "10.1126/sciadv.aea2862", "pmid": "42497266", "labels": {"NGI Long read": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13398488"}], "notes": [], "created": "2026-08-12T15:15:29.174Z", "modified": "2026-08-12T15:15:29.409Z"}, {"entity": "publication", "iuid": "817f65055c534d8196be40bc8a8e308c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/817f65055c534d8196be40bc8a8e308c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/817f65055c534d8196be40bc8a8e308c"}}, "title": "Equal in death: Ancient genomic analysis of children's early Christian burials.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0001-8964-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3a47cc07e9d4b8592dba430785681b5.json"}}, {"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kempe Lagerholm", "given": "Vendela", "initials": "V"}, {"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2250-0463", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ed3c5d3aa804b7085c4f8a4036c09e1.json"}}, {"family": "Zachrisson", "given": "Torun", "initials": "T", "orcid": "0000-0001-7755-4982", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bdaee9400b347088474cc8a9147026b.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Sobrado", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T", "orcid": "0009-0009-3553-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a32a4e171454874a03920c915d3265f.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}], "type": "journal article", "published": "2026-07-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "28", "pages": "eaeb8588", "issn-l": "2375-2548"}, "abstract": "Sexing the skeletal remains of young individuals is crucial yet notoriously difficult in archaeology. Children, who cannot be reliably sexed morphologically, are often excluded from gender-related research, limiting our understanding of past childhood. This issue is compounded in contexts lacking grave goods, such as early Christian burials. We conducted genomic screening of 142 individuals from Sweden dating from the late Viking Age to the Medieval period, including 68 subadults and 74 adults from 27 single and 50 multiple burials. To investigate the treatment of children in death and the role of collective graves, we applied genomic sexing and kinship analyses to individuals from three sites. Contrary to the assumption that collective burials reflect close kinship, our results show that children interred with adults rarely shared close biological ties. Burial patterns indicate that gender roles were established early, with both boys and most girls mirroring adult spatial patterns. However, flexibility existed, and extended kinship likely played a central role in structuring these communities.", "doi": "10.1126/sciadv.aeb8588", "pmid": "42430491", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13353417"}], "notes": [], "created": "2026-07-14T17:36:38.635Z", "modified": "2026-07-14T17:36:39.114Z"}, {"entity": "publication", "iuid": "819b75ef395d4a20bf5a47b2d1857d36", "links": {"self": {"href": "https://publications.scilifelab.se/publication/819b75ef395d4a20bf5a47b2d1857d36.json"}, "display": {"href": "https://publications.scilifelab.se/publication/819b75ef395d4a20bf5a47b2d1857d36"}}, "title": "Open and closed forms of assembled henipavirus nucleoprotein suggest structural basis of genome access", "authors": [{"family": "Jayachandran", "given": "Rupesh Balaji", "initials": "RB", "orcid": "0009-0000-4969-6991", "researcher": {"href": "https://publications.scilifelab.se/researcher/871970f1ea9641518a8e76e8c4d9e028.json"}}, {"family": "Quignon", "given": "Erwan", "initials": "E", "orcid": "0000-0001-7929-8847", "researcher": {"href": "https://publications.scilifelab.se/researcher/87589236770e400bbe113139d9c04d62.json"}}, {"family": "Renner", "given": "Max", "initials": "M", "orcid": "0000-0001-9885-8256", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dec10d9f96e400b800647eb4437a6c9.json"}}], "type": "journal-article", "published": "2026-05-15", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "20", "pages": "eaed8300", "issn-l": "2375-2548"}, "abstract": "Henipaviruses, such as Nipah virus, can cause deadly illness and constitute WHO blueprint priorities due to their pandemic potential. Their genomes are packaged within a nucleocapsid consisting of viral nucleoproteins (N). Now, it is unclear how the encapsidated genome is released from N to allow the viral polymerase to read its sequence. Here, we present the high-resolution cryo-EM structure of a helical N-RNA filament from Langya henipavirus (LayV), allowing us to identify vertical interactions crucial for assembly. We show that assembly efficiency is sequence-dependent and prefers 5'-genomic sequences. Further, we solve the structure of an RNA-free assembly of LayV-N. Structural comparison of the RNA-bound and RNA-free LayV-N shows a conformational opening and closing, even within the assembled state. Our data suggest that N within nucleocapsids may undergo local conformational changes, switching between closed and open states, to temporarily allow access to the encapsidated RNA without nucleocapsid disruption.", "doi": "10.1126/sciadv.aed8300", "pmid": "42127178", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13170654"}], "notes": [], "created": "2026-06-23T07:54:07.878Z", "modified": "2026-08-09T18:35:16.012Z"}, {"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": "27c51de324ea427da6d1ca7c145e1cb6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/27c51de324ea427da6d1ca7c145e1cb6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/27c51de324ea427da6d1ca7c145e1cb6"}}, "title": "Near-infrared MINFLUX imaging enabled by suppression of fluorophore blinking.", "authors": [{"family": "Srambickal", "given": "Chinmaya V", "initials": "CV", "orcid": "0009-0005-3541-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/83d10a808edf4d34a5ee39d5ae20bd49.json"}}, {"family": "Esmaeeli", "given": "Hanie M", "initials": "HM", "orcid": "0000-0003-3806-0255", "researcher": {"href": "https://publications.scilifelab.se/researcher/b00222b6b4f84c9987d4f30e778da180.json"}}, {"family": "Piguet", "given": "Joachim", "initials": "J", "orcid": "0000-0002-4762-4887", "researcher": {"href": "https://publications.scilifelab.se/researcher/3733dec61dc54d91a52d73b853dddc1d.json"}}, {"family": "Reinkensmeier", "given": "Lenny", "initials": "L", "orcid": "0009-0008-8315-6268", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b753b7873924481bbfdb7d03ce42de2.json"}}, {"family": "Siegmund", "given": "Ren\u00e9", "initials": "R", "orcid": "0009-0004-9010-6067", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1ee32987df6479f86e27cc8c79bb52d.json"}}, {"family": "Agostinho", "given": "Ana", "initials": "A", "orcid": "0000-0001-6270-7384", "researcher": {"href": "https://publications.scilifelab.se/researcher/b66ed948cad14e0c9bd35e487a48d330.json"}}, {"family": "Bates", "given": "Mark", "initials": "M", "orcid": "0000-0003-0668-5277", "researcher": {"href": "https://publications.scilifelab.se/researcher/681d6d1b70ad4879b3bb9a1e458d2960.json"}}, {"family": "Egner", "given": "Alexander", "initials": "A", "orcid": "0000-0001-5248-3858", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6b7bdedf9fa4c08b11701f9643d4f9c.json"}}, {"family": "Widengren", "given": "Jerker", "initials": "J", "orcid": "0000-0003-3200-0374", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5db653aece8408bb5aff6531edff22c.json"}}], "type": "journal article", "published": "2025-12-05", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "49", "pages": "eadw3149", "issn-l": "2375-2548"}, "abstract": "MINimal photon FLUXes (MINFLUX) offers nanometer localization precision, with lower fluorophore requirements than for other super-resolution microscopy (SRM) techniques. Nonetheless, low localization probabilities hamper its application, and use of less bright and photostable fluorophores, including near-infrared (NIR) fluorophores has been difficult to realize. Here, we devised strategies overcoming these limitations. We systematically studied the blinking properties of far-red and NIR cyanine fluorophores, followed by simulations of MINFLUX localizations, over typical time scales (microsecond to 10 milliseconds), sample and excitation conditions for MINFLUX imaging. We identified fluorophore blinking via photoisomerization and photoreduction as the main cause of localization errors, and that use of balanced redox buffers and repetitive excitation beam scans can suppress such errors. Implementing these strategies, we could demonstrate NIR-MINFLUX imaging with nanometer localization precision, thereby also presenting an overall strategy to design optimal sample and excitation conditions, for MINFLUX imaging and for SRM in general.", "doi": "10.1126/sciadv.adw3149", "pmid": "41348895", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-12-06T16:23:27.052Z", "modified": "2025-12-06T16:23:28.621Z"}, {"entity": "publication", "iuid": "d2a2d6d880234ac78144a60503cbbe20", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d2a2d6d880234ac78144a60503cbbe20.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d2a2d6d880234ac78144a60503cbbe20"}}, "title": "Ultrafast, remote-controlled protonation reaction enables structural changes in a phytochrome.", "authors": [{"family": "Shankar", "given": "Madan Kumar", "initials": "MK", "orcid": "0000-0002-7944-1081", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd956823ccdf480a8f079fbc11a6815a.json"}}, {"family": "Grunewald", "given": "Lukas", "initials": "L", "orcid": "0009-0006-2976-8680", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc954183b184d28b1de95594ab07564.json"}}, {"family": "Wahlgren", "given": "Weixiao Yuan", "initials": "WY", "orcid": "0000-0003-0413-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/18c55c12fa894dffa8f95f325affa529.json"}}, {"family": "Stucki-Buchli", "given": "Brigitte", "initials": "B", "orcid": "0000-0002-6756-0665", "researcher": {"href": "https://publications.scilifelab.se/researcher/7755ea9da8ee490fa808a0ff505406c6.json"}}, {"family": "Nimmrich", "given": "Amke", "initials": "A", "orcid": "0000-0003-0425-2101", "researcher": {"href": "https://publications.scilifelab.se/researcher/72e8a83ab0cb4d7dad20f00784045ba4.json"}}, {"family": "Kurttila", "given": "Moona", "initials": "M"}, {"family": "Fischer", "given": "Anna-Lena", "initials": "AL", "orcid": "0009-0009-3310-5021", "researcher": {"href": "https://publications.scilifelab.se/researcher/979212c2ef024d249845258e2b322f0e.json"}}, {"family": "Salvadori", "given": "Giacomo", "initials": "G", "orcid": "0000-0001-7330-6228", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f6eae0cdb9e45f99874d6bd200b81c6.json"}}, {"family": "Cellini", "given": "Andrea", "initials": "A"}, {"family": "Maj", "given": "Piotr", "initials": "P", "orcid": "0000-0002-9832-2344", "researcher": {"href": "https://publications.scilifelab.se/researcher/70b8070ad9c349aa875c84d6e101c97a.json"}}, {"family": "Anindya", "given": "Atsarina Larasati", "initials": "AL"}, {"family": "Claesson", "given": "Elin", "initials": "E", "orcid": "0000-0001-8232-7725", "researcher": {"href": "https://publications.scilifelab.se/researcher/10fe8a3b1cc3431384cd9dbe7c9e3865.json"}}, {"family": "Luo", "given": "Fangjia", "initials": "F", "orcid": "0000-0003-0631-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c5507f74fe84eee866fdf2ee3a82b44.json"}}, {"family": "Malla", "given": "Tek Narsingh", "initials": "TN", "orcid": "0000-0002-1387-0801", "researcher": {"href": "https://publications.scilifelab.se/researcher/800976e6911240d080bbf9602f26ce7c.json"}}, {"family": "Pandey", "given": "Suraj", "initials": "S", "orcid": "0000-0002-7097-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/85d34f3408e14d3a9bd538656c3220ab.json"}}, {"family": "Tosha", "given": "Takehiko", "initials": "T", "orcid": "0000-0002-8971-0759", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1075f4e3f1d4966bee737cea1060f75.json"}}, {"family": "Nipawan", "given": "Nuemket", "initials": "N"}, {"family": "Owada", "given": "Shigeki", "initials": "S", "orcid": "0000-0002-1451-7612", "researcher": {"href": "https://publications.scilifelab.se/researcher/78948368f25e4fffba5f79203efb84d9.json"}}, {"family": "Tono", "given": "Kensuke", "initials": "K", "orcid": "0000-0003-1218-3759", "researcher": {"href": "https://publications.scilifelab.se/researcher/3afc0496078b4d719b0653069800e667.json"}}, {"family": "Tanaka", "given": "Rie", "initials": "R", "orcid": "0000-0003-1062-4792", "researcher": {"href": "https://publications.scilifelab.se/researcher/69908679d76c42d6ad9aa42264c60de0.json"}}, {"family": "Stojkovi\u0107", "given": "Emina A", "initials": "EA", "orcid": "0000-0002-4971-5213", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e203482fbc54cbbbcd4a712f6184dd9.json"}}, {"family": "Mozorov", "given": "Dmitry", "initials": "D", "orcid": "0000-0001-9524-948X", "researcher": {"href": "https://publications.scilifelab.se/researcher/fce1c5072a0a445f918e621e23e4687b.json"}}, {"family": "Myllyperki\u00f6", "given": "Pasi", "initials": "P", "orcid": "0000-0003-1651-1676", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e10ceedb7594f5698b53af01f444a21.json"}}, {"family": "Kumpulainen", "given": "Tatu", "initials": "T", "orcid": "0000-0001-9469-9294", "researcher": {"href": "https://publications.scilifelab.se/researcher/e94b734da6774d0fb880f361b50892e9.json"}}, {"family": "Takala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-2518-8583", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf65baa23c3349caa07bc0f44cb52d88.json"}}, {"family": "Schmidt", "given": "Marius", "initials": "M", "orcid": "0000-0002-0962-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e24cc255b246e8a44c52d4002eb46c.json"}}, {"family": "Ihalainen", "given": "Janne A", "initials": "JA", "orcid": "0000-0002-8741-1587", "researcher": {"href": "https://publications.scilifelab.se/researcher/4730f17c203e496bb52a8812767bf37b.json"}}, {"family": "Westenhoff", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6961-8015", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f1519bb234b43c6a13833b04e6720b8.json"}}], "type": "journal article", "published": "2025-10-17", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "42", "pages": "eady0499", "issn-l": "2375-2548"}, "abstract": "In photoactive proteins, coupling between the chromophore and protein matrix is exquisitely tuned. Proton transfer reactions can mediate this coupling, as in proton-coupled electron transfer and excited-state proton transfer. Additional mechanisms involving proton dislocations may exist but remain undiscovered. Here, we present a femtosecond crystallographic movie of the phytochrome from Deinococcus radiodurans. The structures reveal a space-conserving mechanism for rotation of the D-ring in the excited state. We observe rearrangement of a conserved hydrogen bond network within 300 fs, which precedes the isomerization reaction of the chromophore. Aided by molecular modeling and independently confirmed by femtosecond infrared spectroscopy, we attribute these changes to a protonation shift of the strictly conserved histidine-260. Although this histidine lies close to the photoexcited \u03c0-orbitals of the chromophore, it is not directly part of them. We propose that this \"remote-controlled\" proton transfer relays photoexcitation near-instantaneously to the protein matrix. This mechanism may be widely used to transduce cofactor signals to their hosting enzymes.", "doi": "10.1126/sciadv.ady0499", "pmid": "41105772", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12533598"}], "notes": [], "created": "2025-11-28T10:51:47.654Z", "modified": "2025-11-28T10:51:48.542Z"}, {"entity": "publication", "iuid": "89a9d81b95104d2ead4db6caebd4990c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89a9d81b95104d2ead4db6caebd4990c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89a9d81b95104d2ead4db6caebd4990c"}}, "title": "Scalable deep learning reconstruction for accelerated multidimensional nuclear magnetic resonance spectroscopy of proteins", "authors": [{"family": "Huang", "given": "Yihui", "initials": "Y", "orcid": "0000-0002-5035-7687", "researcher": {"href": "https://publications.scilifelab.se/researcher/773bedbe71644bb3adab46fba3477c24.json"}}, {"family": "Gao", "given": "Yuncheng", "initials": "Y", "orcid": "0009-0005-8549-1789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b568fae51f86472487896e51029f0c6f.json"}}, {"family": "Tu", "given": "Zhangren", "initials": "Z", "orcid": "0000-0002-0863-2454", "researcher": {"href": "https://publications.scilifelab.se/researcher/e450c06cfb6d4ff3847e5d98dc818d2b.json"}}, {"family": "Agback", "given": "Tatiana", "initials": "T", "orcid": "0000-0003-1325-6024", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ded0891ca3d4bdda4082ffa347ca37a.json"}}, {"family": "Orekhov", "given": "Vladislav", "initials": "V", "orcid": "0000-0002-7892-6896", "researcher": {"href": "https://publications.scilifelab.se/researcher/77382c412de04fa08ff7c3bc7087b77e.json"}}, {"family": "Hyberts", "given": "Sven G", "initials": "SG", "orcid": "0000-0002-3169-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a0d5dc0f7b040f1b979312bf59a5daf.json"}}, {"family": "Wagner", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-2063-4401", "researcher": {"href": "https://publications.scilifelab.se/researcher/ab6dec04566246c28cfd076fb667f929.json"}}, {"family": "Lin", "given": "Yanqin", "initials": "Y", "orcid": "0000-0003-0596-0740", "researcher": {"href": "https://publications.scilifelab.se/researcher/92d8757206c6419c97d3e6699cc1a8d0.json"}}, {"family": "Chen", "given": "Zhong", "initials": "Z", "orcid": "0000-0002-1473-2224", "researcher": {"href": "https://publications.scilifelab.se/researcher/c95d3606af9b4826a6a298c5ddcdc01e.json"}}, {"family": "Guo", "given": "Di", "initials": "D", "orcid": "0000-0002-9910-5720", "researcher": {"href": "https://publications.scilifelab.se/researcher/0450ec43a296466d8a31387fa3bd9ea6.json"}}, {"family": "Qu", "given": "Xiaobo", "initials": "X", "orcid": "0000-0002-8675-5820", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0bbb61a58d4218ac29f5ec08ed3520.json"}}], "type": "journal-article", "published": "2025-09-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "39", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.adw8122", "pmid": null, "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:02:33.748Z", "modified": "2025-11-27T08:02:34.801Z"}, {"entity": "publication", "iuid": "588352e9404f4729b0d75cdc614fd16e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588352e9404f4729b0d75cdc614fd16e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588352e9404f4729b0d75cdc614fd16e"}}, "title": "Structure of the complete 14-subunit botulinum neurotoxin B complex reveals a unique anchoring through the narrow central pore of HA70.", "authors": [{"family": "Kr\u010d", "given": "Ajda", "initials": "A", "orcid": "0009-0007-5842-8527", "researcher": {"href": "https://publications.scilifelab.se/researcher/cda5c360c20149279692c5d69df7a694.json"}}, {"family": "Ko\u0161enina", "given": "Sara Persson", "initials": "SP", "orcid": "0000-0001-7893-0249", "researcher": {"href": "https://publications.scilifelab.se/researcher/9370d4ecf19c438bb205c43c23f94f26.json"}}, {"family": "Nowakowska", "given": "Maria B", "initials": "MB", "orcid": "0000-0003-2592-2442", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d7fb5e257e941fd8738d9ff147d6b61.json"}}, {"family": "Masuyer", "given": "Geoffrey", "initials": "G", "orcid": "0000-0002-9527-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/41dcc0806dba4a56bb04725812f3a000.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}], "type": "journal article", "published": "2025-08-29", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "35", "pages": "eadx5058", "issn-l": "2375-2548"}, "abstract": "Botulinum neurotoxin serotype B1 (BoNT/B) is a highly potent neurotoxin and therapeutic agent. Here, we present the structure of the complete 14-subunit (780 kDa) progenitor toxin complex (L-PTC) and of five subcomplexes. The structures show how the toxin interacts with its associated components in their role to protect and deliver BoNT/B across epithelial barriers. Each subcomplex, including the M-PTC, M-PTC-HA70, NTNH-HA70, and HA70 trimer, provides detailed understanding of the assembly mechanism, in which the NTNH-nLoop adopts a unique fold that locks the M-PTC into a central pore formed by HA70. The HA subcomplex presents a tripod architecture with flexible legs that may adapt to the rugged cell surface. Mass photometry reveals the pH dependence of BoNT/B release from the complex which is unexpectedly influenced by the presence of HA70. This study provides the complete L-PTC structure, offering insights into its assemblage and supporting the development of countermeasures and therapeutic applications.", "doi": "10.1126/sciadv.adx5058", "pmid": "40864696", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12383256"}], "notes": [], "created": "2025-09-03T12:07:51.156Z", "modified": "2025-11-24T10:54:02.699Z"}, {"entity": "publication", "iuid": "a8fbcd4a221c4de2a1151348bd4c9304", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8fbcd4a221c4de2a1151348bd4c9304.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8fbcd4a221c4de2a1151348bd4c9304"}}, "title": "Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.", "authors": [{"family": "Kauko", "given": "Otto", "initials": "O", "orcid": "0000-0001-8948-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5390cad42a0409f8b66f56ab23ca232.json"}}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Pihlajamaa", "given": "P\u00e4ivi", "initials": "P", "orcid": "0000-0001-9725-6907", "researcher": {"href": "https://publications.scilifelab.se/researcher/1171591a6a724f50a631d34948c6f14a.json"}}, {"family": "H\u00e4kkinen", "given": "Antti", "initials": "A", "orcid": "0000-0002-8081-1588", "researcher": {"href": "https://publications.scilifelab.se/researcher/b00bca666f344d4980a97bbdba20361e.json"}}, {"family": "Queiroz", "given": "Rayner M L", "initials": "RML"}, {"family": "P\u00e4\u00e4kk\u00f6nen", "given": "Mirva", "initials": "M"}, {"family": "Ventel\u00e4", "given": "Sami", "initials": "S"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b58e5cef5224fdcbdcd626fb798b169.json"}}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL", "orcid": "0000-0003-2363-4287", "researcher": {"href": "https://publications.scilifelab.se/researcher/916e190e150e465c9e6afc11911bae04.json"}}, {"family": "Murgia", "given": "Antonio", "initials": "A"}, {"family": "Sahu", "given": "Biswajyoti", "initials": "B", "orcid": "0000-0001-6576-5440", "researcher": {"href": "https://publications.scilifelab.se/researcher/283b12ad225d4fb2b4e38b7f10c026d4.json"}}, {"family": "Routila", "given": "Johannes", "initials": "J", "orcid": "0000-0001-5385-7065", "researcher": {"href": "https://publications.scilifelab.se/researcher/71ee18226e6e4a42ae83b7106ca8b343.json"}}, {"family": "Wei", "given": "Gong-Hong", "initials": "G"}, {"family": "Irjala", "given": "Heikki", "initials": "H", "orcid": "0000-0003-3054-4677", "researcher": {"href": "https://publications.scilifelab.se/researcher/bf759b807e9640aab8fcadbad0c60662.json"}}, {"family": "Griffin", "given": "Julian L", "initials": "JL", "orcid": "0000-0003-1336-7744", "researcher": {"href": "https://publications.scilifelab.se/researcher/98e91146412f4bd2a0bed9331efee8d2.json"}}, {"family": "Lilley", "given": "Kathryn S", "initials": "KS", "orcid": "0000-0003-0594-6543", "researcher": {"href": "https://publications.scilifelab.se/researcher/77b4e7e18a88455199308070d6da7ea3.json"}}, {"family": "Kivioja", "given": "Teemu", "initials": "T", "orcid": "0000-0002-7732-2177", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c318f57c5ce4f4bb747e19514caa907.json"}}, {"family": "Hautaniemi", "given": "Sampsa", "initials": "S", "orcid": "0000-0002-7749-2694", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29cabf8ec5e4f78b9d14984a60c3e84.json"}}, {"family": "Taipale", "given": "Jussi", "initials": "J", "orcid": "0000-0003-4204-0951", "researcher": {"href": "https://publications.scilifelab.se/researcher/43111333f8a84b2cbbceb64d4e1e3bc5.json"}}], "type": "journal article", "published": "2025-08-22", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "11", "issue": "34", "pages": "eadt1798"}, "abstract": "Mutations in numerous genes contribute to human cancer, with different oncogenic lesions prevalent in different cancer types. However, the malignant phenotype is simple, characterized by unrestricted cell growth, invasion, and often metastasis. One possible hypothesis explaining this dichotomy is that cancer genes regulate common targets, which then function as master regulators of essential cancer phenotypes. To identify mechanisms that drive the most fundamental feature shared by all tumors-unrestricted cell proliferation-we used a multiomic approach, which identified translation and ribosome biogenesis as common targets of major oncogenic pathways across cancer types. Proteomic analysis of tumors and functional studies of cell cultures established nucleolar and coiled-body phosphoprotein 1 as a key node, whose convergent regulation, both transcriptionally and posttranslationally, is critical for tumor cell proliferation. Our results indicate that lineage-specific oncogenic pathways regulate the same set of targets for growth control, revealing key downstream nodes that could be targeted for therapy or chemoprevention.", "doi": "10.1126/sciadv.adt1798", "pmid": "40834066", "labels": {"Chemical Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC13155486"}], "notes": [], "created": "2025-11-25T16:41:01.046Z", "modified": "2026-05-25T19:26:02.282Z"}, {"entity": "publication", "iuid": "d086ca68d3ff42dc9c2f5eaa0834b478", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d086ca68d3ff42dc9c2f5eaa0834b478.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d086ca68d3ff42dc9c2f5eaa0834b478"}}, "title": "Droplet microfluidics-based detection of rare antibiotic-resistant subpopulations in Escherichia coli from bloodstream infections.", "authors": [{"family": "Agnihotri", "given": "Sagar N", "initials": "SN", "orcid": "0000-0003-0943-6751", "researcher": {"href": "https://publications.scilifelab.se/researcher/c42c1834bf5247a38d98b8bab8b4914d.json"}}, {"family": "Fatsis-Kavalopoulos", "given": "Nikos", "initials": "N", "orcid": "0000-0002-5081-0138", "researcher": {"href": "https://publications.scilifelab.se/researcher/c173faa59bde4b908da82e02a23d4b70.json"}}, {"family": "Windhager", "given": "Jonas", "initials": "J", "orcid": "0000-0002-2111-5291", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbdf2ef632c740cdaba02c8ee61f2b62.json"}}, {"family": "Tenje", "given": "Maria", "initials": "M", "orcid": "0000-0002-1264-1337", "researcher": {"href": "https://publications.scilifelab.se/researcher/18affd576ee84f62a7a40f678a600058.json"}}, {"family": "Andersson", "given": "Dan I", "initials": "DI", "orcid": "0000-0001-6640-2174", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb042b3dfa21450e862a29951ea0c1eb.json"}}], "type": "journal article", "published": "2025-07-04", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "27", "pages": "eadv4558", "issn-l": "2375-2548"}, "abstract": "Population heterogeneity in bacterial phenotypes, such as antibiotic resistance, is increasingly recognized as a medical concern. Heteroresistance occurs when a predominantly susceptible bacterial population harbors a rare resistant subpopulation. During antibiotic exposure, these resistant bacteria can be selected and lead to treatment failure. Standard antibiotic susceptibility testing methods often fail to reliably detect these subpopulations due to their low frequency, highlighting the need for improved diagnostic approaches. Here, we present a droplet microfluidics method where bacteria are encapsulated in droplets containing growth medium and antibiotics. The growth of rare resistant cells is detected by observing droplet shrinkage under microscopy. We validated this method for three clinically important antibiotics in Escherichia coli isolates obtained from bloodstream infections and showed that it can detect resistant subpopulations as infrequent as 10-6 using only 200 to 300 droplets. In addition, we designed a multiplex microfluidic chip to increase the throughput of the assay.", "doi": "10.1126/sciadv.adv4558", "pmid": "40614180", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12227044"}], "notes": [], "created": "2025-11-25T12:57:58.095Z", "modified": "2025-11-25T12:57:58.278Z"}, {"entity": "publication", "iuid": "5677316fa2684bbba44365a528fe26fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5677316fa2684bbba44365a528fe26fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5677316fa2684bbba44365a528fe26fb"}}, "title": "Three-dimensional cell-cell interactions promote direct reprogramming of patient fibroblasts into functional and transplantable neurons.", "authors": [{"family": "Kajtez", "given": "Janko", "initials": "J", "orcid": "0000-0001-9997-2325", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b3315d47d804d8cb1dc7f6ff2b31731.json"}}, {"family": "Laurin", "given": "Kerstin", "initials": "K", "orcid": "0000-0002-3267-1111", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fabb942c9c540de9e23f5e79018535c.json"}}, {"family": "Nilsson", "given": "Fredrik", "initials": "F"}, {"family": "Bruzelius", "given": "Andreas", "initials": "A"}, {"family": "Cepeda-Prado", "given": "Efrain", "initials": "E", "orcid": "0000-0001-9781-3742", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0ee87e59e144bd6b8a0cce5b1e29194.json"}}, {"family": "Birtele", "given": "Marcella", "initials": "M", "orcid": "0000-0003-2123-6453", "researcher": {"href": "https://publications.scilifelab.se/researcher/5597264e465b4396b0016336b46a7fb1.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Herborg", "given": "Freja", "initials": "F", "orcid": "0000-0002-0159-4598", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ab2173b0ed34bf48a77880e33146a05.json"}}, {"family": "Rylander Ottosson", "given": "Daniella", "initials": "D", "orcid": "0000-0002-9270-3576", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ebb28287f4725b41a4bbf981d0e40.json"}}, {"family": "Storm", "given": "Petter", "initials": "P", "orcid": "0000-0002-7655-3731", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5af5462a2c04920bb43120d429ac386.json"}}, {"family": "Fiorenzano", "given": "Alessandro", "initials": "A", "orcid": "0000-0003-2478-5941", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a17c87028884ff8b5bf3da42a0d63fe.json"}}, {"family": "Habekost", "given": "Mette", "initials": "M", "orcid": "0000-0002-5987-2909", "researcher": {"href": "https://publications.scilifelab.se/researcher/f50503763ece48ba851a3031aade3256.json"}}, {"family": "Parmar", "given": "Malin", "initials": "M", "orcid": "0000-0001-5002-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48b5aaff3bc4832a96fda4f2cf127cb.json"}}], "type": "journal article", "published": "2025-06-06", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "23", "pages": "eadq7855", "issn-l": "2375-2548"}, "abstract": "Direct reprogramming of somatic cells into induced neurons (iNs) has become an attractive strategy for the generation of patient-specific neurons for disease modeling and regenerative neuroscience. To this end, adult human dermal fibroblasts (hDFs) present one of the most relevant cell sources. However, iNs generated from adult hDFs using two-dimensional cultures are difficult to maintain in vitro and face challenges in survival upon transplantation into the adult brain, thus imposing constraints on biomedical applications of iN technology. Here, we present a platform for direct in vitro reprogramming of adult hDFs inside three-dimensional suspension microcultures (3D-iNs). We show that the 3D environment favors neuronal over fibroblast cellular identity to yield more robust conversion into functional neurons with extended culturing span. The 3D reprogramming approach also provides a platform for fusion into induced assembloids. 3D-iNs can be gently harvested and transplanted into the adult rodent brain to reproducibly generate neuron-rich grafts, thus eliminating a major bottleneck in the direct reprogramming field.", "doi": "10.1126/sciadv.adq7855", "pmid": "40479059", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12143395"}], "notes": [], "created": "2025-09-08T07:10:49.448Z", "modified": "2025-09-08T07:10:50.125Z"}, {"entity": "publication", "iuid": "313624c3b36d4a3d8322a45a9a99729e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/313624c3b36d4a3d8322a45a9a99729e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/313624c3b36d4a3d8322a45a9a99729e"}}, "title": "Open-flask, ambient temperature direct arylation synthesis of mixed ionic-electronic conductors", "authors": [{"family": "Kimpel", "given": "Joost", "initials": "J", "orcid": "0000-0002-3576-6132", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c64c9e6e6c84e848cde84461fb55d24.json"}}, {"family": "Kim", "given": "Youngseok", "initials": "Y", "orcid": "0000-0002-9584-821X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4046f508d954f36a6c938aa94a454ca.json"}}, {"family": "Schomaker", "given": "Hannes", "initials": "H"}, {"family": "Hinojosa", "given": "Diego R", "initials": "DR", "orcid": "0000-0002-4849-2062", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2bafd0c86f44253856168aedff62ca2.json"}}, {"family": "Asatryan", "given": "Jesika", "initials": "J", "orcid": "0000-0002-8504-1332", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf89c915fd474fe1937f91d6042e0a08.json"}}, {"family": "Mart\u00edn", "given": "Jaime", "initials": "J"}, {"family": "Kroon", "given": "Renee", "initials": "R", "orcid": "0000-0001-8053-4288", "researcher": {"href": "https://publications.scilifelab.se/researcher/26f7dc50e9284f87ad913e893f14e69e.json"}}, {"family": "Sommer", "given": "Michael", "initials": "M", "orcid": "0000-0002-2377-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c0656ed9bca4ea28c9810b08ee61d64.json"}}, {"family": "M\u00fcller", "given": "Christian", "initials": "C", "orcid": "0000-0001-7859-7909", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fc06198eb0c4a3eb17d052d8ef124ae.json"}}], "type": "journal-article", "published": "2025-05-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "19", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.adv8168", "pmid": null, "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-27T08:06:19.926Z", "modified": "2025-11-27T08:06:20.867Z"}, {"entity": "publication", "iuid": "3c683e5542c844658749a288caaa0a26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c683e5542c844658749a288caaa0a26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c683e5542c844658749a288caaa0a26"}}, "title": "Dephosphorylation and ion binding in prokaryotic calcium transport.", "authors": [{"family": "Prabudiansyah", "given": "Irfan", "initials": "I", "orcid": "0000-0001-7133-6933", "researcher": {"href": "https://publications.scilifelab.se/researcher/1748e78da4b0468692908009c32eaac1.json"}}, {"family": "Or\u00e4dd", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0706-7414", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66f5bb420b4e3c8d706350f86b38ff.json"}}, {"family": "Magkakis", "given": "Konstantinos", "initials": "K", "orcid": "0009-0006-3715-1170", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e26e8739b574fe0b6089d1ad22870a9.json"}}, {"family": "Pounot", "given": "Kevin", "initials": "K", "orcid": "0000-0003-2217-1081", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3ef4f67c86441cbba8ebcb9b2773bc3.json"}}, {"family": "Levantino", "given": "Matteo", "initials": "M", "orcid": "0000-0002-1224-4809", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe97c47f66247d88ae00cfe6edde53e.json"}}, {"family": "Andersson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3364-6647", "researcher": {"href": "https://publications.scilifelab.se/researcher/08ef723036544a65806f0c46d5b44f61.json"}}], "type": "journal article", "published": "2024-10-11", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "41", "pages": "eadp2916", "issn-l": "2375-2548"}, "abstract": "Calcium (Ca2+) signaling is fundamental to cellular processes in both eukaryotic and prokaryotic organisms. While the mechanisms underlying eukaryotic Ca2+ transport are well documented, an understanding of prokaryotic transport remains nascent. LMCA1, a Ca2+ adenosine triphosphatase (ATPase) from Listeria monocytogenes, has emerged as a prototype for elucidating structure and dynamics in prokaryotic Ca2+ transport. Here, we used a multidisciplinary approach integrating kinetics, structure, and dynamics to unravel the intricacies of LMCA1 function. A cryo-electron microscopy (cryo-EM) structure of a Ca2+-bound E1 state showed ion coordination by Asp720, Asn716, and Glu292. Time-resolved x-ray solution scattering experiments identified phosphorylation as the rate-determining step. A cryo-EM E2P state structure exhibited remarkable similarities to a SERCA1a E2-P* state, which highlights the essential role of the unique P-A domain interface in enhancing dephosphorylation rates and reconciles earlier proposed mechanisms. Our study underscores the distinctiveness between eukaryotic and prokaryotic Ca2+ ATPase transport systems and positions LMCA1 as a promising drug target for developing antimicrobial strategies.", "doi": "10.1126/sciadv.adp2916", "pmid": "39908574", "labels": {"Cryo-EM": "Service", "Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11468904"}], "notes": [], "created": "2024-11-27T13:05:37.487Z", "modified": "2025-10-29T14:39:43.384Z"}, {"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": "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": "0c4b50f79cdd44fb8628da5a345f1b64", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c4b50f79cdd44fb8628da5a345f1b64.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c4b50f79cdd44fb8628da5a345f1b64"}}, "title": "Reprogramming Yarrowia lipolytica metabolism for efficient synthesis of itaconic acid from flask to semipilot scale.", "authors": [{"family": "Fu", "given": "Jing", "initials": "J", "orcid": "0000-0001-8651-0658", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec025bf22f943c7add91f987548bb2a.json"}}, {"family": "Zaghen", "given": "Simone", "initials": "S", "orcid": "0000-0002-8964-718X", "researcher": {"href": "https://publications.scilifelab.se/researcher/55013b85227b4cee8eecf11979850d71.json"}}, {"family": "Lu", "given": "Hongzhong", "initials": "H", "orcid": "0009-0005-8555-1841", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ba5d929d8fa4c769648238a6dec119e.json"}}, {"family": "Konzock", "given": "Oliver", "initials": "O", "orcid": "0000-0001-5253-5961", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6a94621516b44f3a01ea7c4a09d0905.json"}}, {"family": "Poorinmohammad", "given": "Naghmeh", "initials": "N"}, {"family": "Kornberg", "given": "Alexander", "initials": "A", "orcid": "0009-0002-3029-1702", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e2b335f86314fc0b25ce6e5e0733048.json"}}, {"family": "Ledesma-Amaro", "given": "Rodrigo", "initials": "R", "orcid": "0000-0003-2631-5898", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffd34c116bbf43a08620103ade906075.json"}}, {"family": "Koseto", "given": "Deni", "initials": "D", "orcid": "0000-0002-0253-1468", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fcdb63d2de64afcb509c6b77bcfd4e7.json"}}, {"family": "Wentzel", "given": "Alexander", "initials": "A", "orcid": "0000-0002-9420-1959", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b0e329fb874c8a8c7cb5721c365352.json"}}, {"family": "Di Bartolomeo", "given": "Francesca", "initials": "F"}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ", "orcid": "0000-0002-3593-5792", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df361f8014144e79479631fcbffad53.json"}}], "type": "journal article", "published": "2024-08-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "32", "pages": "eadn0414", "issn-l": "2375-2548"}, "abstract": "Itaconic acid is an emerging platform chemical with extensive applications. Itaconic acid is currently produced by Aspergillus terreus through biological fermentation. However, A. terreus is a fungal pathogen that needs additional morphology controls, making itaconic acid production on industrial scale problematic. Here, we reprogrammed the Generally Recognized As Safe (GRAS) yeast Yarrowia lipolytica for competitive itaconic acid production. After preventing carbon sink into lipid accumulation, we evaluated itaconic acid production both inside and outside the mitochondria while fine-tuning its biosynthetic pathway. We then mimicked the regulation of nitrogen limitation in nitrogen-replete conditions by down-regulating NAD+-dependent isocitrate dehydrogenase through weak promoters, RNA interference, or CRISPR interference. Ultimately, we optimized fermentation parameters for fed-batch cultivations and produced itaconic acid titers of 130.1 grams per liter in 1-liter bioreactors and 94.8 grams per liter in a 50-liter bioreactor on semipilot scale. Our findings provide effective approaches to harness the GRAS microorganism Y. lipolytica for competitive industrial-scale production of itaconic acid.", "doi": "10.1126/sciadv.adn0414", "pmid": "39121230", "labels": {"Chalmers Mass Spectrometry Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11313960"}], "notes": [], "created": "2024-11-27T15:32:15.067Z", "modified": "2024-11-27T15:32:15.482Z"}, {"entity": "publication", "iuid": "4e32b1a69fb9494d8f947125c273d792", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4e32b1a69fb9494d8f947125c273d792.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4e32b1a69fb9494d8f947125c273d792"}}, "title": "AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1.", "authors": [{"family": "D\u00edaz-Holgu\u00edn", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-3449-5086", "researcher": {"href": "https://publications.scilifelab.se/researcher/335c8b7a0b6043fc984a1d21b77f721b.json"}}, {"family": "Saarinen", "given": "Marcus", "initials": "M"}, {"family": "Vo", "given": "Duc Duy", "initials": "DD"}, {"family": "Sturchio", "given": "Andrea", "initials": "A"}, {"family": "Branzell", "given": "Niclas", "initials": "N"}, {"family": "Cabeza de Vaca", "given": "Israel", "initials": "I", "orcid": "0000-0002-6208-1091", "researcher": {"href": "https://publications.scilifelab.se/researcher/65628edbdaa448b8ab37d5eb4e100aee.json"}}, {"family": "Hu", "given": "Huabin", "initials": "H"}, {"family": "Mitjavila-Dom\u00e8nech", "given": "N\u00faria", "initials": "N"}, {"family": "Lindqvist", "given": "Annika", "initials": "A", "orcid": "0009-0003-2587-8434", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6e7610970e64dcba383e49b60df4f50.json"}}, {"family": "Baranczewski", "given": "Pawel", "initials": "P", "orcid": "0000-0001-5772-6791", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f7af2466c14275a42aad4a431b2dcb.json"}}, {"family": "Millan", "given": "Mark J", "initials": "MJ"}, {"family": "Yang", "given": "Yunting", "initials": "Y", "orcid": "0000-0001-5700-1547", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f8478fd3a4d4a2c8280843835b543d9.json"}}, {"family": "Carlsson", "given": "Jens", "initials": "J", "orcid": "0000-0003-4623-2977", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7d91087358e46e38bb1b7110dc0b214.json"}}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}], "type": "journal article", "published": "2024-08-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "32", "pages": "eadn1524", "issn-l": "2375-2548"}, "abstract": "Artificial intelligence is revolutionizing protein structure prediction, providing unprecedented opportunities for drug design. To assess the potential impact on ligand discovery, we compared virtual screens using protein structures generated by the AlphaFold machine learning method and traditional homology modeling. More than 16 million compounds were docked to models of the trace amine-associated receptor 1 (TAAR1), a G protein-coupled receptor of unknown structure and target for treating neuropsychiatric disorders. Sets of 30 and 32 highly ranked compounds from the AlphaFold and homology model screens, respectively, were experimentally evaluated. Of these, 25 were TAAR1 agonists with potencies ranging from 12 to 0.03 \u03bcM. The AlphaFold screen yielded a more than twofold higher hit rate (60%) than the homology model and discovered the most potent agonists. A TAAR1 agonist with a promising selectivity profile and drug-like properties showed physiological and antipsychotic-like effects in wild-type but not in TAAR1 knockout mice. These results demonstrate that AlphaFold structures can accelerate drug discovery.", "doi": "10.1126/sciadv.adn1524", "pmid": "39110804", "labels": {"Chemical Biology Consortium Sweden": "Service", "Drug Discovery and Development": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11305387"}], "notes": [], "created": "2024-08-16T12:19:56.237Z", "modified": "2025-10-17T13:05:07.343Z"}, {"entity": "publication", "iuid": "e45d50497d0a46859df9cff25bf95fda", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e45d50497d0a46859df9cff25bf95fda.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e45d50497d0a46859df9cff25bf95fda"}}, "title": "Magnesium induced structural reorganization in the active site of adenylate kinase.", "authors": [{"family": "Nam", "given": "Kwangho", "initials": "K", "orcid": "0000-0003-0723-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/29b33d801f244b6aac48a9d626962770.json"}}, {"family": "Thodika", "given": "Abdul Raafik Arattu", "initials": "ARA", "orcid": "0009-0001-4973-5265", "researcher": {"href": "https://publications.scilifelab.se/researcher/e85cd5c166044d3fb45c07ca33ebc2e9.json"}}, {"family": "Tischlik", "given": "Sonja", "initials": "S", "orcid": "0000-0001-7518-2441", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2677763e4c64cca828e8ae78a1b4645.json"}}, {"family": "Phoeurk", "given": "Chanrith", "initials": "C", "orcid": "0000-0002-8025-4232", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec49e730932846aa96826a5fffbab6c5.json"}}, {"family": "Nagy", "given": "Tam\u00e1s Mil\u00e1n", "initials": "TM", "orcid": "0000-0003-4766-1992", "researcher": {"href": "https://publications.scilifelab.se/researcher/22a9fd6e6a4e46b2ae2bc0166f62e092.json"}}, {"family": "Schierholz", "given": "L\u00e9on", "initials": "L"}, {"family": "\u00c5d\u00e9n", "given": "J\u00f6rgen", "initials": "J", "orcid": "0000-0002-4480-1219", "researcher": {"href": "https://publications.scilifelab.se/researcher/00206abad0de45eb90dc6bd3d5f3cf22.json"}}, {"family": "Rogne", "given": "Per", "initials": "P", "orcid": "0000-0002-3687-9200", "researcher": {"href": "https://publications.scilifelab.se/researcher/31042ecc88a94cd6b97cef0508da93fd.json"}}, {"family": "Drescher", "given": "Malte", "initials": "M", "orcid": "0000-0002-3571-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/35108424964e43fbba3e749d8eca0b5b.json"}}, {"family": "Sauer-Eriksson", "given": "A Elisabeth", "initials": "AE", "orcid": "0000-0003-0124-0199", "researcher": {"href": "https://publications.scilifelab.se/researcher/9435049fbe2745b59e04558cc5201f95.json"}}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9098-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6ea8f5c456428db21b1085ad541538.json"}}], "type": "journal article", "published": "2024-08-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "32", "pages": "eado5504", "issn-l": "2375-2548"}, "abstract": "Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that requires Mg2+ as an essential cofactor. While the primary function of Mg2+ is electrostatic activation of substrates, such as ATP, the full spectrum of catalytic mechanisms exerted by Mg2+ is not known. In this study, we integrate structural biology methods, molecular dynamic (MD) simulations, phylogeny, and enzymology assays to provide molecular insights into Mg2+-dependent structural reorganization in the active site of the metabolic enzyme adenylate kinase. Our results demonstrate that Mg2+ induces a conformational rearrangement of the substrates (ATP and ADP), resulting in a 30\u00b0 adjustment of the angle essential for reversible phosphoryl transfer, thereby optimizing it for catalysis. MD simulations revealed transitions between conformational substates that link the fluctuation of the angle to large-scale enzyme dynamics. The findings contribute detailed insight into Mg2+ activation of enzymes and may be relevant for reversible and irreversible phosphoryl transfer reactions.", "doi": "10.1126/sciadv.ado5504", "pmid": "39121211", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11313852"}], "notes": [], "created": "2024-11-13T19:36:50.332Z", "modified": "2025-10-17T13:03:52.837Z"}, {"entity": "publication", "iuid": "cacf484e41274db9a8d7ab5b3963dc8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cacf484e41274db9a8d7ab5b3963dc8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cacf484e41274db9a8d7ab5b3963dc8d"}}, "title": "The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1.", "authors": [{"family": "Gustavsson", "given": "Emil K", "initials": "EK", "orcid": "0000-0003-0541-7537", "researcher": {"href": "https://publications.scilifelab.se/researcher/996f67ab34fb486aa921970420315b08.json"}}, {"family": "Sethi", "given": "Siddharth", "initials": "S", "orcid": "0000-0002-4398-4295", "researcher": {"href": "https://publications.scilifelab.se/researcher/433a0df98347474897c6c63975206b58.json"}}, {"family": "Gao", "given": "Yujing", "initials": "Y", "orcid": "0000-0002-4542-7062", "researcher": {"href": "https://publications.scilifelab.se/researcher/213e239576ee4891adbc3a1971d29c7b.json"}}, {"family": "Brenton", "given": "Jonathan W", "initials": "JW", "orcid": "0000-0002-2381-8484", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1aabde514394f66be925aa9aa10e25b.json"}}, {"family": "Garc\u00eda-Ruiz", "given": "Sonia", "initials": "S", "orcid": "0000-0003-4913-5312", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0e93d9df684439892ef30ff73200a2.json"}}, {"family": "Zhang", "given": "David", "initials": "D"}, {"family": "Garza", "given": "Raquel", "initials": "R", "orcid": "0000-0002-2524-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d53399af304283ba62e0646acdc612.json"}}, {"family": "Reynolds", "given": "Regina H", "initials": "RH", "orcid": "0000-0001-6470-7919", "researcher": {"href": "https://publications.scilifelab.se/researcher/4397a45fd4cb4ea7a2a1706a0411f0d4.json"}}, {"family": "Evans", "given": "James R", "initials": "JR", "orcid": "0000-0003-2923-281X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fbc42acb41341ebba1b572af6751786.json"}}, {"family": "Chen", "given": "Zhongbo", "initials": "Z", "orcid": "0000-0001-6668-7202", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e05d1f791410d933bca331a7309a3.json"}}, {"family": "Grant-Peters", "given": "Melissa", "initials": "M", "orcid": "0000-0003-0585-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ae1ca65912b4142ac5e8a55b0bfa936.json"}}, {"family": "Macpherson", "given": "Hannah", "initials": "H", "orcid": "0000-0002-9535-4025", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b53a05c7f194155bf828cfa1723d4dd.json"}}, {"family": "Montgomery", "given": "Kylie", "initials": "K", "orcid": "0000-0001-6090-0703", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc6e3ca875354f79a54971e5341235f4.json"}}, {"family": "Dore", "given": "Rhys", "initials": "R", "orcid": "0000-0001-8417-8743", "researcher": {"href": "https://publications.scilifelab.se/researcher/a11f7079ca7740029a876c2dd5260946.json"}}, {"family": "Wernick", "given": "Anna I", "initials": "AI", "orcid": "0000-0001-9048-9492", "researcher": {"href": "https://publications.scilifelab.se/researcher/09b297e297994740b74d583a37c74e43.json"}}, {"family": "Arber", "given": "Charles", "initials": "C", "orcid": "0000-0002-9743-8134", "researcher": {"href": "https://publications.scilifelab.se/researcher/29b0c152839b4115a6da93dcc1ffb835.json"}}, {"family": "Wray", "given": "Selina", "initials": "S"}, {"family": "Gandhi", "given": "Sonia", "initials": "S", "orcid": "0000-0003-4395-2661", "researcher": {"href": "https://publications.scilifelab.se/researcher/01493b3d90a244149225710c5f61d1ed.json"}}, {"family": "Esselborn", "given": "Julian", "initials": "J", "orcid": "0000-0002-3499-8417", "researcher": {"href": "https://publications.scilifelab.se/researcher/b856091feda54167848a30d759ad11ea.json"}}, {"family": "Blauwendraat", "given": "Cornelis", "initials": "C", "orcid": "0000-0001-9358-8111", "researcher": {"href": "https://publications.scilifelab.se/researcher/6dd14eb697a94083a02bbc7d522ea87b.json"}}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM", "orcid": "0000-0002-6158-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2c36afdcd3147f39ad6e34623dbec6c.json"}}, {"family": "Kouli", "given": "Antonina", "initials": "A", "orcid": "0000-0001-6553-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/6894568633154da5aad7f93413297f43.json"}}, {"family": "Quaegebeur", "given": "Annelies", "initials": "A"}, {"family": "Barker", "given": "Roger A", "initials": "RA", "orcid": "0000-0001-8843-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/125769a66f77471da6266577717a6395.json"}}, {"family": "Englund", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-2708-2443", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c98fa2b2e7e4e318cd00eb1e8e3ac7a.json"}}, {"family": "Platt", "given": "Frances", "initials": "F"}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}, {"family": "Wood", "given": "Nicholas W", "initials": "NW", "orcid": "0000-0002-9500-3348", "researcher": {"href": "https://publications.scilifelab.se/researcher/850e5336e5c946d29c3375d616a01836.json"}}, {"family": "Houlden", "given": "Henry", "initials": "H", "orcid": "0000-0002-2866-7777", "researcher": {"href": "https://publications.scilifelab.se/researcher/72a57dac09a341ffb23a2ceb9762e1e3.json"}}, {"family": "Saini", "given": "Harpreet", "initials": "H"}, {"family": "Bento", "given": "Carla F", "initials": "CF", "orcid": "0000-0001-8377-4543", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e028035dc8245d9bc33274cd656358a.json"}}, {"family": "Hardy", "given": "John", "initials": "J", "orcid": "0000-0002-3122-0423", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa5b456a58b40a48d97f0be528c0855.json"}}, {"family": "Ryten", "given": "Mina", "initials": "M", "orcid": "0000-0001-9520-6957", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff7e1cb1b3c640449ea0571c4b3a01ac.json"}}], "type": "journal article", "published": "2024-06-28", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "26", "pages": "eadk1296", "issn-l": "2375-2548"}, "abstract": "Mutations in GBA1 cause Gaucher disease and are the most important genetic risk factor for Parkinson's disease. However, analysis of transcription at this locus is complicated by its highly homologous pseudogene, GBAP1. We show that >50% of short RNA-sequencing reads mapping to GBA1 also map to GBAP1. Thus, we used long-read RNA sequencing in the human brain, which allowed us to accurately quantify expression from both GBA1 and GBAP1. We discovered significant differences in expression compared to short-read data and identify currently unannotated transcripts of both GBA1 and GBAP1. These included protein-coding transcripts from both genes that were translated in human brain, but without the known lysosomal function-yet accounting for almost a third of transcription. Analyzing brain-specific cell types using long-read and single-nucleus RNA sequencing revealed region-specific variations in transcript expression. Overall, these findings suggest nonlysosomal roles for GBA1 and GBAP1 with implications for our understanding of the role of GBA1 in health and disease.", "doi": "10.1126/sciadv.adk1296", "pmid": "38924406", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11204300"}], "notes": [], "created": "2024-11-15T06:28:56.936Z", "modified": "2024-11-15T06:28:59.191Z"}, {"entity": "publication", "iuid": "2327ce3d72bd48d988b4642d35ae1d05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2327ce3d72bd48d988b4642d35ae1d05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2327ce3d72bd48d988b4642d35ae1d05"}}, "title": "MOXD1 is a lineage-specific gene and a tumor suppressor in neuroblastoma.", "authors": [{"family": "Fredlund", "given": "Elina", "initials": "E", "orcid": "0009-0006-1986-1267", "researcher": {"href": "https://publications.scilifelab.se/researcher/49c035ee375d466e8cb10b230ca51395.json"}}, {"family": "Andersson", "given": "Stina", "initials": "S", "orcid": "0000-0003-3226-4740", "researcher": {"href": "https://publications.scilifelab.se/researcher/13415a4a70654146ac1c56e009ee31c4.json"}}, {"family": "Hilgert", "given": "Elien", "initials": "E", "orcid": "0000-0002-4715-6972", "researcher": {"href": "https://publications.scilifelab.se/researcher/a09fe68866854929a507cc66f721392b.json"}}, {"family": "Monferrer", "given": "Ezequiel", "initials": "E"}, {"family": "\u00c1lvarez-Hern\u00e1n", "given": "Guadalupe", "initials": "G", "orcid": "0000-0001-5725-6515", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5c136f13154416b8aa895db485856de.json"}}, {"family": "Karakaya", "given": "Sinan", "initials": "S"}, {"family": "Loontiens", "given": "Siebe", "initials": "S", "orcid": "0000-0002-4602-4580", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e652c656ace4c8f947a2d84b4bfa8b5.json"}}, {"family": "Bek", "given": "Jan Willem", "initials": "JW", "orcid": "0000-0003-1337-1970", "researcher": {"href": "https://publications.scilifelab.se/researcher/908c4fb4652842f8b8ea436a2265eaf4.json"}}, {"family": "Gregor", "given": "Tomas", "initials": "T", "orcid": "0000-0002-7974-1316", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c2c049df61f4fe3a4a2918e99158dd2.json"}}, {"family": "Lecomte", "given": "Estelle", "initials": "E"}, {"family": "Magnusson", "given": "Emma", "initials": "E"}, {"family": "Miltenyte", "given": "Enrika", "initials": "E"}, {"family": "Cabirol", "given": "Marie", "initials": "M"}, {"family": "Kyknas", "given": "Michail", "initials": "M", "orcid": "0009-0004-0813-2670", "researcher": {"href": "https://publications.scilifelab.se/researcher/c67634dfede84d038c0d0dc8535eba15.json"}}, {"family": "Engstr\u00f6m", "given": "Niklas", "initials": "N", "orcid": "0000-0003-2399-985X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a002fa86f9c46fea630c84b02419d6a.json"}}, {"family": "Henriksson", "given": "Marie Arsenian", "initials": "MA", "orcid": "0000-0001-6376-7792", "researcher": {"href": "https://publications.scilifelab.se/researcher/e78a2e958a7b4eaaa9aecad01f0e7c57.json"}}, {"family": "Hammarlund", "given": "Emma", "initials": "E", "orcid": "0000-0001-7625-4793", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2b34455bcd94586a8be8a7adeefe7cc.json"}}, {"family": "Rosenblum", "given": "Jared S", "initials": "JS", "orcid": "0000-0001-5941-9082", "researcher": {"href": "https://publications.scilifelab.se/researcher/49b3dd45a5cd494191b4d24e6edb721f.json"}}, {"family": "Noguera", "given": "Rosa", "initials": "R", "orcid": "0000-0003-4546-7459", "researcher": {"href": "https://publications.scilifelab.se/researcher/91dc687d57f947ba9dde1d129e6c8222.json"}}, {"family": "Speleman", "given": "Frank", "initials": "F"}, {"family": "van Nes", "given": "Johan", "initials": "J"}, {"family": "Mohlin", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2458-3963", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e095a99e2c84d52b13973c9d46d128a.json"}}], "type": "journal article", "published": "2024-06-21", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "25", "pages": "eado1583", "issn-l": "2375-2548"}, "abstract": "Neuroblastoma is a childhood developmental cancer; however, its embryonic origins remain poorly understood. Moreover, in-depth studies of early tumor-driving events are limited because of the lack of appropriate models. Herein, we analyzed RNA sequencing data obtained from human neuroblastoma samples and found that loss of expression of trunk neural crest-enriched gene MOXD1 associates with advanced disease and worse outcome. Further, by using single-cell RNA sequencing data of human neuroblastoma cells and fetal adrenal glands and creating in vivo models of zebrafish, chick, and mouse, we show that MOXD1 is a determinate of tumor development. In addition, we found that MOXD1 expression is highly conserved and restricted to mesenchymal neuroblastoma cells and Schwann cell precursors during healthy development. Our findings identify MOXD1 as a lineage-restricted tumor-suppressor gene in neuroblastoma, potentiating further stratification of these tumors and development of novel therapeutic interventions.", "doi": "10.1126/sciadv.ado1583", "pmid": "38905335", "labels": {"Clinical Genomics Lund": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11192077"}], "notes": [], "created": "2024-11-17T16:35:21.203Z", "modified": "2025-11-10T13:57:53.132Z"}, {"entity": "publication", "iuid": "7d3c4336130e450099e81cfa741064ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7d3c4336130e450099e81cfa741064ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7d3c4336130e450099e81cfa741064ec"}}, "title": "Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.", "authors": [{"family": "Feiner", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-4648-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/4dfa523d52b348359775994be5d69640.json"}}, {"family": "Yang", "given": "Weizhao", "initials": "W"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "While", "given": "Geoffrey M", "initials": "GM", "orcid": "0000-0001-8122-9322", "researcher": {"href": "https://publications.scilifelab.se/researcher/b40ba32f8185473fa3543815e8a539fe.json"}}, {"family": "Uller", "given": "Tobias", "initials": "T", "orcid": "0000-0003-1293-5842", "researcher": {"href": "https://publications.scilifelab.se/researcher/6346267a5c3e41c6a6825b7b20a53fa5.json"}}], "type": "journal article", "published": "2024-04-05", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "10", "issue": "14", "pages": "eadk9315", "issn-l": "2375-2548"}, "abstract": "The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such \"phenotypic syndromes\" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a ~400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.", "doi": "10.1126/sciadv.adk9315", "pmid": "38569035", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10990284"}], "notes": [], "created": "2024-04-09T12:41:11.047Z", "modified": "2024-11-25T10:28:12.121Z"}, {"entity": "publication", "iuid": "49731da5fcb34c8ea7886628fc04fb77", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49731da5fcb34c8ea7886628fc04fb77.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49731da5fcb34c8ea7886628fc04fb77"}}, "title": "LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification.", "authors": [{"family": "Garza", "given": "Raquel", "initials": "R", "orcid": "0000-0002-2524-3055", "researcher": {"href": "https://publications.scilifelab.se/researcher/67d53399af304283ba62e0646acdc612.json"}}, {"family": "Atacho", "given": "Diahann A M", "initials": "DAM", "orcid": "0000-0002-6158-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2c36afdcd3147f39ad6e34623dbec6c.json"}}, {"family": "Adami", "given": "Anita", "initials": "A", "orcid": "0000-0002-9421-7942", "researcher": {"href": "https://publications.scilifelab.se/researcher/174398a7905b490ba8a41108d65bfe1d.json"}}, {"family": "Gerdes", "given": "Patricia", "initials": "P", "orcid": "0000-0002-1148-9134", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8571bfad113498c8fdb09fb74d7b2bd.json"}}, {"family": "Vinod", "given": "Meghna", "initials": "M", "orcid": "0009-0008-9057-6834", "researcher": {"href": "https://publications.scilifelab.se/researcher/de9ee947419d440f82ea756abb28d7f9.json"}}, {"family": "Hsieh", "given": "PingHsun", "initials": "P", "orcid": "0000-0001-8294-6227", "researcher": {"href": "https://publications.scilifelab.se/researcher/00e1f1a68324444ea4e89ec62fc12d64.json"}}, {"family": "Karlsson", "given": "Ofelia", "initials": "O"}, {"family": "Horvath", "given": "Vivien", "initials": "V", "orcid": "0000-0001-6536-1710", "researcher": {"href": "https://publications.scilifelab.se/researcher/7be63bec9f4a4bf2a0fa907973cef28d.json"}}, {"family": "Johansson", "given": "Pia A", "initials": "PA", "orcid": "0000-0002-6938-4060", "researcher": {"href": "https://publications.scilifelab.se/researcher/28206ae896f34a2c85c2ed863d4eb53e.json"}}, {"family": "Pandiloski", "given": "Ninoslav", "initials": "N", "orcid": "0000-0002-1204-5359", "researcher": {"href": "https://publications.scilifelab.se/researcher/156ba4836c234d739d10e0da00acce9b.json"}}, {"family": "Matas-Fuentes", "given": "Jon", "initials": "J", "orcid": "0009-0000-9253-1172", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a4d7313057548238c742aefc9c07ca8.json"}}, {"family": "Quaegebeur", "given": "Annelies", "initials": "A", "orcid": "0000-0001-5357-9341", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2f37a3920374d37a1d5508b580ddac2.json"}}, {"family": "Kouli", "given": "Antonina", "initials": "A", "orcid": "0000-0001-6553-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/6894568633154da5aad7f93413297f43.json"}}, {"family": "Sharma", "given": "Yogita", "initials": "Y"}, {"family": "J\u00f6nsson", "given": "Marie E", "initials": "ME", "orcid": "0000-0002-1184-6269", "researcher": {"href": "https://publications.scilifelab.se/researcher/73ddc70ea52e4bfc82f97a3fc35c09cd.json"}}, {"family": "Monni", "given": "Emanuela", "initials": "E", "orcid": "0000-0003-0083-1050", "researcher": {"href": "https://publications.scilifelab.se/researcher/3becd99e5a7d4d5e8a4d893045dcb590.json"}}, {"family": "Englund", "given": "Elisabet", "initials": "E", "orcid": "0000-0002-2708-2443", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c98fa2b2e7e4e318cd00eb1e8e3ac7a.json"}}, {"family": "Eichler", "given": "Evan E", "initials": "EE", "orcid": "0000-0002-8246-4014", "researcher": {"href": "https://publications.scilifelab.se/researcher/43901cc9fc3b4f5c9a18260e36558eb9.json"}}, {"family": "Gale Hammell", "given": "Molly", "initials": "M", "orcid": "0000-0003-0405-8392", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecbbae421ea14d5c983755df8f519930.json"}}, {"family": "Barker", "given": "Roger A", "initials": "RA"}, {"family": "Kokaia", "given": "Zaal", "initials": "Z"}, {"family": "Douse", "given": "Christopher H", "initials": "CH", "orcid": "0000-0002-1604-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/d645238072a64ecdae736e3194b536c2.json"}}, {"family": "Jakobsson", "given": "Johan", "initials": "J", "orcid": "0000-0003-0669-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b08f33ec79b4a36a5f62223d7174201.json"}}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "44", "pages": "eadh9543", "issn-l": "2375-2548"}, "abstract": "The genetic mechanisms underlying the expansion in size and complexity of the human brain remain poorly understood. Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. Using multiomics profiling, we here demonstrate that L1 promoters are dynamically active in the developing and the adult human brain. L1s generate hundreds of developmentally regulated and cell type-specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPR interference silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.", "doi": "10.1126/sciadv.adh9543", "pmid": "37910626", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Long read": "Service", "Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10619931"}], "notes": [], "created": "2023-11-02T13:41:55.614Z", "modified": "2023-11-21T18:50:22.968Z"}, {"entity": "publication", "iuid": "20ef745a74824ae895660affb2537907", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20ef745a74824ae895660affb2537907.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20ef745a74824ae895660affb2537907"}}, "title": "Decoding pancreatic endocrine cell differentiation and \u03b2 cell regeneration in zebrafish.", "authors": [{"family": "Mi", "given": "Jiarui", "initials": "J", "orcid": "0000-0001-6498-3817", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca048a5e8eb24bbbb09d6ea07475dad5.json"}}, {"family": "Liu", "given": "Ka-Cheuk", "initials": "KC", "orcid": "0000-0001-6082-8801", "researcher": {"href": "https://publications.scilifelab.se/researcher/5495387725884c8a969b53cad833258a.json"}}, {"family": "Andersson", "given": "Olov", "initials": "O", "orcid": "0000-0001-6715-781X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f796ff515c95491e9cd47018e02220c0.json"}}], "type": "journal article", "published": "2023-08-18", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "33", "pages": "eadf5142", "issn-l": "2375-2548"}, "abstract": "In contrast to mice, zebrafish have an exceptional yet elusive ability to replenish lost \u03b2 cells in adulthood. Understanding this framework would provide mechanistic insights for \u03b2 cell regeneration, which may be extrapolated to humans. Here, we characterize a krt4-expressing ductal cell type, which is distinct from the putative Notch-responsive cells, showing neogenic competence and giving rise to the majority of endocrine cells during postembryonic development. Furthermore, we demonstrate a marked ductal remodeling process featuring a Notch-responsive to krt4+ luminal duct transformation during late development, indicating several origins of krt4+ ductal cells displaying similar transcriptional patterns. Single-cell transcriptomics upon a series of time points during \u03b2 cell regeneration unveil a previously unrecognized dlb+ transitional endocrine precursor cell, distinct regulons, and a differentiation trajectory involving cellular shuffling through differentiation and dedifferentiation dynamics. These results establish a model of zebrafish pancreatic endocrinogenesis and highlight key values of zebrafish for translational studies of \u03b2 cell regeneration.", "doi": "10.1126/sciadv.adf5142", "pmid": "37595046", "labels": {"NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10438462"}], "notes": [], "created": "2024-10-15T11:03:41.228Z", "modified": "2024-10-15T11:03:41.918Z"}, {"entity": "publication", "iuid": "ee06f5e7b1734f8bbe85e081d1a2649b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee06f5e7b1734f8bbe85e081d1a2649b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee06f5e7b1734f8bbe85e081d1a2649b"}}, "title": "Creation of distinctive Bax-lipid complexes at mitochondrial membrane surfaces drives pore formation to initiate apoptosis.", "authors": [{"family": "Clifton", "given": "Luke A", "initials": "LA", "orcid": "0000-0001-8754-362X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e26f83508bc7451a9d66123eb9ea747c.json"}}, {"family": "Wacklin-Knecht", "given": "Hanna P", "initials": "HP", "orcid": "0000-0002-5248-1147", "researcher": {"href": "https://publications.scilifelab.se/researcher/962e09a261294bcea30f21ae45b23177.json"}}, {"family": "\u00c5d\u00e9n", "given": "J\u00f6rgen", "initials": "J", "orcid": "0000-0002-4480-1219", "researcher": {"href": "https://publications.scilifelab.se/researcher/00206abad0de45eb90dc6bd3d5f3cf22.json"}}, {"family": "Mushtaq", "given": "Ameeq Ul", "initials": "AU", "orcid": "0000-0002-5636-2567", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b77280f8a9463a9af768275bc80ae9.json"}}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Gr\u00f6bner", "given": "Gerhard", "initials": "G", "orcid": "0000-0001-7380-8797", "researcher": {"href": "https://publications.scilifelab.se/researcher/85bd86ebc85d4653bc880bc9be25bc80.json"}}], "type": "journal article", "published": "2023-06-02", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "22", "pages": "eadg7940", "issn-l": "2375-2548"}, "abstract": "Apotosis is an essential process tightly regulated by the Bcl-2 protein family where proapoptotic Bax triggers cell death by perforating the mitochondrial outer membrane. Although intensively studied, the molecular mechanism by which these proteins create apoptotic pores remains elusive. Here, we show that Bax creates pores by extracting lipids from outer mitochondrial membrane mimics by formation of Bax/lipid clusters that are deposited on the membrane surface. Time-resolved neutron reflectometry and Fourier transform infrared spectroscopy revealed two kinetically distinct phases in the pore formation process, both of which were critically dependent on cardiolipin levels. The initially fast adsorption of Bax on the mitochondrial membrane surface is followed by a slower formation of pores and Bax-lipid clusters on the membrane surface. Our findings provide a robust molecular understanding of mitochondrial membrane perforation by cell-killing Bax protein and illuminate the initial phases of programmed cellular death.", "doi": "10.1126/sciadv.adg7940", "pmid": "37267355", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10413641"}], "notes": [], "created": "2023-06-03T11:52:12.695Z", "modified": "2025-10-17T13:03:53.830Z"}, {"entity": "publication", "iuid": "b4a18704cfbc4ac4a6d0e4d56abbcea3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4a18704cfbc4ac4a6d0e4d56abbcea3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4a18704cfbc4ac4a6d0e4d56abbcea3"}}, "title": "Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.", "authors": [{"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Delgado", "given": "Luis Fernando", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Deng", "given": "Ziling", "initials": "Z", "orcid": "0000-0002-6970-6453", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0e06ceb2acf478598cc7080e732cd2b.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.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": "2023-05-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "21", "pages": "eadg2059", "issn-l": "2375-2548"}, "abstract": "The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.", "doi": "10.1126/sciadv.adg2059", "pmid": "37235649", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10219603"}], "notes": [], "created": "2023-11-27T21:57:15.016Z", "modified": "2024-01-16T13:48:33.355Z"}, {"entity": "publication", "iuid": "c47a067012124fd3b1e0a4b3a87b6c30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c47a067012124fd3b1e0a4b3a87b6c30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c47a067012124fd3b1e0a4b3a87b6c30"}}, "title": "Cross-reactive EBNA1 immunity targets alpha-crystallin B and is associated with 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": "Bronge", "given": "Mattias", "initials": "M", "orcid": "0000-0002-1258-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/691b77352a57408896ef1fb486980ccd.json"}}, {"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Akpinar", "given": "Birce", "initials": "B"}, {"family": "Nilsson", "given": "Ola B", "initials": "OB"}, {"family": "Holmgren", "given": "Erik", "initials": "E", "orcid": "0000-0002-2656-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/6160949c45cf4daaab3991d051db5a16.json"}}, {"family": "Hessa", "given": "Tara", "initials": "T"}, {"family": "Gafvelin", "given": "Guro", "initials": "G", "orcid": "0000-0003-1618-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/870294f4604744ccb212a3c299887ecc.json"}}, {"family": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Alfredsson", "given": "Lars", "initials": "L", "orcid": "0000-0003-1688-6697", "researcher": {"href": "https://publications.scilifelab.se/researcher/6df230614a8a448e8607e03480169658.json"}}, {"family": "Martin", "given": "Roland", "initials": "R", "orcid": "0000-0002-0982-1329", "researcher": {"href": "https://publications.scilifelab.se/researcher/64b3f80280694b0399130e6eb26caf72.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": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2938-1877", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9a20a941214f97a22f010df37cd8e1.json"}}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}], "type": "journal article", "published": "2023-05-19", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "20", "pages": "eadg3032", "issn-l": "2375-2548"}, "abstract": "Multiple sclerosis (MS) is an inflammatory disease of the central nervous system, for which and Epstein-Barr virus (EBV) infection is a likely prerequisite. Due to the homology between Epstein-Barr nuclear antigen 1 (EBNA1) and alpha-crystallin B (CRYAB), we examined antibody reactivity to EBNA1 and CRYAB peptide libraries in 713 persons with MS (pwMS) and 722 matched controls (Con). Antibody response to CRYAB amino acids 7 to 16 was associated with MS (OR = 2.0), and combination of high EBNA1 responses with CRYAB positivity markedly increased disease risk (OR = 9.0). Blocking experiments revealed antibody cross-reactivity between the homologous EBNA1 and CRYAB epitopes. Evidence for T cell cross-reactivity was obtained in mice between EBNA1 and CRYAB, and increased CRYAB and EBNA1 CD4+ T cell responses were detected in natalizumab-treated pwMS. This study provides evidence for antibody cross-reactivity between EBNA1 and CRYAB and points to a similar cross-reactivity in T cells, further demonstrating the role of EBV adaptive immune responses in MS development.", "doi": "10.1126/sciadv.adg3032", "pmid": "37196088", "labels": {"Autoimmunity and Serology Profiling": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10191428"}], "notes": [], "created": "2023-06-25T20:13:34.600Z", "modified": "2023-06-25T20:13:34.874Z"}, {"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": "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": "a32fa37af48b40c9a81d99ba853f4d5e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a32fa37af48b40c9a81d99ba853f4d5e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a32fa37af48b40c9a81d99ba853f4d5e"}}, "title": "Endoreplication mediates cell size control via mechanochemical signaling from cell wall.", "authors": [{"family": "Ma", "given": "Yuan", "initials": "Y", "orcid": "0000-0001-8975-1975", "researcher": {"href": "https://publications.scilifelab.se/researcher/70c584ab33de460cba088c3e594c03e8.json"}}, {"family": "Jonsson", "given": "Kristoffer", "initials": "K", "orcid": "0000-0001-7445-7378", "researcher": {"href": "https://publications.scilifelab.se/researcher/85292632eddf41218242a477b217c15e.json"}}, {"family": "Aryal", "given": "Bibek", "initials": "B", "orcid": "0000-0003-0840-6956", "researcher": {"href": "https://publications.scilifelab.se/researcher/1288059c6a6f46d39ef870de260ff44c.json"}}, {"family": "De Veylder", "given": "Lieven", "initials": "L", "orcid": "0000-0003-1150-4426", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e15711bd16e4c0c8b20c1c26e581d77.json"}}, {"family": "Hamant", "given": "Olivier", "initials": "O", "orcid": "0000-0001-6906-6620", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a3175ff25f4423ba8c1a8049b570376.json"}}, {"family": "Bhalerao", "given": "Rishikesh P", "initials": "RP", "orcid": "0000-0003-4384-7036", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0696f50e5c545e9b1c6e48df4689d61.json"}}], "type": "journal article", "published": "2022-12-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "49", "pages": "eabq2047", "issn-l": "2375-2548"}, "abstract": "Endoreplication is an evolutionarily conserved mechanism for increasing nuclear DNA content (ploidy). Ploidy frequently scales with final cell and organ size, suggesting a key role for endoreplication in these processes. However, exceptions exist, and, consequently, the endoreplication-size nexus remains enigmatic. Here, we show that prolonged tissue folding at the apical hook in Arabidopsis requires endoreplication asymmetry under the control of an auxin gradient. We identify a molecular pathway linking endoreplication levels to cell size through cell wall remodeling and stiffness modulation. We find that endoreplication is not only permissive for growth: Endoreplication reduction enhances wall stiffening, actively reducing cell size. The cell wall integrity kinase THESEUS plays a key role in this feedback loop. Our data thus explain the nonlinearity between ploidy levels and size while also providing a molecular mechanism linking mechanochemical signaling with endoreplication-mediated dynamic control of cell growth.", "doi": "10.1126/sciadv.abq2047", "pmid": "36490331", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9733919"}], "notes": [], "created": "2024-11-27T13:04:03.139Z", "modified": "2024-11-27T13:04:03.589Z"}, {"entity": "publication", "iuid": "0fa6a6d0d98e4cdc824c41a447297873", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0fa6a6d0d98e4cdc824c41a447297873.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0fa6a6d0d98e4cdc824c41a447297873"}}, "title": "Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.", "authors": [{"family": "Verma", "given": "Apoorv", "initials": "A", "orcid": "0000-0002-8726-0870", "researcher": {"href": "https://publications.scilifelab.se/researcher/570887d2afe6478da2130ad606cf94e9.json"}}, {"family": "\u00c5berg-Zingmark", "given": "Emma", "initials": "E", "orcid": "0000-0002-5052-5214", "researcher": {"href": "https://publications.scilifelab.se/researcher/82284b92733343d7ba9c03be8bc85fca.json"}}, {"family": "Sparrman", "given": "Tobias", "initials": "T", "orcid": "0000-0002-4442-6367", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0d27dbd2f014795b1f7aa164d34bada.json"}}, {"family": "Mushtaq", "given": "Ameeq Ul", "initials": "AU", "orcid": "0000-0002-5636-2567", "researcher": {"href": "https://publications.scilifelab.se/researcher/d8b77280f8a9463a9af768275bc80ae9.json"}}, {"family": "Rogne", "given": "Per", "initials": "P", "orcid": "0000-0002-3687-9200", "researcher": {"href": "https://publications.scilifelab.se/researcher/31042ecc88a94cd6b97cef0508da93fd.json"}}, {"family": "Grundstr\u00f6m", "given": "Christin", "initials": "C"}, {"family": "Berntsson", "given": "Ronnie", "initials": "R", "orcid": "0000-0001-6848-322X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e78d8a69e46241bc8a79ede3df38ebdf.json"}}, {"family": "Sauer", "given": "Uwe H", "initials": "UH", "orcid": "0000-0002-3420-439X", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d011e944ae54d47aed374d548007812.json"}}, {"family": "Backman", "given": "Lars", "initials": "L", "orcid": "0000-0003-3044-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/99a60ee46b814b5a822c9c93e46ffe42.json"}}, {"family": "Nam", "given": "Kwangho", "initials": "K", "orcid": "0000-0003-0723-7839", "researcher": {"href": "https://publications.scilifelab.se/researcher/29b33d801f244b6aac48a9d626962770.json"}}, {"family": "Sauer-Eriksson", "given": "Elisabeth", "initials": "E", "orcid": "0000-0003-0124-0199", "researcher": {"href": "https://publications.scilifelab.se/researcher/9435049fbe2745b59e04558cc5201f95.json"}}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9098-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6ea8f5c456428db21b1085ad541538.json"}}], "type": "journal article", "published": "2022-11-04", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "44", "pages": "eabm4089", "issn-l": "2375-2548"}, "abstract": "Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from <i>Odinarchaeota<\/i> (OdinAK). <i>Odinarchaeota<\/i> belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while <sup>19<\/sup>F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be \"atypical.\" On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.", "doi": "10.1126/sciadv.abm4089", "pmid": "36332013", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9635829"}], "notes": [], "created": "2022-11-28T13:05:26.193Z", "modified": "2025-10-17T13:03:54.457Z"}, {"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": "ed05b16509414bc8b557611000e36d26", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ed05b16509414bc8b557611000e36d26.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ed05b16509414bc8b557611000e36d26"}}, "title": "Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.", "authors": [{"family": "Ma\u00f1as", "given": "Adriana", "initials": "A", "orcid": "0000-0002-6955-1754", "researcher": {"href": "https://publications.scilifelab.se/researcher/7220571c605044f980abf2933374aa1a.json"}}, {"family": "Aaltonen", "given": "Kristina", "initials": "K", "orcid": "0000-0001-5104-735X", "researcher": {"href": "https://publications.scilifelab.se/researcher/68a63e2719d246a99fc51e8e3ed05cee.json"}}, {"family": "Andersson", "given": "Natalie", "initials": "N", "orcid": "0000-0002-3643-4404", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7ef3a8564354a78a23180c7550a03ff.json"}}, {"family": "Hansson", "given": "Karin", "initials": "K", "orcid": "0000-0002-6993-7673", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c0c991068644f61b10c986deff8fb7f.json"}}, {"family": "Adamska", "given": "Aleksandra", "initials": "A", "orcid": "0000-0002-7152-4149", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f2fab5686a542fdb1286417685bc7a4.json"}}, {"family": "Seger", "given": "Alexandra", "initials": "A", "orcid": "0000-0003-3191-5302", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfcd0a0a226c417eac8e0a48eedd4e7c.json"}}, {"family": "Yasui", "given": "Hiroaki", "initials": "H"}, {"family": "van den Bos", "given": "Hilda", "initials": "H", "orcid": "0000-0001-9787-8597", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3f0fd58a2714db5bcd89642f92c0158.json"}}, {"family": "Radke", "given": "Katarzyna", "initials": "K", "orcid": "0000-0002-4460-0812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad483c946ce244fa898cadb6238e970d.json"}}, {"family": "Esfandyari", "given": "Javanshir", "initials": "J"}, {"family": "Bhave", "given": "Madhura Satish", "initials": "MS"}, {"family": "Karlsson", "given": "Jenny", "initials": "J", "orcid": "0000-0001-7681-0059", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e2ccecaff1d41bfa863dde6616eeadd.json"}}, {"family": "Spierings", "given": "Diana", "initials": "D", "orcid": "0000-0001-8403-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/62825465dc084c7ebd10b71e274d5eb2.json"}}, {"family": "Foijer", "given": "Floris", "initials": "F", "orcid": "0000-0003-0989-3127", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ef3e70e2b5249029ff65894fd11b851.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D"}, {"family": "Bexell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-9426-9550", "researcher": {"href": "https://publications.scilifelab.se/researcher/dda650768a264d93a80f40da6cb8d7e1.json"}}], "type": "journal article", "published": "2022-10-28", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "43", "pages": "eabq4617", "issn-l": "2375-2548"}, "abstract": "Chemotherapy resistance and relapses are common in high-risk neuroblastoma (NB). Here, we developed a clinically relevant in vivo treatment protocol mimicking the first-line five-chemotherapy treatment regimen of high-risk NB and applied this protocol to mice with MYCN-amplified NB patient-derived xenografts (PDXs). Genomic and transcriptomic analyses were used to reveal NB chemoresistance mechanisms. Intrinsic resistance was associated with high genetic diversity and an embryonic phenotype. Relapsed NB with acquired resistance showed a decreased adrenergic phenotype and an enhanced immature mesenchymal-like phenotype, resembling multipotent Schwann cell precursors. NBs with a favorable treatment response presented a lineage-committed adrenergic phenotype similar to normal neuroblasts. Novel integrated phenotypic gene signatures reflected treatment response and patient prognosis. NB organoids established from relapsed PDX tumors retained drug resistance, tumorigenicity, and transcriptional cell states. This work sheds light on the mechanisms of NB chemotherapy response and emphasizes the importance of transcriptional cell states in chemoresistance.", "doi": "10.1126/sciadv.abq4617", "pmid": "36306349", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9616506"}], "notes": [], "created": "2022-11-15T12:56:52.046Z", "modified": "2023-06-01T06:43:02.747Z"}, {"entity": "publication", "iuid": "7aa0f32803b94812952a1ad8388a0b27", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7aa0f32803b94812952a1ad8388a0b27.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7aa0f32803b94812952a1ad8388a0b27"}}, "title": "Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes.", "authors": [{"family": "Pillon", "given": "Nicolas J", "initials": "NJ", "orcid": "0000-0003-1107-9490", "researcher": {"href": "https://publications.scilifelab.se/researcher/4b917d3e521149ec9d695c62ac2d1b85.json"}}, {"family": "Smith", "given": "Jonathon A B", "initials": "JAB", "orcid": "0000-0003-2452-1655", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffd42f562b3485fb50090c02aceeaef.json"}}, {"family": "Alm", "given": "Petter S", "initials": "PS"}, {"family": "Chibalin", "given": "Alexander V", "initials": "AV", "orcid": "0000-0002-6339-6271", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ac028a96dd746c5896f7e5536f978c1.json"}}, {"family": "Alhusen", "given": "Julia", "initials": "J"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Carninci", "given": "Piero", "initials": "P", "orcid": "0000-0001-7202-7243", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3fce15806ba4fb9bc1fda7e52470fad.json"}}, {"family": "Fritz", "given": "Tomas", "initials": "T"}, {"family": "Otten", "given": "Julia", "initials": "J", "orcid": "0000-0001-9016-1139", "researcher": {"href": "https://publications.scilifelab.se/researcher/0038b9a380164700b77cda3879133a29.json"}}, {"family": "Olsson", "given": "Tommy", "initials": "T"}, {"family": "van Doorslaer de Ten Ryen", "given": "Sophie", "initials": "S", "orcid": "0000-0003-4452-1361", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5612041bba948f18e7b795369b2f4f2.json"}}, {"family": "Deldicque", "given": "Louise", "initials": "L", "orcid": "0000-0003-3393-5278", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2d95c5f9ecc4fa8b8661810177085d1.json"}}, {"family": "Caidahl", "given": "Kenneth", "initials": "K", "orcid": "0000-0002-5079-9696", "researcher": {"href": "https://publications.scilifelab.se/researcher/c54c79603a954f9e81d2b82470e3ec36.json"}}, {"family": "Wallberg-Henriksson", "given": "Harriet", "initials": "H", "orcid": "0000-0001-7681-1537", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b84ac00890a44ddb3b6732687003281.json"}}, {"family": "Krook", "given": "Anna", "initials": "A", "orcid": "0000-0002-0891-0258", "researcher": {"href": "https://publications.scilifelab.se/researcher/f43339bcd571486b845a3b10e241bcc4.json"}}, {"family": "Zierath", "given": "Juleen R", "initials": "JR", "orcid": "0000-0001-6891-7497", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ef2b94ba2d44dd9b41192567a7af53.json"}}], "type": "journal article", "published": "2022-09-09", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "36", "pages": "eabo3192", "issn-l": "2375-2548"}, "abstract": "Mechanistic insights into the molecular events by which exercise enhances the skeletal muscle phenotype are lacking, particularly in the context of type 2 diabetes. Here, we unravel a fundamental role for exercise-responsive cytokines (exerkines) on skeletal muscle development and growth in individuals with normal glucose tolerance or type 2 diabetes. Acute exercise triggered an inflammatory response in skeletal muscle, concomitant with an infiltration of immune cells. These exercise effects were potentiated in type 2 diabetes. In response to contraction or hypoxia, cytokines were mainly produced by endothelial cells and macrophages. The chemokine CXCL12 was induced by hypoxia in endothelial cells, as well as by conditioned medium from contracted myotubes in macrophages. We found that CXCL12 was associated with skeletal muscle remodeling after exercise and differentiation of cultured muscle. Collectively, acute aerobic exercise mounts a noncanonical inflammatory response, with an atypical production of exerkines, which is potentiated in type 2 diabetes.", "doi": "10.1126/sciadv.abo3192", "pmid": "36070371", "labels": {"Spatial Proteomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9451165"}], "notes": [], "created": "2023-11-21T15:13:19.754Z", "modified": "2023-11-21T15:13:19.970Z"}, {"entity": "publication", "iuid": "ae4ff1411a31429f8d1c53a6fc16ed11", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ae4ff1411a31429f8d1c53a6fc16ed11.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ae4ff1411a31429f8d1c53a6fc16ed11"}}, "title": "PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.", "authors": [{"family": "Toskas", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-5897-9501", "researcher": {"href": "https://publications.scilifelab.se/researcher/687adc14acf7400eaa552f41eb39807e.json"}}, {"family": "Yaghmaeian-Salmani", "given": "Behzad", "initials": "B", "orcid": "0000-0002-4221-6243", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb9b5976d0b34622aff0e9a564b3ae54.json"}}, {"family": "Skiteva", "given": "Olga", "initials": "O"}, {"family": "Paslawski", "given": "Wojciech", "initials": "W", "orcid": "0000-0003-2141-4547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce039c7e5e774d66a8c0331a3c990ccc.json"}}, {"family": "Gillberg", "given": "Linda", "initials": "L"}, {"family": "Skara", "given": "Vasiliki", "initials": "V", "orcid": "0000-0002-0017-6116", "researcher": {"href": "https://publications.scilifelab.se/researcher/e412dda73e2e40a380e10775f45fbd66.json"}}, {"family": "Antoniou", "given": "Irene", "initials": "I", "orcid": "0000-0002-3616-9049", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a00a046dece4cae9afa12a5c7caa723.json"}}, {"family": "S\u00f6dersten", "given": "Erik", "initials": "E"}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Chergui", "given": "Karima", "initials": "K", "orcid": "0000-0001-5702-0422", "researcher": {"href": "https://publications.scilifelab.se/researcher/be439b7cafce4d919881a7b0ef7d6340.json"}}, {"family": "Ringn\u00e9r", "given": "Markus", "initials": "M", "orcid": "0000-0001-5469-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0308e6d9c534033b431d2552cfe2af6.json"}}, {"family": "Perlmann", "given": "Thomas", "initials": "T"}, {"family": "Holmberg", "given": "Johan", "initials": "J", "orcid": "0000-0002-3018-001X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f84bece88a264d228d3770ca634b4a19.json"}}], "type": "journal article", "published": "2022-08-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "34", "pages": "eabo1543"}, "abstract": "How neurons can maintain cellular identity over an entire life span remains largely unknown. Here, we show that maintenance of identity in differentiated dopaminergic and serotonergic neurons is critically reliant on the Polycomb repressive complex 2 (PRC2). Deletion of the obligate PRC2 component, Eed, in these neurons resulted in global loss of H3K27me3, followed by a gradual activation of genes harboring both H3K27me3 and H3K9me3 modifications. Notably, H3K9me3 was lost at these PRC2 targets before gene activation. Neuronal survival was not compromised; instead, there was a reduction in subtype-specific gene expression and a progressive impairment of dopaminergic and serotonergic neuronal function, leading to behavioral deficits characteristic of Parkinson's disease and anxiety. Single-cell analysis revealed subtype-specific vulnerability to loss of PRC2 repression in dopamine neurons of the substantia nigra. Our study reveals that a PRC2-dependent nonpermissive chromatin state is essential to maintain the subtype identity and function of dopaminergic and serotonergic neurons.", "doi": "10.1126/sciadv.abo1543", "pmid": "36026451", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "NGI Single cell": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9417181"}], "notes": [], "created": "2022-08-30T11:39:49.253Z", "modified": "2024-10-14T11:50:28.807Z"}, {"entity": "publication", "iuid": "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": "7f08b122459149d9ac2a582fcc398431", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f08b122459149d9ac2a582fcc398431.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f08b122459149d9ac2a582fcc398431"}}, "title": "Rapid adaptive radiation of Darwin's finches depends on ancestral genetic modules.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "CJ", "orcid": "0000-0001-8238-5052", "researcher": {"href": "https://publications.scilifelab.se/researcher/0bd98ada4083444e8336ef3ec53df488.json"}}, {"family": "Enbody", "given": "Erik D", "initials": "ED", "orcid": "0000-0003-1349-628X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a4df51b279746539cae2fa83c37456d.json"}}, {"family": "Dobreva", "given": "Mariya P", "initials": "MP", "orcid": "0000-0002-7152-1044", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7264631debb4687be22a07e768c4a07.json"}}, {"family": "Abzhanov", "given": "Arhat", "initials": "A"}, {"family": "Davis", "given": "Brian W", "initials": "BW", "orcid": "0000-0002-6121-135X", "researcher": {"href": "https://publications.scilifelab.se/researcher/63981f53ab2e4dc09a4a2a62ae0b7a84.json"}}, {"family": "Lamichhaney", "given": "Sangeet", "initials": "S", "orcid": "0000-0003-4826-0349", "researcher": {"href": "https://publications.scilifelab.se/researcher/602a2f371eae45e4b9d8f9748f285ef4.json"}}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Sendell-Price", "given": "Ashley T", "initials": "AT"}, {"family": "Sprehn", "given": "C Grace", "initials": "CG"}, {"family": "Valle", "given": "Carlos A", "initials": "CA", "orcid": "0000-0002-5523-634X", "researcher": {"href": "https://publications.scilifelab.se/researcher/69b5e00396c5482786b9eeeea2316cfb.json"}}, {"family": "Vasco", "given": "Karla", "initials": "K", "orcid": "0000-0002-4617-5864", "researcher": {"href": "https://publications.scilifelab.se/researcher/e080c032415840ca864356927ac7fda9.json"}}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"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": "2022-07-08", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "27", "pages": "eabm5982", "issn-l": "2375-2548"}, "abstract": "Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is the relative importance of new mutations, ancestral variants, and introgressive hybridization for phenotypic evolution and speciation. Here, we address this issue using Darwin's finches and investigate the genomic architecture underlying their phenotypic diversity. Admixture mapping for beak and body size in the small, medium, and large ground finches revealed 28 loci showing strong genetic differentiation. These loci represent ancestral haplotype blocks with origins predating speciation events during the Darwin's finch radiation. Genes expressed in the developing beak are overrepresented in these genomic regions. Ancestral haplotypes constitute genetic modules for selection and act as key determinants of the unusual phenotypic diversity of Darwin's finches. Such ancestral haplotype blocks can be critical for how species adapt to environmental variability and change.", "doi": "10.1126/sciadv.abm5982", "pmid": "35857449", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9269886"}], "notes": [], "created": "2022-11-09T15:47:58.882Z", "modified": "2024-01-16T13:48:35.858Z"}, {"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": "387be3d37549490b96f97b6b0818f875", "links": {"self": {"href": "https://publications.scilifelab.se/publication/387be3d37549490b96f97b6b0818f875.json"}, "display": {"href": "https://publications.scilifelab.se/publication/387be3d37549490b96f97b6b0818f875"}}, "title": "Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis.", "authors": [{"family": "Bronge", "given": "Mattias", "initials": "M", "orcid": "0000-0002-1258-3982", "researcher": {"href": "https://publications.scilifelab.se/researcher/691b77352a57408896ef1fb486980ccd.json"}}, {"family": "H\u00f6gelin", "given": "Klara Asplund", "initials": "KA"}, {"family": "Thomas", "given": "Olivia G", "initials": "OG", "orcid": "0000-0002-2011-1344", "researcher": {"href": "https://publications.scilifelab.se/researcher/ea07f812ffee4db893c6f98548563525.json"}}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Carvalho-Queiroz", "given": "Claudia", "initials": "C"}, {"family": "Nilsson", "given": "Ola B", "initials": "OB"}, {"family": "Kaiser", "given": "Andreas", "initials": "A"}, {"family": "Zeitelhofer", "given": "Manuel", "initials": "M"}, {"family": "Holmgren", "given": "Erik", "initials": "E", "orcid": "0000-0002-2656-1864", "researcher": {"href": "https://publications.scilifelab.se/researcher/6160949c45cf4daaab3991d051db5a16.json"}}, {"family": "Linnerbauer", "given": "Mathias", "initials": "M", "orcid": "0000-0002-5528-5141", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c1386bf72f4371acb131d333314da2.json"}}, {"family": "Adzemovic", "given": "Milena Z", "initials": "MZ"}, {"family": "Hellstr\u00f6m", "given": "Cecilia", "initials": "C", "orcid": "0000-0003-0880-5375", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbf3f75938f0442a9b1ae5c98565f44a.json"}}, {"family": "Jelcic", "given": "Ivan", "initials": "I", "orcid": "0000-0002-6187-7098", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b5547919d474434bddd217865f1fb8e.json"}}, {"family": "Liu", "given": "Hao", "initials": "H", "orcid": "0000-0001-6572-2870", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3f8f259e77d4e208a4c838de8a7c7de.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Hillert", "given": "Jan", "initials": "J", "orcid": "0000-0002-7386-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb4f3ad8831d430e8327dd457d43834b.json"}}, {"family": "Brundin", "given": "Lou", "initials": "L", "orcid": "0000-0003-4408-7817", "researcher": {"href": "https://publications.scilifelab.se/researcher/9181d700c722427099d882b3b40eb91e.json"}}, {"family": "Fink", "given": "Katharina", "initials": "K"}, {"family": "Kockum", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-0867-4726", "researcher": {"href": "https://publications.scilifelab.se/researcher/03ebcc6a01ef4d0db4e4673aff8de5d8.json"}}, {"family": "Tengvall", "given": "Katarina", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Martin", "given": "Roland", "initials": "R"}, {"family": "Tegel", "given": "Hanna", "initials": "H", "orcid": "0000-0002-7067-9173", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3d733dbd7b84a6b88f7f5fcff7165f6.json"}}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T", "orcid": "0000-0002-5391-600X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52adbc739e274652bbf877facf4f0959.json"}}, {"family": "Al Nimer", "given": "Faiez", "initials": "F", "orcid": "0000-0003-0937-5995", "researcher": {"href": "https://publications.scilifelab.se/researcher/743a318b1c64432280e3999fb57c9a18.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": "Khademi", "given": "Mohsen", "initials": "M", "orcid": "0000-0003-0801-1444", "researcher": {"href": "https://publications.scilifelab.se/researcher/5446d6d754bc4c429d0e48ade419413c.json"}}, {"family": "Gafvelin", "given": "Guro", "initials": "G", "orcid": "0000-0003-1618-4011", "researcher": {"href": "https://publications.scilifelab.se/researcher/870294f4604744ccb212a3c299887ecc.json"}}, {"family": "Olsson", "given": "Tomas", "initials": "T", "orcid": "0000-0002-2938-1877", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd9a20a941214f97a22f010df37cd8e1.json"}}, {"family": "Gr\u00f6nlund", "given": "Hans", "initials": "H", "orcid": "0000-0003-4882-7624", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e701613f60249b793f2def737168a05.json"}}], "type": "journal article", "published": "2022-04-29", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "17", "pages": "eabn1823", "issn-l": "2375-2548"}, "abstract": "Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS), in which pathological T cells, likely autoimmune, play a key role. Despite its central importance, the autoantigen repertoire remains largely uncharacterized. Using a novel in vitro antigen delivery method combined with the Human Protein Atlas library, we screened for T cell autoreactivity against 63 CNS-expressed proteins. We identified four previously unreported autoantigens in MS: fatty acid-binding protein 7, prokineticin-2, reticulon-3, and synaptosomal-associated protein 91, which were verified to induce interferon-\u03b3 responses in MS in two cohorts. Autoreactive profiles were heterogeneous, and reactivity to several autoantigens was MS-selective. Autoreactive T cells were predominantly CD4+ and human leukocyte antigen-DR restricted. Mouse immunization induced antigen-specific responses and CNS leukocyte infiltration. This represents one of the largest systematic efforts to date in the search for MS autoantigens, demonstrates the heterogeneity of autoreactive profiles, and highlights promising targets for future diagnostic tools and immunomodulatory therapies in MS.", "doi": "10.1126/sciadv.abn1823", "pmid": "35476434", "labels": {"Autoimmunity and Serology Profiling": "Collaborative"}, "xrefs": [], "notes": [], "created": "2022-04-28T11:23:43.022Z", "modified": "2022-04-28T11:23:43.509Z"}, {"entity": "publication", "iuid": "6563c0614cbe470791aceee0c8571317", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6563c0614cbe470791aceee0c8571317.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6563c0614cbe470791aceee0c8571317"}}, "title": "Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies.", "authors": [{"family": "Hanke", "given": "Leo", "initials": "L", "orcid": "0000-0001-5514-2418", "researcher": {"href": "https://publications.scilifelab.se/researcher/ece050a286f946f6807170cffc9320e7.json"}}, {"family": "Sheward", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0002-0227-5636", "researcher": {"href": "https://publications.scilifelab.se/researcher/6105f3617cdf4241bf335299ac957ee5.json"}}, {"family": "Pankow", "given": "Alec", "initials": "A", "orcid": "0000-0001-9108-1683", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bea0dd4229242aeb696a03e4f6976b1.json"}}, {"family": "Vidakovics", "given": "Laura Perez", "initials": "LP", "orcid": "0000-0003-4283-812X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f8d317c1bf74fd5bfb3e63936f5ab5e.json"}}, {"family": "Karl", "given": "Vivien", "initials": "V", "orcid": "0000-0001-7026-7622", "researcher": {"href": "https://publications.scilifelab.se/researcher/777268eb24884ee48b344e2e22731f5a.json"}}, {"family": "Kim", "given": "Changil", "initials": "C", "orcid": "0000-0003-4977-4384", "researcher": {"href": "https://publications.scilifelab.se/researcher/f2212e39632b4184b3dfa8f985b87221.json"}}, {"family": "Urgard", "given": "Egon", "initials": "E"}, {"family": "Smith", "given": "Natalie L", "initials": "NL"}, {"family": "Astorga-Wells", "given": "Juan", "initials": "J", "orcid": "0000-0003-1017-8841", "researcher": {"href": "https://publications.scilifelab.se/researcher/14530d9aa03747858976b4889e959fe5.json"}}, {"family": "Ekstr\u00f6m", "given": "Simon", "initials": "S"}, {"family": "Coquet", "given": "Jonathan M", "initials": "JM", "orcid": "0000-0002-5967-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b74959951024d6ea9712b55f115652e.json"}}, {"family": "McInerney", "given": "Gerald M", "initials": "GM", "orcid": "0000-0003-2257-7241", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ac2f68095fe4426b97ec070865e5091.json"}}, {"family": "Murrell", "given": "Ben", "initials": "B", "orcid": "0000-0002-0393-4445", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a899203048943489bf7b6310a32b19f.json"}}], "type": "journal article", "published": "2022-03-25", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "12", "pages": "eabm0220", "issn-l": "2375-2548"}, "abstract": "Conventional approaches to isolate and characterize nanobodies are laborious. We combine phage display, multivariate enrichment, next-generation sequencing, and a streamlined screening strategy to identify numerous anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nanobodies. We characterize their potency and specificity using neutralization assays and hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most potent nanobodies bind to the receptor binding motif of the receptor binding domain (RBD), and we identify two exceptionally potent members of this category (with monomeric half-maximal inhibitory concentrations around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the Beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 \u03bcg/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.", "doi": "10.1126/sciadv.abm0220", "pmid": "35333580", "labels": {"Structural Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8956255"}], "notes": [], "created": "2022-04-27T14:23:39.598Z", "modified": "2023-06-19T13:00:53.317Z"}, {"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": "fc11fc0561274cad8b75a6b4042e1ae4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc11fc0561274cad8b75a6b4042e1ae4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc11fc0561274cad8b75a6b4042e1ae4"}}, "title": "Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter.", "authors": [{"family": "Chaptal", "given": "Vincent", "initials": "V", "orcid": "0000-0003-2603-0294", "researcher": {"href": "https://publications.scilifelab.se/researcher/417117a3671f42cfaa9d0e6af6962264.json"}}, {"family": "Zampieri", "given": "Veronica", "initials": "V", "orcid": "0000-0002-8292-2951", "researcher": {"href": "https://publications.scilifelab.se/researcher/97d59bc8c12a4244839094cb090fb792.json"}}, {"family": "Wiseman", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-2994-5839", "researcher": {"href": "https://publications.scilifelab.se/researcher/2098646fa9de4dbc8f7cca8aeabad319.json"}}, {"family": "Orelle", "given": "C\u00e9dric", "initials": "C", "orcid": "0000-0003-3418-3290", "researcher": {"href": "https://publications.scilifelab.se/researcher/535f40a445ce4b4ca5f14c3c68bb7695.json"}}, {"family": "Martin", "given": "Juliette", "initials": "J", "orcid": "0000-0002-4787-0885", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ed31b14b464bb9a733989dc6c026dd.json"}}, {"family": "Nguyen", "given": "Kim-Anh", "initials": "KA", "orcid": "0000-0001-5143-507X", "researcher": {"href": "https://publications.scilifelab.se/researcher/992134f693644a70a6fe03d38bddd3c7.json"}}, {"family": "Gobet", "given": "Alexia", "initials": "A"}, {"family": "Di Cesare", "given": "Margot", "initials": "M", "orcid": "0000-0002-7883-852X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b28e57b6b8104eeea44a290272dffaa4.json"}}, {"family": "Magnard", "given": "Sandrine", "initials": "S", "orcid": "0000-0003-1195-1840", "researcher": {"href": "https://publications.scilifelab.se/researcher/04df653ff50f4bc7ba6d1cf0ae74261e.json"}}, {"family": "Javed", "given": "Waqas", "initials": "W", "orcid": "0000-0002-3381-4794", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a3cbad57a404e269b7d3ecba3ab520a.json"}}, {"family": "Eid", "given": "Jad", "initials": "J"}, {"family": "Kilburg", "given": "Arnaud", "initials": "A", "orcid": "0000-0003-4803-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/977a2544bc0240a3bf8eb3ccbee19863.json"}}, {"family": "Peuchmaur", "given": "Marine", "initials": "M"}, {"family": "Marcoux", "given": "Julien", "initials": "J", "orcid": "0000-0001-7321-7436", "researcher": {"href": "https://publications.scilifelab.se/researcher/9916769d1e0c43379123c00472e672b6.json"}}, {"family": "Monticelli", "given": "Luca", "initials": "L", "orcid": "0000-0002-6352-4595", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d10f84721bc4214bf9350d0587e1cfc.json"}}, {"family": "Hogbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}, {"family": "Schoehn", "given": "Guy", "initials": "G", "orcid": "0000-0002-1459-3201", "researcher": {"href": "https://publications.scilifelab.se/researcher/0df30761c33d4c8db05a3f47f998f93b.json"}}, {"family": "Jault", "given": "Jean-Michel", "initials": "JM", "orcid": "0000-0003-1743-2777", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1a639dd1caf46f2a076c8b10e9e5fea.json"}}, {"family": "Boumendjel", "given": "Ahc\u00e8ne", "initials": "A"}, {"family": "Falson", "given": "Pierre", "initials": "P", "orcid": "0000-0002-9760-4577", "researcher": {"href": "https://publications.scilifelab.se/researcher/f633a18c37cf4cdba35101a956ceb492.json"}}], "type": "journal article", "published": "2022-01-28", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "8", "issue": "4", "pages": "eabg9215", "issn-l": "2375-2548"}, "abstract": "Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.", "doi": "10.1126/sciadv.abg9215", "pmid": "35080979", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8791611"}], "notes": [], "created": "2022-02-03T21:05:51.843Z", "modified": "2022-12-02T10:10:31.688Z"}, {"entity": "publication", "iuid": "bbbef057569645bdafa2067f2ae47efc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbbef057569645bdafa2067f2ae47efc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbbef057569645bdafa2067f2ae47efc"}}, "title": "Structural basis of DegP protease temperature-dependent activation.", "authors": [{"family": "\u0160ulskis", "given": "Darius", "initials": "D", "orcid": "0000-0002-6925-4469", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f96dc2852dc41dd93310a4e33d3c216.json"}}, {"family": "Thoma", "given": "Johannes", "initials": "J", "orcid": "0000-0003-3584-8274", "researcher": {"href": "https://publications.scilifelab.se/researcher/98d27ad4d2224fbaa840469f85a596e4.json"}}, {"family": "Burmann", "given": "Bj\u00f6rn M", "initials": "BM", "orcid": "0000-0002-3135-7964", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7a6d61fc1a64677874973c3247b1eb4.json"}}], "type": "journal article", "published": "2021-12-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "7", "issue": "50", "pages": "eabj1816"}, "abstract": "Protein quality control is an essential cellular function mainly executed by a vast array of different proteases and molecular chaperones. One of the bacterial high temperature requirement A (HtrA) protein family members, the homo-oligomeric DegP protease, plays a crucial role in the Escherichia coli protein quality control machinery by removing unfolded proteins or preventing their aggregation and chaperoning them to their final folded state within the periplasm. DegP contains two regulatory PDZ domains, which play key roles in substrate recognition and in the transformation of DegP between inactive hexameric and proteolytic active cage-like structures. Here, we analyze the interaction and dynamics of the DegP PDZ domains underlying this transformation by high-resolution NMR spectroscopy complemented with biochemical cleavage assays. We identify an interdomain molecular lock, which controls the interactions between the two PDZ domains, regulated by fine-tuned temperature-dependent protein dynamics, and which is potentially conserved in proteins harboring tandem PDZ domains.", "doi": "10.1126/sciadv.abj1816", "pmid": "34878848", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8654288"}], "notes": [], "created": "2020-12-11T09:06:12.338Z", "modified": "2025-10-17T13:03:55.266Z"}, {"entity": "publication", "iuid": "eaa395c68f0b4f77a2b97246718702be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaa395c68f0b4f77a2b97246718702be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaa395c68f0b4f77a2b97246718702be"}}, "title": "Causal effects of inflammatory protein biomarkers on inflammatory diseases.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE", "orcid": "0000-0003-2194-496X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7398a2bfa9154e15a4295828bc0f5bb8.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.json"}}, {"family": "H\u00f6glund", "given": "Julia", "initials": "J", "orcid": "0000-0001-8061-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b02049b625d47a69324be23e35f5b58.json"}}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-8008-4659", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd09a995c7240c78bfe4ba6690847cc.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": "2021-12-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "50", "pages": "eabl4359", "issn-l": "2375-2548"}, "abstract": "Many circulating proteins are associated with the presence or severity of disease. However, whether these protein biomarkers are causal for disease development is usually unknown. We investigated the causal effect of 21 well-known or exploratory protein biomarkers of inflammation on 18 inflammatory diseases using two-sample Mendelian randomization. We identified six proteins to have causal effects on any of 11 inflammatory diseases (FDR < 0.05, corresponding to P < 1.4 \u00d7 10\u20133). IL-12B protects against psoriasis and psoriatic arthropathy, LAP-TGF-\u03b2-1 protects against osteoarthritis, TWEAK protects against asthma, VEGF-A protects against ulcerative colitis, and LT-\u03b1 protects against both type 1 diabetes and rheumatoid arthritis. In contrast, IL-18R1 increases the risk of developing allergy, hay fever, and eczema. Most proteins showed protective effects against development of disease rather than increasing disease risk, which indicates that many disease-related biomarkers are expressed to protect from tissue damage. These proteins represent potential intervention points for disease prevention and treatment.", "doi": "10.1126/sciadv.abl4359", "pmid": "34878845", "labels": {"Affinity Proteomics Uppsala": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8654293"}], "notes": [], "created": "2022-12-02T08:53:54.595Z", "modified": "2022-12-02T08:53:54.660Z"}, {"entity": "publication", "iuid": "707f5e508c434c7a9243a9968c9a6bdb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/707f5e508c434c7a9243a9968c9a6bdb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/707f5e508c434c7a9243a9968c9a6bdb"}}, "title": "Tracking the ATP-binding response in adenylate kinase in real time.", "authors": [{"family": "Or\u00e4dd", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0706-7414", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d66f5bb420b4e3c8d706350f86b38ff.json"}}, {"family": "Ravishankar", "given": "Harsha", "initials": "H", "orcid": "0000-0002-8795-6309", "researcher": {"href": "https://publications.scilifelab.se/researcher/4594172ba2a44b7da58137b052922ee0.json"}}, {"family": "Goodman", "given": "Jack", "initials": "J"}, {"family": "Rogne", "given": "Per", "initials": "P"}, {"family": "Backman", "given": "Lars", "initials": "L", "orcid": "0000-0003-3044-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/99a60ee46b814b5a822c9c93e46ffe42.json"}}, {"family": "Duelli", "given": "Annette", "initials": "A"}, {"family": "Nors Pedersen", "given": "Martin", "initials": "M"}, {"family": "Levantino", "given": "Matteo", "initials": "M", "orcid": "0000-0002-1224-4809", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe97c47f66247d88ae00cfe6edde53e.json"}}, {"family": "Wulff", "given": "Michael", "initials": "M", "orcid": "0000-0003-3784-9019", "researcher": {"href": "https://publications.scilifelab.se/researcher/1116a777db76465f829a73d6e76dc268.json"}}, {"family": "Wolf-Watz", "given": "Magnus", "initials": "M", "orcid": "0000-0002-9098-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c6ea8f5c456428db21b1085ad541538.json"}}, {"family": "Andersson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3364-6647", "researcher": {"href": "https://publications.scilifelab.se/researcher/08ef723036544a65806f0c46d5b44f61.json"}}], "type": "journal article", "published": "2021-11-19", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "47", "pages": "eabi5514", "issn-l": "2375-2548"}, "abstract": "[Figure: see text].", "doi": "10.1126/sciadv.abi5514", "pmid": "34788091", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8597995"}], "notes": [], "created": "2021-12-05T14:24:29.343Z", "modified": "2025-10-17T13:03:55.324Z"}, {"entity": "publication", "iuid": "8d8a7c48cf414bbd9c480513a1994913", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8d8a7c48cf414bbd9c480513a1994913.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8d8a7c48cf414bbd9c480513a1994913"}}, "title": "The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation.", "authors": [{"family": "Lindehell", "given": "Henrik", "initials": "H", "orcid": "0000-0003-1195-2341", "researcher": {"href": "https://publications.scilifelab.se/researcher/bffc62dbca3145d8849c0dbbb16d44b3.json"}}, {"family": "Glotov", "given": "Alexander", "initials": "A"}, {"family": "Dorafshan", "given": "Eshagh", "initials": "E"}, {"family": "Schwartz", "given": "Yuri B", "initials": "YB", "orcid": "0000-0003-4790-3920", "researcher": {"href": "https://publications.scilifelab.se/researcher/2751a236629d4b8bb9fff42cad6ff614.json"}}, {"family": "Larsson", "given": "Jan", "initials": "J", "orcid": "0000-0003-4373-6790", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d6f8e41628d4534879edaf229575dec.json"}}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "40", "pages": "eabh4390", "issn-l": "2375-2548"}, "abstract": "[Figure: see text].", "doi": "10.1126/sciadv.abh4390", "pmid": "34597135", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-06T13:49:37.169Z", "modified": "2024-01-16T13:48:38.326Z"}, {"entity": "publication", "iuid": "f18d7672bbbb4e5dbcd524fde4fbc995", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f18d7672bbbb4e5dbcd524fde4fbc995.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f18d7672bbbb4e5dbcd524fde4fbc995"}}, "title": "The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.", "authors": [{"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "Espinoza", "given": "Jaime A", "initials": "JA", "orcid": "0000-0002-0731-2715", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cdf2cd80f5b4f87adf6d936b6390ee8.json"}}, {"family": "Zisi", "given": "Asimina", "initials": "A", "orcid": "0000-0002-4253-0275", "researcher": {"href": "https://publications.scilifelab.se/researcher/5cf82380ca6e4cd1985bc9dd23789539.json"}}, {"family": "Sakkas", "given": "Elpidoforos", "initials": "E"}, {"family": "Bartkova", "given": "Jirina", "initials": "J"}, {"family": "Katsori", "given": "Anna-Maria", "initials": "AM", "orcid": "0000-0002-5975-2931", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a338e7f888b4e7fa663fdd87d667713.json"}}, {"family": "Bostr\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0001-5252-4023", "researcher": {"href": "https://publications.scilifelab.se/researcher/2af59464d2c74c27af7a43fb5d1a670e.json"}}, {"family": "Dyrskj\u00f8t", "given": "Lars", "initials": "L"}, {"family": "Broholm", "given": "Helle", "initials": "H", "orcid": "0000-0002-6029-822X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6d1ef8a71f24d1694aee57b47c22198.json"}}, {"family": "Altun", "given": "Mikael", "initials": "M", "orcid": "0000-0002-6937-6124", "researcher": {"href": "https://publications.scilifelab.se/researcher/4317b773615e476694840e907b7b1a0c.json"}}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications.scilifelab.se/researcher/5aa942fbfbee4257a129b3e7888f5b6d.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd0d4d98261f41268c76dd91345a1857.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "32", "issn-l": "2375-2548"}, "abstract": "Eukaryotic initiation factor 4A-III (eIF4A3), a core helicase component of the exon junction complex, is essential for splicing, mRNA trafficking, and nonsense-mediated decay processes emerging as targets in cancer therapy. Here, we unravel eIF4A3's tumor-promoting function by demonstrating its role in ribosome biogenesis (RiBi) and p53 (de)regulation. Mechanistically, eIF4A3 resides in nucleoli within the small subunit processome and regulates rRNA processing via R-loop clearance. EIF4A3 depletion induces cell cycle arrest through impaired RiBi checkpoint-mediated p53 induction and reprogrammed translation of cell cycle regulators. Multilevel omics analysis following eIF4A3 depletion pinpoints pathways of cell death regulation and translation of alternative mouse double minute homolog 2 (MDM2) transcript isoforms that control p53. EIF4A3 expression and subnuclear localization among clinical cancer specimens correlate with the RiBi status rendering eIF4A3 an exploitable vulnerability in high-RiBi tumors. We propose a concept of eIF4A3's unexpected role in RiBi, with implications for cancer pathogenesis and treatment.", "doi": "10.1126/sciadv.abf7561", "pmid": "34348895", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Global Proteomics and Proteogenomics": "Service"}, "xrefs": [{"db": "pii", "key": "7/32/eabf7561"}, {"db": "pmc", "key": "PMC8336962"}], "notes": [], "created": "2021-10-01T09:03:24.915Z", "modified": "2023-06-19T11:42:22.695Z"}, {"entity": "publication", "iuid": "2fa2f808b1704aa48c255a9d72580b1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2fa2f808b1704aa48c255a9d72580b1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2fa2f808b1704aa48c255a9d72580b1f"}}, "title": "The mitochondrial single-stranded DNA binding protein is essential for initiation of mtDNA replication.", "authors": [{"family": "Jiang", "given": "Min", "initials": "M", "orcid": "0000-0002-7005-937X", "researcher": {"href": "https://publications.scilifelab.se/researcher/862b43b10af944108db18b48d57ba4a1.json"}}, {"family": "Xie", "given": "Xie", "initials": "X", "orcid": "0000-0002-8021-9875", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0feb563228e42579c5aee512d250e5d.json"}}, {"family": "Zhu", "given": "Xuefeng", "initials": "X", "orcid": "0000-0002-4759-4446", "researcher": {"href": "https://publications.scilifelab.se/researcher/eebd5f32ac0c48869c90ba2d2ba94fa9.json"}}, {"family": "Jiang", "given": "Shan", "initials": "S", "orcid": "0000-0003-2020-6447", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bd8b6e66470485f9978b3db1bb3b765.json"}}, {"family": "Milenkovic", "given": "Dusanka", "initials": "D", "orcid": "0000-0003-0151-8760", "researcher": {"href": "https://publications.scilifelab.se/researcher/7667a08efad244b88892a772f51ccf50.json"}}, {"family": "Misic", "given": "Jelena", "initials": "J", "orcid": "0000-0002-1562-0582", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed5101973de04ee896ee41a2657612c4.json"}}, {"family": "Shi", "given": "Yonghong", "initials": "Y"}, {"family": "Tandukar", "given": "Nirwan", "initials": "N", "orcid": "0000-0001-7769-5304", "researcher": {"href": "https://publications.scilifelab.se/researcher/6fc8863a94e6450c9218b97453380785.json"}}, {"family": "Li", "given": "Xinping", "initials": "X", "orcid": "0000-0002-7427-0017", "researcher": {"href": "https://publications.scilifelab.se/researcher/836410d8d48f47fbb5bfd46deac8f6e8.json"}}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Jenninger", "given": "Louise", "initials": "L"}, {"family": "Hoberg", "given": "Emily", "initials": "E"}, {"family": "Albarran-Gutierrez", "given": "Sara", "initials": "S", "orcid": "0000-0003-1403-3922", "researcher": {"href": "https://publications.scilifelab.se/researcher/9231ff3b6f994dfaa9bc8f2a52746d78.json"}}, {"family": "Szilagyi", "given": "Zsolt", "initials": "Z"}, {"family": "Macao", "given": "Bertil", "initials": "B"}, {"family": "Siira", "given": "Stefan J", "initials": "SJ", "orcid": "0000-0002-8391-0143", "researcher": {"href": "https://publications.scilifelab.se/researcher/4739679420014daca252a8a6ea68597e.json"}}, {"family": "Carelli", "given": "Valerio", "initials": "V", "orcid": "0000-0003-4923-6404", "researcher": {"href": "https://publications.scilifelab.se/researcher/55d1ecff8faa4f4e90e515a6472f7701.json"}}, {"family": "Griffith", "given": "Jack D", "initials": "JD"}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM"}, {"family": "Nicholls", "given": "Thomas J", "initials": "TJ", "orcid": "0000-0002-3034-4109", "researcher": {"href": "https://publications.scilifelab.se/researcher/46e55e31c134464c8d8f71cc553ef198.json"}}, {"family": "Filipovska", "given": "Aleksandra", "initials": "A", "orcid": "0000-0002-6998-8403", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5130ef46efb4fcd8d3b7bbd5c1e7708.json"}}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG", "orcid": "0000-0001-5100-996X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc68aa2893a4ab8845fc32d8d6bc59a.json"}}, {"family": "Falkenberg", "given": "Maria", "initials": "M", "orcid": "0000-0001-8713-173X", "researcher": {"href": "https://publications.scilifelab.se/researcher/562109b99a5c4eb3bd8b92f30014828b.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "27", "issn-l": "2375-2548"}, "abstract": "We report a role for the mitochondrial single-stranded DNA binding protein (mtSSB) in regulating mitochondrial DNA (mtDNA) replication initiation in mammalian mitochondria. Transcription from the light-strand promoter (LSP) is required both for gene expression and for generating the RNA primers needed for initiation of mtDNA synthesis. In the absence of mtSSB, transcription from LSP is strongly up-regulated, but no replication primers are formed. Using deep sequencing in a mouse knockout model and biochemical reconstitution experiments with pure proteins, we find that mtSSB is necessary to restrict transcription initiation to optimize RNA primer formation at both origins of mtDNA replication. Last, we show that human pathological versions of mtSSB causing severe mitochondrial disease cannot efficiently support primer formation and initiation of mtDNA replication.", "doi": "10.1126/sciadv.abf8631", "pmid": "34215584", "labels": {"Integrated Microscopy Technologies Gothenburg": "Service"}, "xrefs": [{"db": "pii", "key": "7/27/eabf8631"}], "notes": [], "created": "2023-02-16T08:17:57.108Z", "modified": "2023-02-16T08:17:57.519Z"}, {"entity": "publication", "iuid": "cee69667064f4aa186925651c58a42f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cee69667064f4aa186925651c58a42f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cee69667064f4aa186925651c58a42f9"}}, "title": "A single-cell type transcriptomics map of human tissues.", "authors": [{"family": "Karlsson", "given": "Max", "initials": "M", "orcid": "0000-0002-7000-4416", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e1bd9a99e5648c3998c6e0106a07fbc.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1b9559ac41749fa91c4025108947e13.json"}}, {"family": "M\u00e9ar", "given": "Loren", "initials": "L", "orcid": "0000-0001-9333-0110", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4f441a799324599953796b467abf95c.json"}}, {"family": "Zhong", "given": "Wen", "initials": "W", "orcid": "0000-0002-7422-6104", "researcher": {"href": "https://publications.scilifelab.se/researcher/a82c3b7da3b8472392d39ca5f6d5bedb.json"}}, {"family": "Digre", "given": "Andreas", "initials": "A", "orcid": "0000-0003-1145-6700", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83918be53c64470a67ab23170b86b11.json"}}, {"family": "Katona", "given": "Borbala", "initials": "B"}, {"family": "Sj\u00f6stedt", "given": "Evelina", "initials": "E", "orcid": "0000-0002-0327-7377", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdcf6ac54d8343838878c1afbafa32b3.json"}}, {"family": "Butler", "given": "Lynn", "initials": "L"}, {"family": "Odeberg", "given": "Jacob", "initials": "J", "orcid": "0000-0003-0996-1644", "researcher": {"href": "https://publications.scilifelab.se/researcher/d1f04395fea84d898a8fe2a9875e79c4.json"}}, {"family": "Dusart", "given": "Philip", "initials": "P"}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f0e8af0b9144bcd9fd566d316008a62.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P", "orcid": "0000-0003-3014-5502", "researcher": {"href": "https://publications.scilifelab.se/researcher/6cdb69ec1f0f428898a2aadceb01062c.json"}}, {"family": "von Feilitzen", "given": "Kalle", "initials": "K", "orcid": "0000-0002-0257-7554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f1e309f8d9247458c59e2ecfbd0c079.json"}}, {"family": "Zwahlen", "given": "Martin", "initials": "M", "orcid": "0000-0002-0064-4776", "researcher": {"href": "https://publications.scilifelab.se/researcher/04fb4e913dfb47b9bee48531db50d64c.json"}}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications.scilifelab.se/researcher/fbe369c4e07c44c09dcf64a3c18d833e.json"}}, {"family": "Altay", "given": "Ozlem", "initials": "O"}, {"family": "Li", "given": "Xiangyu", "initials": "X", "orcid": "0000-0002-8301-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c15b68f3b7f4188b9927c011d586efd.json"}}, {"family": "Ozcan", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-1222-2802", "researcher": {"href": "https://publications.scilifelab.se/researcher/480be47a6ccd4f9ebc66d718997a3462.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A", "orcid": "0000-0002-4254-6090", "researcher": {"href": "https://publications.scilifelab.se/researcher/da756265658c4ed2a8911644583e07a3.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L", "orcid": "0000-0003-0198-7137", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8db0663a10a4d9e9241457609d5952e.json"}}, {"family": "Mulder", "given": "Jan", "initials": "J", "orcid": "0000-0003-3717-5018", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8443b271929476bb2b569e39bae732c.json"}}, {"family": "Luo", "given": "Yonglun", "initials": "Y", "orcid": "0000-0002-0007-7759", "researcher": {"href": "https://publications.scilifelab.se/researcher/0aad9ec706674ed6ab358a445ba1989d.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "31", "pages": "eabh2169", "issn-l": "2375-2548"}, "abstract": "Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.", "doi": "10.1126/sciadv.abh2169", "pmid": "34321199", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7/31/eabh2169"}, {"db": "pmc", "key": "PMC8318366"}], "notes": [], "created": "2021-08-27T07:22:02.009Z", "modified": "2024-01-16T13:48:39.387Z"}, {"entity": "publication", "iuid": "ac498053fd134ab2a54ce6b4b2ed366c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac498053fd134ab2a54ce6b4b2ed366c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac498053fd134ab2a54ce6b4b2ed366c"}}, "title": "Following spatial A\u03b2 aggregation dynamics in evolving Alzheimer's disease pathology by imaging stable isotope labeling kinetics.", "authors": [{"family": "Michno", "given": "Wojciech", "initials": "W", "orcid": "0000-0002-3096-3604", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4307eb6e45426e8176337e88c9c344.json"}}, {"family": "Stringer", "given": "Katie M", "initials": "KM", "orcid": "0000-0003-1616-2437", "researcher": {"href": "https://publications.scilifelab.se/researcher/c2638dd298ce470eb41bb45cbf1501c3.json"}}, {"family": "Enzlein", "given": "Thomas", "initials": "T", "orcid": "0000-0003-1789-4090", "researcher": {"href": "https://publications.scilifelab.se/researcher/8c32c7c836c4417182d0b04ac914e318.json"}}, {"family": "Passarelli", "given": "Melissa K", "initials": "MK", "orcid": "0000-0003-2466-1439", "researcher": {"href": "https://publications.scilifelab.se/researcher/2699b550e880407296571ccfe51a1cee.json"}}, {"family": "Escrig", "given": "Stephane", "initials": "S", "orcid": "0000-0002-7525-4000", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f704fbd587f4a96b272ea9269512c89.json"}}, {"family": "Vitanova", "given": "Karina", "initials": "K", "orcid": "0000-0001-8800-4150", "researcher": {"href": "https://publications.scilifelab.se/researcher/c3c495f6ef37496fbafc13a93a8d50f3.json"}}, {"family": "Wood", "given": "Jack", "initials": "J", "orcid": "0000-0001-6049-4020", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9b71cccc5da4ece9a9f57f0c46eda26.json"}}, {"family": "Blennow", "given": "Kaj", "initials": "K", "orcid": "0000-0002-1890-4193", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e646be026ce42ecbfd4d62eca3f9bce.json"}}, {"family": "Zetterberg", "given": "Henrik", "initials": "H", "orcid": "0000-0003-3930-4354", "researcher": {"href": "https://publications.scilifelab.se/researcher/85efee74eb4a4b38b63cf2823d204529.json"}}, {"family": "Meibom", "given": "Anders", "initials": "A", "orcid": "0000-0002-4542-2819", "researcher": {"href": "https://publications.scilifelab.se/researcher/449ed37aa5ab48ab8b1d93e0ab0f3f9b.json"}}, {"family": "Hopf", "given": "Carsten", "initials": "C", "orcid": "0000-0003-0802-6451", "researcher": {"href": "https://publications.scilifelab.se/researcher/178878399aac4cd6bf793f3720c75365.json"}}, {"family": "Edwards", "given": "Frances A", "initials": "FA", "orcid": "0000-0001-8515-9077", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdb5831ebd95409b9fc30c2410bf8ad3.json"}}, {"family": "Hanrieder", "given": "J\u00f6rg", "initials": "J", "orcid": "0000-0001-6059-198X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e65454100674f98bf8f2575093f2441.json"}}], "type": "journal article", "published": "2021-06-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "25", "issn-l": "2375-2548"}, "abstract": "\u03b2-Amyloid (A\u03b2) plaque formation is the major pathological hallmark of Alzheimer's disease (AD) and constitutes a potentially critical, early inducer driving AD pathogenesis as it precedes other pathological events and cognitive symptoms by decades. It is therefore critical to understand how A\u03b2 pathology is initiated and where and when distinct A\u03b2 species aggregate. Here, we used metabolic isotope labeling in APP knock-in mice together with mass spectrometry imaging to monitor the earliest seeds of A\u03b2 deposition through ongoing plaque development. This allowed visualizing A\u03b2 aggregation dynamics within single plaques across different brain regions. We show that formation of structurally distinct plaques is associated with differential A\u03b2 peptide deposition. Specifically, A\u03b21-42 is forming an initial core structure followed by radial outgrowth and late secretion and deposition of A\u03b21-38. These data describe a detailed picture of the earliest events of precipitating amyloid pathology at scales not previously possible.NL-G-F", "doi": "10.1126/sciadv.abg4855", "pmid": "34134980", "labels": {"Integrated Microscopy Technologies Gothenburg": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8208724"}, {"db": "pii", "key": "7/25/eabg4855"}], "notes": [], "created": "2023-02-16T08:19:47.219Z", "modified": "2023-02-16T08:19:47.531Z"}, {"entity": "publication", "iuid": "8b4bf38b9f4740a3b2864b1a99212dde", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b4bf38b9f4740a3b2864b1a99212dde.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b4bf38b9f4740a3b2864b1a99212dde"}}, "title": "Direct observation of hyperpolarization breaking through the spin diffusion barrier.", "authors": [{"family": "Stern", "given": "Quentin", "initials": "Q", "orcid": "0000-0002-8490-030X", "researcher": {"href": "https://publications.scilifelab.se/researcher/46d71698a5be404c93aa12d17e15a638.json"}}, {"family": "Cousin", "given": "Samuel Fran\u00e7ois", "initials": "SF", "orcid": "0000-0002-7021-478X", "researcher": {"href": "https://publications.scilifelab.se/researcher/696aced06abd460a8fc78514eadb659f.json"}}, {"family": "Mentink-Vigier", "given": "Fr\u00e9d\u00e9ric", "initials": "F", "orcid": "0000-0002-3570-9787", "researcher": {"href": "https://publications.scilifelab.se/researcher/9048df8f85bc4013bfc1bc633cc7914d.json"}}, {"family": "Pinon", "given": "Arthur C\u00e9sar", "initials": "AC"}, {"family": "Elliott", "given": "Stuart James", "initials": "SJ", "orcid": "0000-0002-8726-0635", "researcher": {"href": "https://publications.scilifelab.se/researcher/58f00a9e465b4896b91f83a8349ad726.json"}}, {"family": "Cala", "given": "Olivier", "initials": "O", "orcid": "0000-0003-3579-0973", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57fdc2504be4af8862bafa16931f49d.json"}}, {"family": "Jannin", "given": "Sami", "initials": "S", "orcid": "0000-0002-8877-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/d792b277cbb74068ba4fd8d2f4c60788.json"}}], "type": "journal article", "published": "2021-04-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "18", "issn-l": "2375-2548"}, "abstract": "Dynamic nuclear polarization (DNP) is a widely used tool for overcoming the low intrinsic sensitivity of nuclear magnetic resonance spectroscopy and imaging. Its practical applicability is typically bounded, however, by the so-called \"spin diffusion barrier,\" which relates to the poor efficiency of polarization transfer from highly polarized nuclei close to paramagnetic centers to bulk nuclei. A quantitative assessment of this barrier has been hindered so far by the lack of general methods for studying nuclear polarization flow in the vicinity of paramagnetic centers. Here, we fill this gap and introduce a general set of experiments based on microwave gating that are readily implemented. We demonstrate the versatility of our approach in experiments conducted between 1.2 and 4.2 K in static mode and at 100 K under magic angle spinning (MAS)-conditions typical for dissolution DNP and MAS-DNP-and directly observe the marked dependence of polarization flow on temperature.", "doi": "10.1126/sciadv.abf5735", "pmid": "33931450", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pii", "key": "7/18/eabf5735"}, {"db": "pmc", "key": "PMC8087418"}], "notes": [], "created": "2022-04-25T12:29:02.328Z", "modified": "2025-10-17T13:03:56.086Z"}, {"entity": "publication", "iuid": "131283b276484c18b504aa4dc0115f19", "links": {"self": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19.json"}, "display": {"href": "https://publications.scilifelab.se/publication/131283b276484c18b504aa4dc0115f19"}}, "title": "The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.", "authors": [{"family": "Schober", "given": "Florian A", "initials": "FA", "orcid": "0000-0003-4604-6170", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e9cd9d0742d40e3b5dc1abfde64d5c4.json"}}, {"family": "Moore", "given": "David", "initials": "D"}, {"family": "Atanassov", "given": "Ilian", "initials": "I", "orcid": "0000-0001-8259-2545", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8d22eab41e44364be8966abaf693de1.json"}}, {"family": "Moedas", "given": "Marco F", "initials": "MF", "orcid": "0000-0001-5461-0320", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a9cd9caaa014f4280544a243520e18c.json"}}, {"family": "Clemente", "given": "Paula", "initials": "P"}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications.scilifelab.se/researcher/74be6e7c877e4f0da6c7ed3747f3ef9d.json"}}, {"family": "Fissi", "given": "Najla El", "initials": "NE", "orcid": "0000-0002-6631-4630", "researcher": {"href": "https://publications.scilifelab.se/researcher/dec87cba920947028856aadb5892f7a6.json"}}, {"family": "Filograna", "given": "Roberta", "initials": "R"}, {"family": "Bucher", "given": "Anna-Lena", "initials": "AL", "orcid": "0000-0002-9391-4850", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ec4467fb36b44f0a0b1dfa056ec964d.json"}}, {"family": "Hinze", "given": "Yvonne", "initials": "Y", "orcid": "0000-0002-2966-9862", "researcher": {"href": "https://publications.scilifelab.se/researcher/a922a71f2fde43908945980353ed595a.json"}}, {"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications.scilifelab.se/researcher/7e90cde879dc41eaade439bcf951a646.json"}}, {"family": "Hedman", "given": "Erik", "initials": "E", "orcid": "0000-0003-4017-9749", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffc752d50a6649248c6809ea5aec803d.json"}}, {"family": "Chernogubova", "given": "Ekaterina", "initials": "E"}, {"family": "Begzati", "given": "Arjana", "initials": "A", "orcid": "0000-0002-8770-8022", "researcher": {"href": "https://publications.scilifelab.se/researcher/a15af0dbd68445538bd92c89f6d901df.json"}}, {"family": "Wibom", "given": "Rolf", "initials": "R", "orcid": "0000-0001-6721-4642", "researcher": {"href": "https://publications.scilifelab.se/researcher/c7d5fc666ef84a8784d8b28ecf233146.json"}}, {"family": "Jain", "given": "Mohit", "initials": "M"}, {"family": "Nilsson", "given": "Roland", "initials": "R", "orcid": "0000-0002-6020-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/0667c6d082934d818445fe0187dbb23e.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Freyer", "given": "Christoph", "initials": "C", "orcid": "0000-0003-0418-1673", "researcher": {"href": "https://publications.scilifelab.se/researcher/888298d25fb94acca7639063d3592373.json"}}, {"family": "Wredenberg", "given": "Anna", "initials": "A", "orcid": "0000-0002-2500-6121", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ea9ee7305424cdb8c238ef569e5be03.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "8", "issn-l": "2375-2548"}, "abstract": "Induction of the one-carbon cycle is an early hallmark of mitochondrial dysfunction and cancer metabolism. Vital intermediary steps are localized to mitochondria, but it remains unclear how one-carbon availability connects to mitochondrial function. Here, we show that the one-carbon metabolite and methyl group donor S-adenosylmethionine (SAM) is pivotal for energy metabolism. A gradual decline in mitochondrial SAM (mitoSAM) causes hierarchical defects in fly and mouse, comprising loss of mitoSAM-dependent metabolites and impaired assembly of the oxidative phosphorylation system. Complex I stability and iron-sulfur cluster biosynthesis are directly controlled by mitoSAM levels, while other protein targets are predominantly methylated outside of the organelle before import. The mitoSAM pool follows its cytosolic production, establishing mitochondria as responsive receivers of one-carbon units. Thus, we demonstrate that cellular methylation potential is required for energy metabolism, with direct relevance for pathophysiology, aging, and cancer.", "doi": "10.1126/sciadv.abf0717", "pmid": "33608280", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/8/eabf0717"}, {"db": "pmc", "key": "PMC7895438"}], "notes": [], "created": "2021-12-06T13:45:25.780Z", "modified": "2024-01-16T13:48:40.799Z"}, {"entity": "publication", "iuid": "aab5be8b28f949029e6e9dafb461eca8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aab5be8b28f949029e6e9dafb461eca8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aab5be8b28f949029e6e9dafb461eca8"}}, "title": "Mass spectrometry imaging identifies abnormally elevated brain l-DOPA levels and extrastriatal monoaminergic dysregulation in l-DOPA-induced dyskinesia.", "authors": [{"family": "Fridjonsdottir", "given": "Elva", "initials": "E", "orcid": "0000-0002-3779-3556", "researcher": {"href": "https://publications.scilifelab.se/researcher/d39a6e68683d4414bb87a0dc7033a7a4.json"}}, {"family": "Shariatgorji", "given": "Reza", "initials": "R", "orcid": "0000-0001-9484-0921", "researcher": {"href": "https://publications.scilifelab.se/researcher/7762e9f6779c4780a4077c557eb7a3b6.json"}}, {"family": "Nilsson", "given": "Anna", "initials": "A", "orcid": "0000-0002-6183-6931", "researcher": {"href": "https://publications.scilifelab.se/researcher/79c9fe163d31414e8b66aa0834538627.json"}}, {"family": "Vallianatou", "given": "Theodosia", "initials": "T", "orcid": "0000-0002-1477-7756", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae610b7669754328a119654fdfcd6af4.json"}}, {"family": "Odell", "given": "Luke R", "initials": "LR", "orcid": "0000-0001-7658-5103", "researcher": {"href": "https://publications.scilifelab.se/researcher/7653ba79ce9d4e4a80be4b42f516680b.json"}}, {"family": "Schembri", "given": "Luke S", "initials": "LS", "orcid": "0000-0001-5588-1077", "researcher": {"href": "https://publications.scilifelab.se/researcher/9dc760b581324125816ed40eb748104c.json"}}, {"family": "Svenningsson", "given": "Per", "initials": "P", "orcid": "0000-0001-6727-3802", "researcher": {"href": "https://publications.scilifelab.se/researcher/5199496295334771ba3c5621a83a6f43.json"}}, {"family": "Fernagut", "given": "Pierre-Olivier", "initials": "P"}, {"family": "Crossman", "given": "Alan R", "initials": "AR"}, {"family": "Bezard", "given": "Erwan", "initials": "E", "orcid": "0000-0002-0410-4638", "researcher": {"href": "https://publications.scilifelab.se/researcher/c33e3029113549ea96e60c7952e5a19a.json"}}, {"family": "Andr\u00e9n", "given": "Per E", "initials": "PE", "orcid": "0000-0002-4062-7743", "researcher": {"href": "https://publications.scilifelab.se/researcher/64f6381de42949db8d30b56b526f3e26.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "7", "issue": "2", "pages": null}, "abstract": "l-DOPA treatment for Parkinson's disease frequently leads to dyskinesias, the pathophysiology of which is poorly understood. We used MALDI-MSI to map the distribution of l-DOPA and monoaminergic pathways in brains of dyskinetic and nondyskinetic primates. We report elevated levels of l-DOPA, and its metabolite 3-O-methyldopa, in all measured brain regions of dyskinetic animals and increases in dopamine and metabolites in all regions analyzed except the striatum. In dyskinesia, dopamine levels correlated well with l-DOPA levels in extrastriatal regions, such as hippocampus, amygdala, bed nucleus of the stria terminalis, and cortical areas, but not in the striatum. Our results demonstrate that l-DOPA-induced dyskinesia is linked to a dysregulation of l-DOPA metabolism throughout the brain. The inability of extrastriatal brain areas to regulate the formation of dopamine during l-DOPA treatment introduces the potential of dopamine or even l-DOPA itself to modulate neuronal signaling widely across the brain, resulting in unwanted side effects.", "doi": "10.1126/sciadv.abe5948", "pmid": "33523980", "labels": {"Spatial Mass Spectrometry": "Technology development"}, "xrefs": [{"db": "pii", "key": "7/2/eabe5948"}, {"db": "pmc", "key": "PMC7787486"}], "notes": [], "created": "2021-03-26T12:47:07.296Z", "modified": "2024-02-09T14:58:49.154Z"}, {"entity": "publication", "iuid": "e78358779455418ba9c1128f301841ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e78358779455418ba9c1128f301841ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e78358779455418ba9c1128f301841ef"}}, "title": "Human population dynamics and Yersinia pestis in ancient northeast Asia.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef101ca28384bfabb088e7c87d0749e.json"}}, {"family": "D\u00f6nerta\u015f", "given": "Handan Melike", "initials": "HM", "orcid": "0000-0002-9788-6535", "researcher": {"href": "https://publications.scilifelab.se/researcher/99f355027fbd4691af8a17e78f1554f8.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Shergin", "given": "Dmitrij", "initials": "D"}, {"family": "Ivanov", "given": "Grigorij", "initials": "G", "orcid": "0000-0003-4316-7372", "researcher": {"href": "https://publications.scilifelab.se/researcher/f098ecc1f60d44e185f590c7f3b98a3d.json"}}, {"family": "Kichigin", "given": "Dmitrii", "initials": "D", "orcid": "0000-0003-3382-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fbe657eebfa460eb6eabd47c6f55384.json"}}, {"family": "Pestereva", "given": "Kjunnej", "initials": "K", "orcid": "0000-0001-6270-1230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c267495499114556b837c66845be6247.json"}}, {"family": "Volkov", "given": "Denis", "initials": "D", "orcid": "0000-0001-6064-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ce5ce75417640b4b778687b0dbd94a8.json"}}, {"family": "Mandryka", "given": "Pavel", "initials": "P", "orcid": "0000-0002-8647-3823", "researcher": {"href": "https://publications.scilifelab.se/researcher/5832247ccd844904b4421f7c89836815.json"}}, {"family": "Kharinskii", "given": "Artur", "initials": "A", "orcid": "0000-0002-4815-6069", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d0f94fca6d4c2388c64486891d28a4.json"}}, {"family": "Tishkin", "given": "Alexey", "initials": "A", "orcid": "0000-0002-7769-136X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff988500a4ec4fddb2b3f79b95127f77.json"}}, {"family": "Ineshin", "given": "Evgenij", "initials": "E"}, {"family": "Kovychev", "given": "Evgeniy", "initials": "E"}, {"family": "Stepanov", "given": "Aleksandr", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "2", "issn-l": "2375-2548"}, "abstract": "We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.", "doi": "10.1126/sciadv.abc4587", "pmid": "33523963", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/2/eabc4587"}, {"db": "pmc", "key": "PMC7787494"}], "notes": [], "created": "2021-06-09T12:15:48.048Z", "modified": "2024-01-16T13:48:41.043Z"}, {"entity": "publication", "iuid": "f2cdfa285b444ec9b4e48be0907149d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2cdfa285b444ec9b4e48be0907149d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2cdfa285b444ec9b4e48be0907149d9"}}, "title": "The structure of enteric human adenovirus 41-A leading cause of diarrhea in children.", "authors": [{"family": "Rafie", "given": "K", "initials": "K", "orcid": "0000-0003-2418-0061", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c32b813de00417e8fa716ea5c6059c7.json"}}, {"family": "Lenman", "given": "A", "initials": "A", "orcid": "0000-0001-5109-9408", "researcher": {"href": "https://publications.scilifelab.se/researcher/c41b8142e00444afa728b6e4a2ae331a.json"}}, {"family": "Fuchs", "given": "J", "initials": "J"}, {"family": "Rajan", "given": "A", "initials": "A", "orcid": "0000-0002-4873-8528", "researcher": {"href": "https://publications.scilifelab.se/researcher/261182551e72486895b04cebcaa22d69.json"}}, {"family": "Arnberg", "given": "N", "initials": "N", "orcid": "0000-0002-7069-6678", "researcher": {"href": "https://publications.scilifelab.se/researcher/8764d7981e174798ab8411d36e7d0f1b.json"}}, {"family": "Carlson", "given": "L-A", "initials": "LA", "orcid": "0000-0003-2342-6488", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba0e366ce21e49b48212bbed5a0a7bd1.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "2", "issn-l": "2375-2548"}, "abstract": "Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present the first structure of an enteric HAdV-HAdV-F41-determined by cryo-electron microscopy to a resolution of 3.8 \u00c5. The structure reveals extensive alterations to the virion exterior as compared to nonenteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of core protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation of enteric HAdVs to a fundamentally different tissue tropism.", "doi": "10.1126/sciadv.abe0974", "pmid": "33523995", "labels": {"Cryo-EM": "Service", "Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7793593"}, {"db": "pii", "key": "7/2/eabe0974"}], "notes": [], "created": "2022-04-01T06:47:38.187Z", "modified": "2024-01-16T13:46:30.920Z"}, {"entity": "publication", "iuid": "2a387a31c3c54f2f9d3abce4e7efdfe2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2a387a31c3c54f2f9d3abce4e7efdfe2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2a387a31c3c54f2f9d3abce4e7efdfe2"}}, "title": "A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.", "authors": [{"family": "Dias", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-1402-0323", "researcher": {"href": "https://publications.scilifelab.se/researcher/82499805c5c24c46b8c2ec6427345c89.json"}}, {"family": "Alekseenko", "given": "Zhanna", "initials": "Z", "orcid": "0000-0002-6560-9699", "researcher": {"href": "https://publications.scilifelab.se/researcher/d78aae6139714fa3ae8221f3fb380b5a.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications.scilifelab.se/researcher/083131be9eab46df9c789fb018316dff.json"}}, {"family": "Boareto", "given": "Marcelo", "initials": "M", "orcid": "0000-0002-9915-6376", "researcher": {"href": "https://publications.scilifelab.se/researcher/992734ee2f564e51b65c3d24770cc337.json"}}, {"family": "Vollmer", "given": "Jannik", "initials": "J", "orcid": "0000-0001-8341-7730", "researcher": {"href": "https://publications.scilifelab.se/researcher/793924a7af814c28a4ad66ff2fabf136.json"}}, {"family": "Kozhevnikova", "given": "Mariya", "initials": "M", "orcid": "0000-0001-9177-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/a7a4bfdfbcc54403b818b31b24934151.json"}}, {"family": "Wang", "given": "Hui", "initials": "H", "orcid": "0000-0002-5444-1579", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fc15d279b34209a72be7bd71a9338c.json"}}, {"family": "Matise", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-2998-9927", "researcher": {"href": "https://publications.scilifelab.se/researcher/f861ea74deb9478fa475c5036333dfd9.json"}}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A", "orcid": "0000-0001-8812-6481", "researcher": {"href": "https://publications.scilifelab.se/researcher/54b6c0ff12c148dd803f7f72c8af0d14.json"}}, {"family": "Iber", "given": "Dagmar", "initials": "D", "orcid": "0000-0001-8051-1035", "researcher": {"href": "https://publications.scilifelab.se/researcher/26137676787f477fb374d629819d898b.json"}}, {"family": "Ericson", "given": "Johan", "initials": "J", "orcid": "0000-0002-8019-7127", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a093b1609b74f74a8a8546f02946782.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "6", "issue": "38", "pages": null}, "abstract": "How time is measured by neural stem cells during temporal neurogenesis has remained unresolved. By combining experiments and computational modeling, we define a Shh/Gli-driven three-node timer underlying the sequential generation of motor neurons (MNs) and serotonergic neurons in the brainstem. The timer is founded on temporal decline of Gli-activator and Gli-repressor activities established through down-regulation of Gli transcription. The circuitry conforms an incoherent feed-forward loop, whereby Gli proteins not only promote expression of Phox2b and thereby MN-fate but also account for a delayed activation of a self-promoting transforming growth factor-\u03b2 (Tgf\u03b2) node triggering a fate switch by repressing Phox2b. Hysteresis and spatial averaging by diffusion of Tgf\u03b2 counteract noise and increase temporal accuracy at the population level, providing a functional rationale for the intrinsically programmed activation of extrinsic switch signals in temporal patterning. Our study defines how time is reliably encoded during the sequential specification of neurons.", "doi": "10.1126/sciadv.aba8196", "pmid": "32938678", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "6/38/eaba8196"}, {"db": "pmc", "key": "PMC7494341"}], "notes": [], "created": "2020-12-07T16:28:52.509Z", "modified": "2024-01-16T13:48:41.848Z"}, {"entity": "publication", "iuid": "ca335345d4104805803d58f9c0c2c4cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca335345d4104805803d58f9c0c2c4cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca335345d4104805803d58f9c0c2c4cd"}}, "title": "Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor.", "authors": [{"family": "K\u00f6hler", "given": "C", "initials": "C", "orcid": "0000-0002-4347-3110", "researcher": {"href": "https://publications.scilifelab.se/researcher/1af8128ea267472e980d78545001c86c.json"}}, {"family": "Carlstr\u00f6m", "given": "G", "initials": "G", "orcid": "0000-0003-4981-2440", "researcher": {"href": "https://publications.scilifelab.se/researcher/866dc5a8666e4814ab4ae0f346d9d5d5.json"}}, {"family": "Gunnarsson", "given": "A", "initials": "A"}, {"family": "Weininger", "given": "U", "initials": "U", "orcid": "0000-0003-0841-8332", "researcher": {"href": "https://publications.scilifelab.se/researcher/24384408cc7b4c72bd496b452237d1a5.json"}}, {"family": "T\u00e5ngefjord", "given": "S", "initials": "S", "orcid": "0000-0002-3846-6637", "researcher": {"href": "https://publications.scilifelab.se/researcher/60570e5550a74340af123c498b33609d.json"}}, {"family": "Ullah", "given": "V", "initials": "V"}, {"family": "Lepist\u00f6", "given": "M", "initials": "M"}, {"family": "Karlsson", "given": "U", "initials": "U"}, {"family": "Papavoine", "given": "T", "initials": "T", "orcid": "0000-0002-2359-7159", "researcher": {"href": "https://publications.scilifelab.se/researcher/137909632b77412497f482eb806e342a.json"}}, {"family": "Edman", "given": "K", "initials": "K", "orcid": "0000-0002-2560-2388", "researcher": {"href": "https://publications.scilifelab.se/researcher/a06dff3734a943ca92bc47e3defe55b5.json"}}, {"family": "Akke", "given": "M", "initials": "M", "orcid": "0000-0002-2395-825X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e36b418e03154b90a8722670bed9e81a.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "29", "pages": "eabb5277", "issn-l": "2375-2548"}, "abstract": "Allosteric communication within proteins is a hallmark of biochemical signaling, but the dynamic transmission pathways remain poorly characterized. We combined NMR spectroscopy and surface plasmon resonance to reveal these pathways and quantify their energetics in the glucocorticoid receptor, a transcriptional regulator controlling development, metabolism, and immune response. Our results delineate a dynamic communication network of residues linking the ligand-binding pocket to the activation function-2 interface, where helix 12, a switch for transcriptional activation, exhibits ligand- and coregulator-dependent dynamics coupled to graded activation. The allosteric free energy responds to variations in ligand structure: subtle changes gradually tune allostery while preserving the transmission pathway, whereas substitution of the entire pharmacophore leads to divergent allosteric control by apparently rewiring the communication network. Our results provide key insights that should aid in the design of mechanistically differentiated ligands.", "doi": "10.1126/sciadv.abb5277", "pmid": "32832645", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "abb5277"}, {"db": "pmc", "key": "PMC7439413"}], "notes": [], "created": "2020-12-11T09:09:31.901Z", "modified": "2025-10-17T13:03:56.813Z"}, {"entity": "publication", "iuid": "4c85c4f3e9624ded9b910cee95bfc2b8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c85c4f3e9624ded9b910cee95bfc2b8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c85c4f3e9624ded9b910cee95bfc2b8"}}, "title": "Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.", "authors": [{"family": "Westbury", "given": "Michael V", "initials": "MV", "orcid": "0000-0003-0478-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c4a764072a0474abe4ca97c7b220676.json"}}, {"family": "Hartmann", "given": "Stefanie", "initials": "S"}, {"family": "Barlow", "given": "Axel", "initials": "A"}, {"family": "Preick", "given": "Michaela", "initials": "M"}, {"family": "Ridush", "given": "Bogdan", "initials": "B", "orcid": "0000-0002-5896-6073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4615423b4a504bdcbfc76429f38b48ea.json"}}, {"family": "Nagel", "given": "Doris", "initials": "D"}, {"family": "Rathgeber", "given": "Thomas", "initials": "T", "orcid": "0000-0001-6549-6543", "researcher": {"href": "https://publications.scilifelab.se/researcher/39c4006697bf419ba19fa020e80de5c4.json"}}, {"family": "Ziegler", "given": "Reinhard", "initials": "R"}, {"family": "Baryshnikov", "given": "Gennady", "initials": "G"}, {"family": "Sheng", "given": "Guilian", "initials": "G", "orcid": "0000-0003-2314-1650", "researcher": {"href": "https://publications.scilifelab.se/researcher/e96cf70da0364db0926d5312a9076a97.json"}}, {"family": "Ludwig", "given": "Arne", "initials": "A", "orcid": "0000-0001-7249-9953", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5bba6af461445c7bd4a2b6ee97bbd2e.json"}}, {"family": "Wiesel", "given": "Ingrid", "initials": "I"}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Bibi", "given": "Faysal", "initials": "F", "orcid": "0000-0002-9414-5547", "researcher": {"href": "https://publications.scilifelab.se/researcher/ac6a6d03a0c440328ca1a58fd70cf0f3.json"}}, {"family": "Werdelin", "given": "Lars", "initials": "L"}, {"family": "Heller", "given": "Rasmus", "initials": "R", "orcid": "0000-0001-6583-6923", "researcher": {"href": "https://publications.scilifelab.se/researcher/0289add03723441ab92592b4e3702a2c.json"}}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "11", "pages": "eaay0456", "issn-l": "2375-2548"}, "abstract": "The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.", "doi": "10.1126/sciadv.aay0456", "pmid": "32201717", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "aay0456"}, {"db": "pmc", "key": "PMC7069707"}], "notes": [], "created": "2020-07-08T13:04:56.878Z", "modified": "2021-11-10T12:53:35.972Z"}, {"entity": "publication", "iuid": "5f926bdd219e419880e434267d225d2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f926bdd219e419880e434267d225d2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f926bdd219e419880e434267d225d2d"}}, "title": "Irreversible TrxR1 inhibitors block STAT3 activity and induce cancer cell death.", "authors": [{"family": "Busker", "given": "S", "initials": "S", "orcid": "0000-0002-7069-3864", "researcher": {"href": "https://publications.scilifelab.se/researcher/78029e78072548688bf306c577738232.json"}}, {"family": "Qian", "given": "W", "initials": "W"}, {"family": "Haraldsson", "given": "M", "initials": "M"}, {"family": "Espinosa", "given": "B", "initials": "B"}, {"family": "Johansson", "given": "L", "initials": "L"}, {"family": "Attarha", "given": "S", "initials": "S", "orcid": "0000-0003-4085-9680", "researcher": {"href": "https://publications.scilifelab.se/researcher/0095bacd15234e8488ecc6056ce0883e.json"}}, {"family": "Kolosenko", "given": "I", "initials": "I"}, {"family": "Liu", "given": "J", "initials": "J"}, {"family": "Dagnell", "given": "M", "initials": "M", "orcid": "0000-0002-5925-6794", "researcher": {"href": "https://publications.scilifelab.se/researcher/c36a6602bc714b878fd34f1f32f65672.json"}}, {"family": "Grand\u00e9r", "given": "D", "initials": "D"}, {"family": "Arn\u00e9r", "given": "E S J", "initials": "ESJ", "orcid": "0000-0002-4807-6114", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a545effced47da8a5192a7472ceb8f.json"}}, {"family": "Tamm", "given": "K Pokrovskaja", "initials": "KP", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Page", "given": "B D G", "initials": "BDG", "orcid": "0000-0002-2101-1329", "researcher": {"href": "https://publications.scilifelab.se/researcher/87dde8251a714d26b3b7cc045b47061f.json"}}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "6", "issue": "12", "pages": "eaax7945", "issn-l": "2375-2548"}, "abstract": "Because of its key role in cancer development and progression, STAT3 has become an attractive target for developing new cancer therapeutics. While several STAT3 inhibitors have progressed to advanced stages of development, their underlying biology and mechanisms of action are often more complex than would be expected from specific binding to STAT3. Here, we have identified and optimized a series of compounds that block STAT3-dependent luciferase expression with nanomolar potency. Unexpectedly, our lead compounds did not bind to cellular STAT3 but to another prominent anticancer drug target, TrxR1. We further identified that TrxR1 inhibition induced Prx2 and STAT3 oxidation, which subsequently blocked STAT3-dependent transcription. Moreover, previously identified inhibitors of STAT3 were also found to inhibit TrxR1, and likewise, established TrxR1 inhibitors block STAT3-dependent transcriptional activity. These results provide new insights into the complexities of STAT3 redox regulation while highlighting a novel mechanism to block aberrant STAT3 signaling in cancer cells.", "doi": "10.1126/sciadv.aax7945", "pmid": "32219156", "labels": {"Protein Science Facility (PSF)": "Service", "Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7083616"}, {"db": "pii", "key": "aax7945"}], "notes": [], "created": "2020-09-25T11:19:23.210Z", "modified": "2025-10-17T13:04:28.359Z"}, {"entity": "publication", "iuid": "f443991f0cc64850a2b0e6cdc57400dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f443991f0cc64850a2b0e6cdc57400dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f443991f0cc64850a2b0e6cdc57400dd"}}, "title": "Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.", "authors": [{"family": "Morales", "given": "Hern\u00e1n E", "initials": "HE"}, {"family": "Faria", "given": "Rui", "initials": "R"}, {"family": "Johannesson", "given": "Kerstin", "initials": "K"}, {"family": "Larsson", "given": "Tomas", "initials": "T"}, {"family": "Panova", "given": "Marina", "initials": "M"}, {"family": "Westram", "given": "Anja M", "initials": "AM"}, {"family": "Butlin", "given": "Roger K", "initials": "RK"}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "5", "issn": "2375-2548", "issue": "12", "pages": "eaav9963", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.", "doi": "10.1126/sciadv.aav9963", "pmid": "31840052", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "aav9963"}, {"db": "pmc", "key": "PMC6892616"}], "notes": [], "created": "2020-01-08T16:48:53.277Z", "modified": "2020-01-21T13:56:16.525Z"}, {"entity": "publication", "iuid": "c4121567e5bb46d5bfee7bf4443780a2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4121567e5bb46d5bfee7bf4443780a2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4121567e5bb46d5bfee7bf4443780a2"}}, "title": "Multiplexed analysis of the secretin-like GPCR-RAMP interactome.", "authors": [{"family": "Lorenzen", "given": "Emily", "initials": "E", "orcid": "0000-0002-0008-0966", "researcher": {"href": "https://publications.scilifelab.se/researcher/e009a3686e804b808372ef5cd3eabaf3.json"}}, {"family": "Dodig-Crnkovi\u0107", "given": "Tea", "initials": "T", "orcid": "0000-0002-2875-896X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf18af5b676b449693945249fc1767e4.json"}}, {"family": "Kotliar", "given": "Ilana B", "initials": "IB", "orcid": "0000-0001-9533-4828", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf97aaf7767453a9a165e6198fda679.json"}}, {"family": "Pin", "given": "Elisa", "initials": "E", "orcid": "0000-0002-2158-2674", "researcher": {"href": "https://publications.scilifelab.se/researcher/ccb4db02b9784587b62020716ab87247.json"}}, {"family": "Ceraudo", "given": "Emilie", "initials": "E", "orcid": "0000-0001-6563-9751", "researcher": {"href": "https://publications.scilifelab.se/researcher/58ba695a85a84fe2a7986ea3f3eff4ab.json"}}, {"family": "Vaughan", "given": "Roger D", "initials": "RD"}, {"family": "Uhl\u00e8n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Huber", "given": "Thomas", "initials": "T", "orcid": "0000-0002-1844-262X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f730be20f6dd4b8db1756bfed4aa1170.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Sakmar", "given": "Thomas P", "initials": "TP", "orcid": "0000-0002-2836-8953", "researcher": {"href": "https://publications.scilifelab.se/researcher/1130157044664f8b994b94e3b199cc30.json"}}], "type": "journal article", "published": "2019-09-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "5", "issue": "9", "pages": "eaaw2778", "issn-l": "2375-2548"}, "abstract": "Receptor activity-modifying proteins (RAMPs) have been shown to modulate the functions of several G protein-coupled receptors (GPCRs), but potential direct interactions among the three known RAMPs and hundreds of GPCRs have never been investigated. Focusing mainly on the secretin-like family of GPCRs, we engineered epitope-tagged GPCRs and RAMPs, and developed a multiplexed suspension bead array (SBA) immunoassay to detect GPCR-RAMP complexes from detergent-solubilized lysates. Using 64 antibodies raised against the native proteins and 4 antibodies targeting the epitope tags, we mapped the interactions among 23 GPCRs and 3 RAMPs. We validated nearly all previously reported secretin-like GPCR-RAMP interactions, and also found previously unidentified RAMP interactions with additional secretin-like GPCRs, chemokine receptors, and orphan receptors. The results provide a complete interactome of secretin-like GPCRs with RAMPs. The SBA strategy will be useful to search for additional GPCR-RAMP complexes and other interacting membrane protein pairs in cell lines and tissues.", "doi": "10.1126/sciadv.aaw2778", "pmid": "31555726", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "aaw2778"}, {"db": "pmc", "key": "PMC6750928"}], "notes": [], "created": "2020-01-08T10:24:44.506Z", "modified": "2021-07-08T12:07:33.919Z"}, {"entity": "publication", "iuid": "85dd2a7538c140dca8f26a21e97f1e3e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85dd2a7538c140dca8f26a21e97f1e3e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85dd2a7538c140dca8f26a21e97f1e3e"}}, "title": "Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain", "authors": [{"family": "Bigalke", "given": "Janna M", "initials": "JM", "orcid": "0000-0002-3473-4390", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bdcb302357c40dda68bb2123075bbc7.json"}}, {"family": "Aibara", "given": "Shintaro", "initials": "S", "orcid": "0000-0003-2221-482X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d66746c4bec5414da78b2a325a13328f.json"}}, {"family": "Roth", "given": "Robert", "initials": "R", "orcid": "0000-0002-7084-6947", "researcher": {"href": "https://publications.scilifelab.se/researcher/65b319b9f0c54690b969c6ff12023ccb.json"}}, {"family": "Dahl", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gordon", "given": "Euan", "initials": "E"}, {"family": "Dorb\u00e9us", "given": "Sarah", "initials": "S"}, {"family": "Amunts", "given": "A", "initials": "A", "orcid": "0000-0002-5302-1740", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7d0bf36ad1a47f5b5b88f78d1e15395.json"}}, {"family": "Sandmark", "given": "Jenny", "initials": "J", "orcid": "0000-0002-3237-2429", "researcher": {"href": "https://publications.scilifelab.se/researcher/d5cc233fa5d946e4a7d8351dd0dd80ff.json"}}], "type": "journal-article", "published": "2019-07-05", "journal": {"volume": "5", "issn": "2375-2548", "issue": "7", "pages": "eaau4202", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Signaling through the receptor tyrosine kinase RET is essential during normal development. Both gain- and loss-of-function mutations are involved in a variety of diseases, yet the molecular details of receptor activation have remained elusive. We have reconstituted the complete extracellular region of the RET signaling complex together with Neurturin (NRTN) and GFR\u03b12 and determined its structure at 5.7-\u00c5 resolution by cryo-EM. The proteins form an assembly through RET-GFR\u03b12 and RET-NRTN interfaces. Two key interaction points required for RET extracellular domain binding were observed: (i) the calcium-binding site in RET that contacts GFR\u03b12 domain 3 and (ii) the RET cysteine-rich domain interaction with NRTN. The structure highlights the importance of the RET cysteine-rich domain and allows proposition of a model to explain how complex formation leads to RET receptor dimerization and its activation. This provides a framework for targeting RET activity and for further exploration of mechanisms underlying neurological diseases.", "doi": "10.1126/sciadv.aau4202", "pmid": "31392261", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6669014"}, {"db": "pii", "key": "aau4202"}], "notes": "The cryo-EM maps have been deposited in the Electron Microscopy Data Bank with accession code EMD-0026. The atomic model has been deposited in the PDB under accession code 6GL7.", "created": "2019-08-21T10:46:44.422Z", "modified": "2023-06-19T08:55:09.348Z"}, {"entity": "publication", "iuid": "d171962fdb334ddb8594478ee9618c44", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d171962fdb334ddb8594478ee9618c44.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d171962fdb334ddb8594478ee9618c44"}}, "title": "Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.", "authors": [{"family": "Hill", "given": "Jason", "initials": "J"}, {"family": "Rastas", "given": "Pasi", "initials": "P"}, {"family": "Hornett", "given": "Emily A", "initials": "EA"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Clark", "given": "Nathan", "initials": "N"}, {"family": "Morehouse", "given": "Nathan", "initials": "N"}, {"family": "de la Paz Celorio-Mancera", "given": "Maria", "initials": "M"}, {"family": "Cols", "given": "Jofre Carnicer", "initials": "JC"}, {"family": "Dircksen", "given": "Heinrich", "initials": "H"}, {"family": "Meslin", "given": "Camille", "initials": "C"}, {"family": "Keehnen", "given": "Naomi", "initials": "N"}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Sikkink", "given": "Kristin", "initials": "K"}, {"family": "Vives", "given": "Maria", "initials": "M"}, {"family": "Vogel", "given": "Heiko", "initials": "H"}, {"family": "Wiklund", "given": "Christer", "initials": "C"}, {"family": "Woronik", "given": "Alyssa", "initials": "A"}, {"family": "Boggs", "given": "Carol L", "initials": "CL"}, {"family": "Nylin", "given": "S\u00f6ren", "initials": "S"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}], "type": "journal article", "published": "2019-06-00", "journal": {"volume": "5", "issn": "2375-2548", "issue": "6", "pages": "eaau3648", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly ( Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.", "doi": "10.1126/sciadv.aau3648", "pmid": "31206013", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "aau3648"}, {"db": "pmc", "key": "PMC6561736"}], "notes": [], "created": "2019-12-02T16:53:05.154Z", "modified": "2020-01-21T13:56:15.532Z"}, {"entity": "publication", "iuid": "d75ef87849e04fe6bb610c383abae7f9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d75ef87849e04fe6bb610c383abae7f9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d75ef87849e04fe6bb610c383abae7f9"}}, "title": "Pervasive hybridizations in the history of wheat relatives.", "authors": [{"family": "Gl\u00e9min", "given": "Sylvain", "initials": "S"}, {"family": "Scornavacca", "given": "Celine", "initials": "C"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Burgarella", "given": "Concetta", "initials": "C"}, {"family": "Viader", "given": "V\u00e9ronique", "initials": "V"}, {"family": "Ardisson", "given": "Morgane", "initials": "M"}, {"family": "Sarah", "given": "Gautier", "initials": "G"}, {"family": "Santoni", "given": "Sylvain", "initials": "S"}, {"family": "David", "given": "Jacques", "initials": "J"}, {"family": "Ranwez", "given": "Vincent", "initials": "V"}], "type": "journal article", "published": "2019-05-00", "journal": {"volume": "5", "issn": "2375-2548", "issue": "5", "pages": "eaav9188", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought- Aegilops mutica, an overlooked wild species-instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.", "doi": "10.1126/sciadv.aav9188", "pmid": "31049399", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "aav9188"}, {"db": "pmc", "key": "PMC6494498"}], "notes": [], "created": "2019-12-05T15:39:13.411Z", "modified": "2020-01-21T13:53:22.787Z"}, {"entity": "publication", "iuid": "c18fc22d368f4c109f76e74dbc4c0d6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d"}}, "title": "Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Shcherbakov", "given": "Nikolai", "initials": "N", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Shuteleva", "given": "Iia", "initials": "I", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Leonova", "given": "Tatiana", "initials": "T"}, {"family": "Kraeva", "given": "Liudmila", "initials": "L", "orcid": "0000-0002-6524-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/f11ac245436b40a88c66740d94f27353.json"}}, {"family": "Sungatov", "given": "Flarit A", "initials": "FA", "orcid": "0000-0001-5982-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bbdcfb0afa84a899f1dead7ff3c5531.json"}}, {"family": "Sultanova", "given": "Alfija N", "initials": "AN", "orcid": "0000-0002-5409-8344", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc71e882ea64d408cb1d5201aae554a.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Sinika", "given": "Vitaly", "initials": "V", "orcid": "0000-0002-1621-9205", "researcher": {"href": "https://publications.scilifelab.se/researcher/64dffb07a3a342d78eb91d9c02f87f83.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-10-00", "journal": {"volume": "4", "issn": "2375-2548", "issue": "10", "pages": "eaat4457", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.", "doi": "10.1126/sciadv.aat4457", "pmid": "30417088", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "aat4457"}, {"db": "pmc", "key": "PMC6223350"}], "notes": [], "created": "2018-10-22T10:10:13.051Z", "modified": "2024-01-16T13:48:45.440Z"}, {"entity": "publication", "iuid": "ab6f9bb6fde644719766160c28d9a3b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab6f9bb6fde644719766160c28d9a3b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab6f9bb6fde644719766160c28d9a3b5"}}, "title": "Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans", "authors": [{"family": "Cedernaes", "given": "Jonathan", "initials": "J"}, {"family": "Sch\u00f6nke", "given": "Milena", "initials": "M"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO"}, {"family": "Mi", "given": "Jia", "initials": "J"}, {"family": "Chibalin", "given": "Alexander", "initials": "A"}, {"family": "Voisin", "given": "Sarah", "initials": "S"}, {"family": "Osler", "given": "Megan", "initials": "M"}, {"family": "Vogel", "given": "Heike", "initials": "H"}, {"family": "H\u00f6rnaeus", "given": "Katarina", "initials": "K"}, {"family": "Dickson", "given": "Suzanne L", "initials": "SL"}, {"family": "Lind", "given": "Sara Bergstr\u00f6m", "initials": "SB"}, {"family": "Bergquist", "given": "Jonas", "initials": "J"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}, {"family": "Zierath", "given": "Juleen R", "initials": "JR"}, {"family": "Benedict", "given": "Christian", "initials": "C"}], "type": "journal-article", "published": "2018-08-00", "journal": {"volume": "4", "issn": "2375-2548", "issue": "8", "pages": "eaar8590", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": null, "doi": "10.1126/sciadv.aar8590", "pmid": "30140739", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Swedish Metabolomics Centre": "Service"}, "xrefs": [], "notes": [], "created": "2018-08-23T08:30:20.679Z", "modified": "2025-10-17T13:03:17.992Z"}, {"entity": "publication", "iuid": "daf09ae6d7c44e24bf34efb14d8edacb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/daf09ae6d7c44e24bf34efb14d8edacb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/daf09ae6d7c44e24bf34efb14d8edacb"}}, "title": "Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.", "authors": [{"family": "Deville", "given": "C\u00e9lia", "initials": "C", "orcid": "0000-0002-0235-6735", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c716cbe85a047c595efdb2a55a7dcb6.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Franke", "given": "Kamila B", "initials": "KB"}, {"family": "Topf", "given": "Maya", "initials": "M", "orcid": "0000-0002-8185-1215", "researcher": {"href": "https://publications.scilifelab.se/researcher/de031511a9374c3f97b14433944dee8c.json"}}, {"family": "Bukau", "given": "Bernd", "initials": "B"}, {"family": "Mogk", "given": "Axel", "initials": "A", "orcid": "0000-0003-3674-5410", "researcher": {"href": "https://publications.scilifelab.se/researcher/56a1d7fc519743029c9ae615086d8093.json"}}, {"family": "Saibil", "given": "Helen R", "initials": "HR", "orcid": "0000-0002-2266-8891", "researcher": {"href": "https://publications.scilifelab.se/researcher/f1d53e27939a416893b968a87fedd92e.json"}}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "3", "issn": "2375-2548", "issue": "8", "pages": "e1701726", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'-O-(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.", "doi": "10.1126/sciadv.1701726", "pmid": "28798962", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pii", "key": "1701726"}, {"db": "pmc", "key": "PMC5544394"}], "notes": [], "created": "2017-10-16T16:20:48.109Z", "modified": "2021-07-05T17:22:20.822Z"}, {"entity": "publication", "iuid": "993f8ce2d05b4f62b7966bf6f4196c5d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/993f8ce2d05b4f62b7966bf6f4196c5d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/993f8ce2d05b4f62b7966bf6f4196c5d"}}, "title": "Analysis of neural crest-derived clones reveals novel aspects of facial development.", "authors": [{"family": "Kaucka", "given": "Marketa", "initials": "M"}, {"family": "Ivashkin", "given": "Evgeny", "initials": "E"}, {"family": "Gyllborg", "given": "Daniel", "initials": "D"}, {"family": "Zikmund", "given": "Tomas", "initials": "T"}, {"family": "Tesarova", "given": "Marketa", "initials": "M"}, {"family": "Kaiser", "given": "Jozef", "initials": "J"}, {"family": "Xie", "given": "Meng", "initials": "M"}, {"family": "Petersen", "given": "Julian", "initials": "J"}, {"family": "Pachnis", "given": "Vassilis", "initials": "V"}, {"family": "Nicolis", "given": "Silvia K", "initials": "SK"}, {"family": "Yu", "given": "Tian", "initials": "T"}, {"family": "Sharpe", "given": "Paul", "initials": "P"}, {"family": "Arenas", "given": "Ernest", "initials": "E"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Blom", "given": "Hans", "initials": "H", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Clevers", "given": "Hans", "initials": "H"}, {"family": "Suter", "given": "Ueli", "initials": "U"}, {"family": "Chagin", "given": "Andrei S", "initials": "AS"}, {"family": "Fried", "given": "Kaj", "initials": "K"}, {"family": "Hellander", "given": "Andreas", "initials": "A"}, {"family": "Adameyko", "given": "Igor", "initials": "I"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "2", "issn": "2375-2548", "issue": "8", "pages": "e1600060", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "Cranial neural crest cells populate the future facial region and produce ectomesenchyme-derived tissues, such as cartilage, bone, dermis, smooth muscle, adipocytes, and many others. However, the contribution of individual neural crest cells to certain facial locations and the general spatial clonal organization of the ectomesenchyme have not been determined. We investigated how neural crest cells give rise to clonally organized ectomesenchyme and how this early ectomesenchyme behaves during the developmental processes that shape the face. Using a combination of mouse and zebrafish models, we analyzed individual migration, cell crowd movement, oriented cell division, clonal spatial overlapping, and multilineage differentiation. The early face appears to be built from multiple spatially defined overlapping ectomesenchymal clones. During early face development, these clones remain oligopotent and generate various tissues in a given location. By combining clonal analysis, computer simulations, mouse mutants, and live imaging, we show that facial shaping results from an array of local cellular activities in the ectomesenchyme. These activities mostly involve oriented divisions and crowd movements of cells during morphogenetic events. Cellular behavior that can be recognized as individual cell migration is very limited and short-ranged and likely results from cellular mixing due to the proliferation activity of the tissue. These cellular mechanisms resemble the strategy behind limb bud morphogenesis, suggesting the possibility of common principles and deep homology between facial and limb outgrowth.", "doi": "10.1126/sciadv.1600060", "pmid": "27493992", "labels": {"Integrated Microscopy Technologies Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1600060"}, {"db": "pmc", "key": "PMC4972470"}], "notes": [], "created": "2017-05-03T12:59:24.371Z", "modified": "2021-07-05T13:48:51.580Z"}], "created": "2017-05-09T09:12:19.165Z", "modified": "2020-11-27T13:14:10.068Z"}